Contacts of the helix formed by residues 63 - 81 (chain B) in PDB entry 2GPC
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 GLY 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LYS* 1.3 76.6 - - - +
64B PRO* 1.3 75.7 - - - +
66B PHE* 3.1 14.4 + - - +
67B ASN* 3.1 20.1 + - - +
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Residues in contact with PRO 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS 4.4 1.6 - - - +
63B GLY* 1.3 83.1 - - - +
65B ILE* 1.3 69.8 + - + +
67B ASN* 3.3 14.8 + - + +
68B LEU* 3.2 27.9 + - + +
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.3 8.1 - - + +
42B ALA* 3.6 29.6 - - + -
49B LEU* 3.8 35.4 - - + -
57B ILE* 4.0 12.1 - - + -
61B GLU* 4.5 10.5 - - + +
62B LYS 4.2 7.6 + - - +
63B GLY 3.2 1.2 - - - -
64B PRO* 1.3 80.6 - - + +
66B PHE* 1.3 67.4 + - - +
68B LEU* 3.3 14.9 + - + +
69B ALA* 3.3 20.4 + - - +
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Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 4.6 7.9 - - - -
58B ILE* 3.3 39.9 - - + -
61B GLU* 3.5 26.0 - - - +
62B LYS* 3.8 10.3 + - - -
63B GLY 3.1 11.6 + - - +
65B ILE* 1.3 78.7 - - - +
67B ASN* 1.3 79.1 + - - +
68B LEU 3.2 0.2 + - - -
69B ALA* 3.2 1.7 + - - +
70B ALA* 2.9 43.4 + - + +
144B ALA 3.8 15.5 - - - -
145B GLY* 4.5 3.6 - - - -
146B CYS* 4.5 7.6 - - + -
149B THR* 3.6 22.2 - - + -
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Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PHE* 3.5 49.9 - - + +
35B TYR* 5.4 0.2 - - - -
63B GLY* 3.1 14.5 + - - +
64B PRO* 3.3 16.0 + - + +
66B PHE* 1.3 92.7 - - - +
68B LEU* 1.3 59.5 + - + +
71B GLN* 3.0 36.7 + - - +
143B ASP* 5.8 0.5 - - - +
144B ALA* 3.6 13.9 + - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 6.0 1.6 - - + -
35B TYR* 3.8 32.9 - - + +
38B LYS* 3.8 36.1 - - + +
39B LEU* 3.8 36.6 - - + +
42B ALA* 4.9 0.9 - - + -
64B PRO* 3.2 17.8 + - + +
65B ILE* 3.6 20.4 - - + +
66B PHE 3.2 0.8 - - - -
67B ASN* 1.3 78.8 - - + +
69B ALA* 1.3 57.7 + - - +
71B GLN* 3.8 2.1 - - - +
72B ILE* 3.0 35.5 + - - +
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.5 3.1 - - + +
54B ILE* 3.4 31.1 - - + +
57B ILE* 3.4 41.7 - - + -
58B ILE* 3.9 5.4 - - + +
65B ILE 3.3 2.5 + - - +
66B PHE 3.2 3.2 + - - +
68B LEU* 1.3 76.6 - - - +
70B ALA* 1.3 60.7 + - - +
72B ILE* 3.2 10.4 + - - +
73B PHE* 3.0 24.1 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 3.7 16.7 - - + +
66B PHE* 2.9 35.4 + - + +
69B ALA* 1.3 75.3 - - - +
71B GLN* 1.3 60.1 + - - +
73B PHE* 3.4 1.2 + - - +
74B ASN* 2.8 37.3 + - - +
144B ALA* 3.1 26.7 - - + +
146B CYS* 4.2 5.6 - - + -
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Residues in contact with GLN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 3.8 10.1 - - + -
35B TYR* 3.1 47.6 + - + -
67B ASN 3.0 25.7 + - - +
68B LEU 3.8 2.0 - - - +
70B ALA* 1.3 73.1 - - - +
72B ILE* 1.3 65.3 + - - +
74B ASN* 3.7 2.3 + - - -
75B HIS* 2.6 48.2 + - - +
124B TRP* 3.2 24.1 + - - -
144B ALA* 3.4 18.0 - - + -
162B TRP* 3.4 27.7 - - - +
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PHE* 5.5 1.3 - - + -
3B SER 5.1 2.5 - - - +
4B ILE* 3.7 23.3 - - + -
32B HIS* 2.9 24.9 + - + -
35B TYR* 3.8 18.8 - - + +
36B VAL* 3.8 31.4 - - + -
39B LEU* 3.5 30.1 - - + -
54B ILE* 3.9 22.2 - - + -
68B LEU 3.0 20.2 + - - +
69B ALA 3.2 6.9 + - - +
71B GLN* 1.3 75.5 - - - +
73B PHE* 1.3 62.3 + - - +
76B THR* 3.2 12.5 + - - +
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 3.9 7.6 - - + -
55B GLU* 3.5 31.2 - - + -
58B ILE* 3.5 23.8 - - + -
69B ALA 3.0 5.6 + - - +
70B ALA 3.7 2.7 - - - +
72B ILE* 1.3 74.6 - - - +
74B ASN* 1.3 75.9 + - - +
76B THR* 3.3 5.6 + - - -
77B PHE* 2.9 48.3 + + - +
126B TRP* 4.3 10.5 - + - -
146B CYS* 3.7 17.3 - - - -
148B LEU* 3.7 19.3 - - + -
155B PRO* 4.1 21.3 - - + -
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Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ALA 2.8 22.6 + - - +
71B GLN* 3.7 4.6 + - - +
73B PHE* 1.3 80.2 - - - +
75B HIS* 1.3 57.5 + - - +
77B PHE* 3.4 5.4 + - - +
78B TYR* 2.9 28.4 + - - +
124B TRP* 3.3 45.4 - - + +
126B TRP* 3.4 24.4 - - - -
144B ALA 3.4 9.3 + - - -
145B GLY 3.2 22.6 + - - -
146B CYS* 3.5 16.3 - - - -
158B THR* 3.8 1.7 - - - +
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Residues in contact with HIS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B HIS* 3.2 21.1 + + - -
31B HIS* 5.0 0.8 - - - +
32B HIS* 3.4 37.5 - + + +
35B TYR* 3.6 17.8 - + - -
71B GLN* 2.6 53.4 + - - +
74B ASN* 1.3 75.3 - - - +
76B THR* 1.3 64.5 + - - +
78B TYR* 3.1 8.2 + + - +
79B TRP* 3.0 29.6 + + - +
124B TRP* 3.5 16.3 - + - -
160B ASP* 3.4 1.2 + - - -
164B HIS* 3.8 1.6 + - - -
195B FE2 2.1 31.8 - - - -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.2 3.3 - - - +
5B PRO* 4.1 28.7 + - + +
32B HIS* 3.3 19.4 - - - -
72B ILE* 3.2 15.2 + - - +
73B PHE* 3.3 6.2 + - - -
75B HIS* 1.3 75.1 - - - +
77B PHE* 1.3 63.4 + - - +
79B TRP* 3.3 9.4 + - + +
80B GLU* 3.0 47.0 + - + +
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B PHE* 2.9 38.7 + + + +
74B ASN* 3.6 6.3 - - - +
76B THR* 1.3 75.6 - - - +
78B TYR* 1.3 53.9 + - - +
80B GLU* 3.4 15.4 + - - +
81B SER* 2.7 42.4 + - - -
126B TRP* 3.8 16.6 - + + -
155B PRO* 3.3 39.5 - - + -
156B LEU* 3.4 11.2 - - - -
157B LEU* 3.3 29.4 - - - -
158B THR* 3.9 6.1 - - + -
189B ASN* 4.8 6.1 - - - -
193B GLN* 4.0 21.5 - - + -
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.0 6.4 - - - +
27B HIS* 3.6 20.3 + + - -
74B ASN 2.9 14.0 + - - +
75B HIS* 3.3 11.9 - + - +
77B PHE* 1.3 74.5 - - - +
79B TRP* 1.3 99.4 + + - +
81B SER* 3.1 14.9 + - - -
82B MET* 3.4 34.3 + - + +
124B TRP* 3.9 4.9 - - + -
158B THR* 3.6 22.4 - - + +
159B CYS* 4.1 4.3 - - - -
160B ASP* 3.5 35.9 - - + -
165B ALA* 4.4 6.2 + - - +
177B TYR* 2.8 31.2 + - - -
181B PHE* 4.4 3.1 - + - -
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Residues in contact with TRP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO 5.7 1.6 - - - -
6B PRO 5.9 0.4 - - - -
7B LEU* 3.4 17.7 - - + -
8B PRO* 3.9 20.4 - - + +
9B TRP* 3.3 36.5 + + + -
19B LEU* 5.8 1.1 - - + -
24B VAL* 4.5 14.1 - - + -
27B HIS* 3.6 39.3 - + + -
28B TYR* 3.5 32.1 - + + -
32B HIS* 3.1 31.4 + + - -
75B HIS* 3.0 22.9 + + + -
76B THR* 3.8 7.9 - - + +
78B TYR* 1.3 95.7 - + - +
80B GLU* 1.3 58.6 + - + +
82B MET* 3.1 35.9 + - + +
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 4.9 5.7 - - - +
8B PRO* 4.6 16.6 - - + -
76B THR* 3.0 41.2 + - + +
77B PHE* 3.6 18.0 - - - +
79B TRP* 1.3 76.5 - - + +
81B SER* 1.3 56.0 + - - +
82B MET 3.2 2.7 - - - -
186B ASN* 3.3 14.1 + - - +
189B ASN* 3.2 43.5 + - - +
193B GLN* 5.7 1.9 + - - -
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 2.7 29.7 + - - -
78B TYR 3.1 8.4 + - - -
80B GLU* 1.3 76.3 - - - +
82B MET* 1.3 60.0 + - - +
156B LEU 4.7 0.5 + - - -
157B LEU* 3.6 23.0 - - - +
158B THR 3.2 33.1 + - - -
181B PHE* 4.5 3.0 - - - -
185B VAL* 3.5 6.8 - - - -
186B ASN* 2.8 23.9 + - - -
189B ASN* 4.7 4.5 + - - -
190B VAL* 6.2 0.2 - - - -
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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) + - + + + + + -
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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