Contacts of the helix formed by residues 96 - 120 (chain B) in PDB entry 3A4I
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 ASP 96 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TYR* 5.2 2.2 - - - -
94B VAL* 3.8 1.2 - - - +
95B THR* 1.3 81.4 + - - +
97B PRO* 1.4 63.5 - - - +
98B GLU* 2.8 44.5 + - - +
99B GLU* 3.1 35.4 + - - +
100B LYS* 3.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 6.4 0.2 - - + -
249A TYR* 3.9 24.0 - - + +
95B THR 3.4 5.8 - - - +
96B ASP* 1.4 90.7 - - - +
98B GLU* 1.3 66.1 + - - +
100B LYS* 3.3 7.2 + - + +
101B ARG* 3.1 29.5 + - - +
195B VAL* 5.1 0.8 - - + +
308B GLU* 3.6 61.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 4.8 9.0 - - - +
247A ARG* 5.4 9.8 + - - -
249A TYR* 3.6 18.2 + - - +
96B ASP* 2.8 20.6 + - - +
97B PRO* 1.3 80.1 - - - +
99B GLU* 1.3 57.3 + - + +
101B ARG* 3.4 14.2 + - - +
102B LYS* 3.0 29.0 + - - +
308B GLU* 4.9 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 3.8 20.3 - - + +
95B THR 5.5 0.2 + - - -
96B ASP* 3.1 33.7 + - + +
98B GLU* 1.3 77.2 - - + +
100B LYS* 1.3 65.2 + - - +
102B LYS* 4.3 11.2 - - + -
103B ILE* 2.9 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.9 18.0 - - + +
94B VAL* 3.7 24.6 - - + +
95B THR 4.4 7.4 - - - -
96B ASP 3.0 14.4 + - - +
97B PRO* 3.5 7.6 - - + +
98B GLU 3.3 0.2 - - - -
99B GLU* 1.3 75.5 - - - +
101B ARG* 1.3 58.2 + - - +
104B ILE* 3.0 41.6 + - + +
194B ALA* 2.9 22.8 + - + +
195B VAL* 4.9 6.3 - - + -
197B VAL 2.7 29.3 + - - -
199B GLY 2.9 20.7 + - - -
201B VAL* 3.8 11.8 - - + +
308B GLU* 2.8 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PRO 3.1 17.2 + - - +
98B GLU* 3.8 13.9 - - - +
100B LYS* 1.3 81.6 - - - +
102B LYS* 1.3 61.7 + - - +
104B ILE* 3.5 6.0 + - - +
105B GLY* 3.1 20.6 + - - -
189B PRO* 5.1 4.8 - - - +
191B PRO* 3.7 24.3 - - + +
195B VAL* 3.8 31.3 - - + +
306B GLU* 4.5 9.9 - - - +
308B GLU* 2.7 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU 3.0 17.6 + - - +
99B GLU* 3.7 12.3 - - + +
101B ARG* 1.3 78.5 - - - +
103B ILE* 1.3 59.4 + - + +
105B GLY* 3.4 1.2 + - - -
106B ARG* 3.0 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 3.7 37.9 - - + +
91B LEU* 4.0 9.4 - - + -
94B VAL* 3.7 31.6 - - + -
99B GLU* 2.9 28.2 + - + +
100B LYS 3.9 2.5 - - - +
102B LYS* 1.3 80.7 - - + +
104B ILE* 1.3 59.3 + - - +
106B ARG* 3.2 31.1 + - - +
107B VAL* 2.8 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR* 5.4 3.6 - - + -
57B PHE* 3.9 12.1 - - + -
87B PHE* 3.5 22.3 - - + -
91B LEU* 3.8 20.9 - - + -
100B LYS* 3.0 25.5 + - + +
101B ARG 3.9 3.1 - - - +
103B ILE* 1.3 76.0 - - + +
105B GLY* 1.3 59.1 + - - +
108B PHE* 2.9 31.2 + - + +
190B GLY 4.6 5.4 - - - +
191B PRO* 3.6 35.7 - - + -
194B ALA* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG 3.1 14.9 + - - -
102B LYS 3.7 3.6 - - - -
104B ILE* 1.3 77.9 - - - +
106B ARG* 1.3 60.0 + - - +
108B PHE* 3.3 6.4 + - - +
109B ILE* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 5.2 3.2 + - - +
102B LYS* 3.0 21.9 + - + +
103B ILE* 3.2 43.2 + - - +
105B GLY* 1.3 74.4 - - - +
107B VAL* 1.3 68.7 + - - +
109B ILE* 3.4 8.5 + - - +
110B GLU* 3.1 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG* 4.5 15.9 - - + +
87B PHE* 3.7 35.7 - - + -
90B ALA* 3.5 27.6 - - + -
103B ILE* 2.8 27.1 + - + +
106B ARG* 1.3 80.4 - - - +
108B PHE* 1.3 66.7 + - - +
110B GLU* 3.3 19.4 + - - +
111B VAL* 3.0 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 4.0 26.0 - - + -
51B VAL 6.0 0.2 - - - -
53B VAL* 3.6 42.6 - - + -
55B THR* 4.9 5.8 - - + -
87B PHE* 3.7 13.8 - + + -
104B ILE* 2.9 21.1 + - + +
105B GLY* 3.6 6.5 - - - +
107B VAL* 1.3 77.2 - - - +
109B ILE* 1.3 72.3 + - + +
111B VAL* 3.3 2.6 + - - +
112B PHE* 2.8 54.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLY 3.1 17.2 + - - +
106B ARG* 3.7 8.7 - - - +
107B VAL 3.3 0.2 - - - -
108B PHE* 1.3 90.9 - - + +
110B GLU* 1.3 53.1 + - - +
112B PHE* 3.9 7.5 - - + +
113B GLU* 2.8 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG* 6.0 2.4 - - - +
106B ARG* 3.1 41.8 + - + +
107B VAL* 3.4 23.4 - - - +
109B ILE* 1.3 76.5 - - - +
111B VAL* 1.3 64.4 + - + +
113B GLU* 3.7 9.1 - - - +
114B GLU* 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 4.3 19.3 - - + -
81B VAL* 3.5 31.6 - - + -
83B ALA* 4.2 9.6 - - + -
86B ARG* 3.7 34.3 - - - +
87B PHE* 4.5 1.3 - - + -
107B VAL* 3.0 25.7 + - + +
108B PHE* 3.8 4.7 - - - +
110B GLU* 1.3 81.6 - - + +
112B PHE* 1.3 62.6 + - - +
114B GLU* 3.2 11.9 - - - +
115B VAL* 3.2 23.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
24B ILE* 3.6 35.2 - - + -
26B ALA* 3.8 28.3 - - + -
51B VAL* 3.8 30.1 - - + -
53B VAL* 5.0 2.5 - - + -
108B PHE* 2.8 42.5 + + + +
109B ILE* 3.9 7.9 - - + +
111B VAL* 1.3 73.5 - - - +
113B GLU* 1.3 60.0 + - - +
115B VAL* 3.3 5.7 + - - +
116B ALA* 2.9 31.7 + - + +
124B LEU* 3.9 27.4 - - + -
155B LEU* 5.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 2.8 33.9 + - + +
110B GLU* 3.7 8.4 - - - +
112B PHE* 1.3 72.3 - - - +
114B GLU* 1.3 65.5 + - - +
116B ALA* 3.7 7.0 - - + +
117B LYS* 3.1 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG* 3.7 23.8 + - - -
110B GLU* 3.0 16.3 + - - +
111B VAL* 3.2 15.6 - - - +
113B GLU* 1.3 78.2 - - - +
115B VAL* 1.3 61.2 + - + +
117B LYS* 3.7 4.3 + - - +
118B LYS* 3.0 52.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 4.1 19.7 - - + -
79B HIS* 4.4 16.2 - - + +
81B VAL* 3.7 29.4 - - + -
111B VAL* 3.2 16.9 + - + +
112B PHE* 3.8 6.7 - - - +
114B GLU* 1.3 78.2 - - + +
116B ALA* 1.3 64.4 + - - +
118B LYS* 3.1 17.4 + - + +
119B ILE* 3.2 31.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
24B ILE* 3.8 25.0 - - + +
112B PHE* 2.9 21.0 + - + +
113B GLU* 3.4 8.7 + - - +
115B VAL* 1.3 75.5 - - - +
117B LYS* 1.3 60.8 + - - +
119B ILE* 3.2 5.9 + - - +
120B GLY* 3.1 19.6 + - - -
121B ALA* 3.9 7.0 + - + +
155B LEU* 4.7 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLU* 3.1 30.7 + - + +
114B GLU* 3.8 7.6 - - - +
115B VAL 3.2 0.2 - - - -
116B ALA* 1.3 77.8 - - - +
118B LYS* 1.3 68.0 + - + +
119B ILE 3.4 0.5 + - - -
120B GLY* 3.6 10.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 3.0 46.0 + - - +
115B VAL* 3.1 12.2 + - + +
117B LYS* 1.3 86.3 - - + +
119B ILE* 1.3 62.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 2.8 31.1 + - + -
24B ILE* 3.8 21.8 - - + -
49B HIS* 3.6 37.5 - - + +
51B VAL* 4.2 0.9 - - + -
79B HIS* 3.9 33.0 - - + +
115B VAL* 3.4 32.8 - - + +
116B ALA* 3.2 6.9 + - - +
117B LYS 3.2 0.8 - - - -
118B LYS* 1.3 81.6 - - + +
120B GLY* 1.3 56.9 + - - +
121B ALA* 4.0 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 4.4 11.3 + - - +
116B ALA 3.1 8.2 + - - -
117B LYS* 3.6 7.4 + - - -
118B LYS 3.5 2.2 - - - -
119B ILE* 1.3 78.9 - - - +
121B ALA* 1.3 66.9 + - - +
122B GLU* 3.8 1.2 + - - +
----------------------------------------------------------
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