Contacts of the helix formed by residues 72 - 94 (chain B) in PDB entry 1P7G
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 72 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS* 4.4 12.0 + - - +
75A ALA* 4.8 2.1 - - - +
76A VAL* 6.1 0.3 - - - +
79A ASP* 4.1 6.2 - - - +
71B ILE* 1.3 71.8 - - - +
73B ILE* 1.3 63.5 + - - +
74B ARG* 3.2 6.4 + - - +
75B ALA* 2.9 30.0 + - + +
76B VAL* 3.1 15.6 + - + +
402B BME 2.9 32.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.2 13.5 - - + -
64B PHE* 5.3 0.9 - - + -
71B ILE* 3.3 24.0 + - + +
72B ASP* 1.3 73.5 + - - +
74B ARG* 1.3 66.3 + - - +
76B VAL 4.8 0.2 - - - +
77B LEU* 3.1 52.7 + - + +
128C GLU* 4.0 26.7 - - + +
131C GLN* 3.4 33.9 - - + +
132C ALA* 3.9 17.0 - - + +
135C ASN* 4.0 17.3 - - + +
157C GLN* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASP* 2.8 28.9 + - - -
83A HIS* 4.8 10.9 - - - -
72B ASP* 3.2 4.2 + - - +
73B ILE* 1.3 84.0 - - + +
75B ALA* 1.3 61.8 + - - +
77B LEU 4.0 0.2 - - - -
78B ARG* 3.0 65.6 + - - +
402B BME 3.0 23.1 + - - +
135C ASN* 2.8 46.4 + - + +
137C GLU* 3.8 24.4 + - - +
157C GLN* 3.3 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 4.7 8.5 - - + +
75A ALA* 3.5 30.3 - - + -
72B ASP* 2.9 27.7 + - + +
74B ARG* 1.3 78.0 - - - +
76B VAL* 1.3 59.5 + - + +
78B ARG* 3.4 1.6 + - - +
79B ASP* 3.0 36.2 + - - +
402B BME 3.7 12.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 3.5 35.0 - - + +
60B LYS* 4.2 22.7 - - + +
61B LEU* 4.0 17.7 - - + -
71B ILE* 3.5 31.4 - - + -
72B ASP* 3.1 11.2 + - + +
73B ILE 4.5 1.3 - - - +
75B ALA* 1.3 77.3 - - + +
77B LEU* 1.3 58.9 + - - +
79B ASP* 3.3 9.2 + - + +
80B LEU* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.2 30.5 - - + -
73B ILE* 3.1 44.6 + - + +
74B ARG 4.4 1.3 - - - +
76B VAL* 1.3 73.7 - - - +
78B ARG* 1.3 65.0 + - - +
80B LEU* 3.9 9.0 - - + +
81B SER* 3.1 24.8 + - - -
128C GLU* 5.0 2.0 - - - +
132C ALA* 3.8 18.6 - - + -
155C ILE* 3.0 32.5 - - + +
156C LEU* 3.9 12.9 - - - +
157C GLN* 3.9 19.7 + - + +
164C MSE 4.8 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 3.8 35.5 - - - +
160A LYS* 3.6 5.1 - - - +
74B ARG* 3.0 43.7 + - + +
75B ALA 3.6 4.5 - - - +
77B LEU* 1.3 77.0 - - - +
79B ASP* 1.3 64.4 + - - +
81B SER* 3.6 1.9 + - - -
82B PHE* 3.3 23.0 + - - +
162B ASN* 4.2 3.3 + - - -
402B BME 2.9 39.6 - - - +
137C GLU* 3.2 28.9 + - - -
157C GLN* 4.7 2.3 - - - +
159C GLU* 2.8 28.1 + - - -
164C MSE 3.7 26.5 - - + -
137D GLU* 4.2 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 4.3 11.1 - - - +
74A ARG* 2.8 34.6 + - - +
78A ARG* 4.7 3.6 + - - -
53B GLY 5.6 0.2 - - - +
57B ALA* 4.6 9.4 - - + -
60B LYS* 4.3 15.9 + - - -
75B ALA* 3.0 23.2 + - - +
76B VAL* 3.5 11.2 - - - +
78B ARG* 1.3 76.4 - - - +
80B LEU* 1.3 62.8 + - - +
82B PHE* 3.3 3.3 + - - +
83B HIS* 3.0 39.1 + - + +
137D GLU* 4.4 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 5.7 0.7 - - + -
54B ALA* 4.1 24.2 - - + +
57B ALA* 3.9 13.0 - - + +
58B LEU* 4.3 10.3 - - + -
61B LEU* 3.8 25.8 - - + -
76B VAL 2.9 17.2 + - - +
77B LEU* 3.9 11.4 - - + +
79B ASP* 1.3 75.7 - - - +
81B SER* 1.3 55.1 + - - +
83B HIS* 4.9 1.8 - - - -
84B LEU* 2.7 57.9 + - + +
154C LEU* 4.3 20.6 - - + -
155C ILE 4.6 1.8 - - - +
156C LEU* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU 3.1 16.4 + - - -
78B ARG 3.9 2.0 - - - -
79B ASP 3.4 0.2 - - - -
80B LEU* 1.3 79.3 - - - +
82B PHE* 1.3 61.7 + - - +
84B LEU* 4.6 4.3 - - - -
85B ASN* 2.5 33.7 + - - +
162B ASN* 3.3 11.4 - - - +
156C LEU* 4.5 12.3 - - - +
157C GLN 5.6 0.4 - - - -
164C MSE 2.5 48.4 + - - -
166C ALA* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 3.8 13.7 - + - -
78B ARG 3.3 7.2 + - - +
79B ASP 3.7 4.3 - - - +
80B LEU 3.2 1.0 - - - -
81B SER* 1.3 80.4 - - - +
83B HIS* 1.3 88.9 + + - +
86B GLY 2.9 22.3 + - - -
160B LYS* 4.1 10.8 - - + -
161B HIS* 3.4 36.9 + + - +
162B ASN* 3.5 25.7 - - - +
178B TRP* 3.7 26.0 - + - -
137D GLU* 3.3 47.8 - - + +
138D GLY 4.6 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 4.8 17.4 + - - -
49B GLY 4.2 3.7 + - - -
50B TYR* 3.3 41.5 - + - +
53B GLY* 3.1 31.5 + - - -
54B ALA* 3.4 10.8 - - - +
79B ASP* 3.0 23.5 + - + +
80B LEU 4.1 0.2 - - - +
82B PHE* 1.3 104.0 - + - +
84B LEU* 1.3 61.3 + - - +
86B GLY 3.1 1.1 + - - +
87B HIS* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 3.8 39.9 - - + +
54B ALA* 4.1 6.2 - - - +
80B LEU* 2.7 37.6 + - + +
81B SER* 4.3 2.7 - - - +
83B HIS* 1.3 73.1 - - - +
85B ASN* 1.3 58.6 + - - +
87B HIS* 3.3 4.5 + - + +
88B ILE* 2.9 52.1 + - + +
147C GLU* 3.9 10.1 - - + -
154C LEU* 3.6 31.4 - - + -
156C LEU* 5.5 3.6 - - + -
166C ALA* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B SER* 2.5 30.9 + - - +
84B LEU* 1.3 73.4 - - - +
86B GLY* 1.3 61.6 + - - +
88B ILE* 4.4 4.5 - - - +
89B LEU* 2.8 34.7 + - - +
161B HIS* 3.0 28.9 - - + +
162B ASN* 3.2 6.2 - - - +
165B HIS* 3.2 21.6 + - - +
165C HIS 2.9 16.0 + - - +
166C ALA* 3.7 7.5 - - - +
167C ALA* 2.9 33.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 3.9 9.9 - - - -
82B PHE 2.9 11.5 + - - -
83B HIS 3.1 5.3 + - - -
85B ASN* 1.3 76.5 - - - +
87B HIS* 1.3 54.4 + - - +
90B HIS* 2.7 38.2 + - - +
161B HIS* 3.3 33.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 3.4 40.1 - + + +
19B THR 3.1 26.6 + - - -
21B PRO* 3.9 3.8 - - + -
47B HIS* 3.0 30.4 + - - -
50B TYR* 3.7 1.8 - - - +
51B VAL* 3.2 25.2 - - + +
54B ALA* 5.5 1.1 - - + -
83B HIS 2.9 12.6 + - - +
84B LEU* 3.5 11.4 - - + +
86B GLY* 1.3 73.4 - - - +
88B ILE* 1.3 55.8 + - - +
91B SER* 2.6 51.7 + - - -
149C LEU* 3.6 22.9 - - + +
150C GLU* 5.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 2.9 49.8 + - + +
85B ASN* 3.9 4.0 - - - +
87B HIS* 1.3 73.9 - - - +
89B LEU* 1.3 64.9 + - - +
91B SER* 3.2 7.7 + - - -
92B ILE* 3.0 39.8 + - + +
220B LEU* 5.1 7.4 - - + -
147C GLU* 4.0 13.2 - - - +
149C LEU* 4.1 18.6 - - + -
166C ALA* 4.5 4.7 - - + -
167C ALA* 3.7 42.8 - - + +
168C ASP* 4.4 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASN 2.8 22.9 + - - +
86B GLY 4.2 0.2 - - - +
88B ILE* 1.3 73.7 - - - +
90B HIS* 1.3 57.7 + - - +
92B ILE* 3.2 7.4 + - + +
93B PHE* 2.8 28.1 + - - +
141B TRP* 3.5 53.6 - - + +
143B ILE* 4.7 6.1 - - + -
158B ILE* 4.5 0.9 - - + -
161B HIS* 3.6 23.3 - - + +
165B HIS* 3.6 27.8 - - + +
171B VAL* 4.4 18.8 - - + -
174B ALA* 4.6 4.8 - - + +
167C ALA* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B HIS* 2.6 45.3 + + - -
47B HIS* 3.3 31.6 - + + +
50B TYR* 3.3 26.8 - + - -
86B GLY 2.7 29.7 + - - +
89B LEU* 1.3 76.4 - - - +
91B SER* 1.3 63.5 + - - +
93B PHE* 3.1 14.7 + + - +
94B TRP* 3.1 34.2 + + - +
141B TRP* 3.4 23.1 - + - -
161B HIS* 3.8 7.2 - - - -
176B ASP* 3.0 6.5 + - - -
180B HIS* 4.3 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PRO* 4.0 11.9 - - - +
47B HIS* 3.6 9.3 - - - -
87B HIS* 2.6 48.0 + - - -
88B ILE* 3.4 8.5 - - - -
90B HIS* 1.3 76.4 - - - +
92B ILE* 1.3 57.3 + - - +
94B TRP* 4.6 2.9 - - - -
95B PRO* 2.9 23.6 - - - +
220B LEU* 6.1 0.4 - - - -
302B ACT 3.4 21.4 - - - +
149C LEU* 4.4 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 3.0 27.6 + - + +
89B LEU* 3.6 10.3 - - + +
91B SER* 1.3 78.9 - - - +
93B PHE* 1.3 64.3 + - - +
95B PRO* 3.3 7.2 - - - +
96B ASN* 3.1 40.2 + - - +
171B VAL* 4.0 37.7 - - + +
172B LEU 4.7 0.4 - - - +
174B ALA* 4.4 3.4 - - + -
205B ASP* 4.3 0.2 - - - +
209B ARG* 4.1 17.3 - - - +
220B LEU* 4.1 17.5 - - + -
302B ACT 4.4 2.7 - - + -
168C ASP* 3.7 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 4.9 4.3 - - + -
39B MSE 5.7 0.7 - - - -
42B HIS* 3.9 21.3 - + - -
89B LEU 2.8 17.8 + - - +
90B HIS* 3.1 11.2 + + - +
92B ILE* 1.3 74.2 - - - +
94B TRP* 1.3 97.4 + + - +
96B ASN* 3.1 19.9 + - - +
97B MSE 3.4 34.0 + - + +
141B TRP* 3.9 13.7 - + + -
174B ALA* 3.1 27.4 - - - -
175B LEU* 4.0 1.3 - - + -
176B ASP* 3.6 17.7 - - + -
181B ALA* 5.4 0.7 - - + -
193B TYR* 3.9 18.4 - - - -
197B TRP* 3.9 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PRO* 5.0 6.3 - - + -
22B PRO 5.5 1.6 - - - +
23B LEU* 3.3 16.8 - - + -
24B PRO* 3.7 21.3 - - + -
25B TYR* 2.8 19.6 + - - -
39B MSE 3.3 33.4 - - + -
42B HIS* 3.5 43.1 - + + -
43B HIS* 3.7 19.1 - + + -
47B HIS* 3.0 27.5 + + - -
90B HIS* 3.1 35.7 + + - -
91B SER* 4.6 3.1 - - - -
93B PHE* 1.3 95.6 - + - +
95B PRO* 1.3 69.0 - - + +
97B MSE 3.1 25.7 + - + +
----------------------------------------------------------
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