Contacts of the helix formed by residues 93 - 119 (chain B) in PDB entry 1H9T
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 93 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ASP* 2.7 30.3 + - - -
92B GLU* 1.3 76.2 - - - +
94B VAL* 1.3 64.2 + - - +
95B PRO* 3.3 3.3 - - - +
96B GLN* 2.9 38.8 + - - +
97B LEU* 3.7 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA* 3.7 26.0 - - + +
90B ASP 3.5 5.3 + - - +
91B HIS* 3.4 36.3 - - + +
93B SER* 1.3 74.6 - - - +
95B PRO* 1.3 73.7 - - + +
97B LEU* 2.9 19.9 + - - +
98B ILE* 3.1 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLU 4.0 8.1 - - - +
93B SER 3.3 4.9 - - - +
94B VAL* 1.3 96.4 - - + +
96B GLN* 1.3 66.0 + - - +
97B LEU 2.9 0.7 + - - -
98B ILE* 3.6 6.4 - - + +
99B ASP* 2.7 27.9 + - - +
223B TRP* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLY 5.4 5.7 + - - -
93B SER* 2.9 30.8 + - - +
95B PRO* 1.3 73.6 - - - +
97B LEU* 1.3 57.8 + - - +
99B ASP* 3.3 7.4 - - - +
100B ASN* 2.9 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PRO* 5.4 7.6 - - + -
160A ILE* 5.4 4.9 - - + -
75B TRP* 6.1 2.0 - - + -
83B LEU* 4.4 20.2 - - + +
86B LEU* 4.3 23.1 - - + -
87B ALA* 3.5 36.1 - - + +
93B SER 3.7 1.9 + - - +
94B VAL* 2.9 15.9 + - - +
95B PRO 2.9 0.6 + - - -
96B GLN* 1.3 75.0 - - - +
98B ILE* 1.3 68.3 + - + +
100B ASN* 2.7 22.3 + - - +
101B LEU* 2.7 21.9 + - + +
171B LEU* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 3.1 29.0 + - + +
95B PRO* 3.6 8.5 - - + +
97B LEU* 1.3 79.5 - - + +
99B ASP* 1.3 68.2 + - - +
101B LEU* 2.6 22.9 + - - +
102B LEU* 2.8 24.8 + - + +
171B LEU* 4.7 16.6 - - + -
175B ILE* 3.3 39.0 - - + -
223B TRP* 4.4 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PRO 2.7 22.8 + - - +
96B GLN* 3.3 8.3 - - - +
98B ILE* 1.3 74.5 - - - +
100B ASN* 1.3 53.7 + - - +
102B LEU* 3.4 9.0 + - - +
103B SER* 2.8 40.8 + - - -
223B TRP* 5.7 2.0 - - - +
224B HIS* 3.0 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLY 4.8 2.1 - - - +
158A ASN* 3.1 41.9 + - - +
159A PRO* 4.1 20.4 - - - +
160A ILE* 3.8 6.5 - - + -
96B GLN* 2.9 43.5 + - - +
97B LEU* 2.7 29.0 + - - +
99B ASP* 1.3 70.3 - - - +
101B LEU* 1.3 52.4 + - - +
103B SER* 2.8 27.0 + - - -
104B VAL* 3.0 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ILE* 3.1 20.6 - - + +
83B LEU* 5.0 10.1 - - + -
97B LEU* 2.7 10.8 + - + +
98B ILE* 2.6 15.0 + - - +
100B ASN* 1.3 71.1 - - - +
102B LEU* 1.3 60.1 + - - +
104B VAL* 2.8 17.8 + - - +
105B ARG* 2.9 16.9 + - + -
168B MET* 3.6 35.0 - - + -
171B LEU* 3.2 41.7 - - + -
172B TYR* 4.3 17.0 - - + +
175B ILE* 4.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 2.8 28.5 + - + +
99B ASP* 3.9 8.1 - - - +
101B LEU* 1.3 69.1 - - - +
103B SER* 1.3 53.5 + - - +
104B VAL 2.7 15.9 + - - -
105B ARG* 3.3 21.4 + - - +
106B THR* 2.8 28.9 + - - -
172B TYR* 3.7 23.8 - - + -
175B ILE* 3.3 37.7 - - + -
219B SER* 5.9 2.2 - - - +
220B GLY* 5.8 5.6 - - - -
223B TRP* 4.4 22.9 - - + -
224B HIS* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASN* 4.2 7.2 + - - -
161A TYR* 3.9 2.8 + - - -
99B ASP* 2.8 22.8 + - - -
100B ASN* 2.8 12.4 + - - -
102B LEU* 1.3 74.7 - - - +
104B VAL* 1.3 55.5 + - - +
106B THR* 4.2 5.2 - - - -
107B ASN* 2.5 35.3 + - - +
213B ARG* 5.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASN* 3.6 15.5 - - - +
160A ILE* 4.0 18.4 - - + -
161A TYR* 3.4 37.0 - - + -
164A ILE* 5.2 1.8 - - + -
100B ASN 3.0 12.5 + - - +
101B LEU* 2.8 10.2 + - - +
102B LEU 2.7 1.8 + - - -
103B SER* 1.3 78.4 - - - +
105B ARG* 1.3 56.2 + - - +
106B THR 2.6 14.4 + - - -
107B ASN 3.2 1.0 + - - -
108B ILE* 2.9 52.4 + - + +
168B MET* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 2.9 14.8 + - + +
102B LEU* 4.0 22.9 + - - +
104B VAL* 1.3 78.3 - - - +
106B THR* 1.3 93.7 + - - +
108B ILE* 4.8 3.8 - - - -
109B SER* 3.0 19.2 + - - -
112B PHE* 5.5 0.5 - - - -
149B PHE* 3.5 36.6 - - + -
165B LEU* 5.0 14.5 - - + +
168B MET* 4.3 14.3 - - + +
172B TYR* 2.8 48.2 + - + +
212B VAL* 5.5 3.4 - - - +
215B TYR* 5.0 14.4 - - - -
216B GLY* 5.2 5.1 - - - -
219B SER* 4.5 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU 2.8 22.1 + - - -
103B SER* 4.2 3.7 - - - -
104B VAL 2.6 0.6 + - - -
105B ARG* 1.3 98.4 + - - +
107B ASN* 1.3 84.8 + - - +
108B ILE 2.9 1.0 + - - -
109B SER* 2.3 28.2 + - - -
110B THR* 3.2 4.7 - - - +
212B VAL* 4.1 23.6 - - + +
213B ARG* 4.6 13.5 - - - +
216B GLY* 4.0 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.1 45.4 - - + +
115A THR* 6.2 0.2 - - - -
161A TYR* 3.5 7.1 + - - +
103B SER* 2.5 38.0 + - - -
104B VAL 3.2 0.4 + - - -
106B THR* 1.3 88.0 - - - +
108B ILE* 1.3 59.0 + - - +
110B THR* 2.6 28.7 + - - +
111B ILE* 3.9 1.6 - - - +
209B TYR* 5.4 3.1 + - + -
213B ARG* 3.5 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ILE* 4.9 11.2 - - + -
111A ILE* 3.9 8.5 - - + -
161A TYR* 4.6 13.9 - - + +
164A ILE* 4.3 18.4 - - + -
104B VAL* 2.9 42.2 + - + +
105B ARG* 4.4 3.6 - - - +
107B ASN* 1.3 73.7 - - - +
109B SER* 1.3 68.0 + - - +
111B ILE* 2.8 23.9 + - - +
112B PHE* 3.5 20.5 + - + -
161B TYR* 4.2 19.5 - - + -
164B ILE* 4.5 16.6 - - + -
165B LEU* 5.0 7.6 - - + -
168B MET* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 3.0 15.1 + - - -
106B THR* 2.3 28.1 + - - -
108B ILE* 1.3 76.3 - - - +
110B THR* 1.3 59.7 + - - +
111B ILE 2.9 1.4 + - - -
112B PHE* 2.9 21.3 + - - -
113B ILE* 2.7 55.0 + - - +
149B PHE* 4.0 14.1 - - - -
212B VAL* 3.6 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B THR* 3.2 12.1 - - + +
107B ASN* 2.6 29.8 + - - +
109B SER* 1.3 74.8 + - - +
111B ILE* 1.3 61.9 + - - +
113B ILE* 4.6 0.2 - - - -
114B ARG* 3.1 28.3 + - - +
208B VAL* 3.9 8.8 - - - +
209B TYR* 3.9 34.6 + - + +
212B VAL* 3.6 29.8 - - + -
213B ARG* 5.6 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASN* 3.4 64.8 - - + +
108A ILE* 3.9 5.4 - - + +
110A THR* 4.6 1.3 - - - +
111A ILE* 3.6 24.7 - - + -
209A TYR* 6.3 4.0 - - + -
213A ARG* 5.7 1.6 - - - +
107B ASN 3.9 2.9 - - - +
108B ILE* 2.8 19.4 + - - +
110B THR* 1.3 82.7 + - - +
112B PHE* 1.3 57.9 + - - +
114B ARG* 3.4 10.3 - - - +
115B THR* 3.1 27.8 + - - +
161B TYR* 4.0 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG 5.5 0.4 - - - -
108B ILE* 3.5 14.5 + - + -
109B SER* 2.9 36.3 + - - -
111B ILE* 1.3 76.9 - - - +
113B ILE* 1.3 68.5 + - + +
115B THR* 3.0 8.0 + - - -
116B ALA* 2.5 36.7 + - - +
149B PHE* 3.4 26.9 - + + -
152B LEU* 3.5 12.1 - - + -
153B ALA* 3.0 39.7 - - + -
156B SER* 3.4 6.5 - - - -
161B TYR* 4.0 35.0 - + + -
165B LEU* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B SER* 2.7 56.0 + - - +
110B THR* 4.2 2.7 - - - +
112B PHE* 1.3 87.8 - - + +
114B ARG* 1.3 65.7 + - - +
116B ALA* 2.7 19.1 + - + +
117B PHE* 3.0 32.1 + - + -
149B PHE* 4.4 10.5 - - + -
152B LEU* 3.6 32.3 - - + -
192B PHE* 5.3 3.8 - - + -
196B LEU* 4.7 18.2 - - + -
208B VAL* 5.0 6.1 - - + -
212B VAL* 4.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 5.3 9.3 + - - -
213A ARG* 5.6 11.8 - - - +
110B THR 3.1 22.3 + - - +
111B ILE* 3.4 7.2 - - - +
113B ILE* 1.3 80.1 - - - +
115B THR* 1.3 70.3 + - - +
117B PHE* 3.0 23.1 + - - +
118B ARG* 3.8 15.8 + - - +
205B HIS* 4.1 42.6 - - + +
206B ASP* 5.5 2.0 - - - +
208B VAL* 4.4 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASN* 5.6 2.6 + - - -
111B ILE* 3.1 15.2 + - - +
112B PHE* 3.0 10.9 + - - -
114B ARG* 1.3 83.4 + - - +
116B ALA* 1.3 52.8 + - - +
117B PHE 2.6 17.7 + - - -
118B ARG* 3.1 36.1 + - - +
119B GLN* 3.4 6.4 + - + +
156B SER* 2.9 31.9 - - - +
158B ASN* 5.8 2.5 - - + -
161B TYR* 6.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE 2.5 17.1 + - - +
113B ILE* 2.7 18.1 + - + +
115B THR* 1.3 70.3 - - - +
117B PHE* 1.3 58.0 + - + +
119B GLN 2.9 16.2 - - - +
120B HIS 3.7 3.8 - - - +
124B ALA* 3.6 20.6 - - + +
152B LEU* 3.4 30.3 - - + +
155B ALA* 4.1 5.5 - - + +
156B SER* 3.4 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 3.0 45.1 + - + -
114B ARG* 3.0 12.9 + - - +
115B THR 2.6 6.3 + - - -
116B ALA* 1.3 75.1 - - + +
118B ARG* 1.3 55.6 + - - +
119B GLN 2.8 15.6 + - - -
121B PRO* 3.1 32.1 - - - +
124B ALA* 4.9 10.3 - - + -
128B LEU* 6.4 2.0 - - + -
196B LEU* 4.4 28.3 - - + -
199B LEU* 3.7 15.0 - - + -
200B CYS* 3.3 45.8 - - + -
203B GLY* 5.5 3.1 - - - -
205B HIS* 4.8 13.9 - - + +
208B VAL* 5.0 9.4 - - + -
1231B AU 3.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 3.8 9.6 + - - +
115B THR* 3.1 32.5 + - - +
117B PHE* 1.3 76.2 - - - +
119B GLN* 1.3 106.8 + - - +
120B HIS 4.2 0.6 + - - -
121B PRO* 4.5 3.6 - - - +
205B HIS* 3.1 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B THR* 3.4 4.9 + - + +
116B ALA* 2.9 17.2 - - - +
117B PHE 2.8 3.0 + - - -
118B ARG* 1.3 123.5 + - - +
120B HIS* 1.3 91.6 + - + +
121B PRO* 4.1 0.2 - - - -
155B ALA 3.6 2.3 - - - +
156B SER 5.0 6.1 - - - +
157B GLY* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il