Contacts of the helix formed by residues 72 - 89 (chain B) in PDB entry 3CTP
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 ASN 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASN* 3.1 25.4 + - - +
70B ILE 3.3 0.2 - - - -
71B SER* 1.3 77.4 - - - +
73B PRO* 1.3 73.8 - - - +
74B PHE* 2.9 18.6 + - - +
75B PHE* 2.8 25.1 + - + +
76B ASN* 3.2 11.6 + - - -
213B ASP* 3.0 28.9 + - - -
214B PHE* 5.3 0.2 - - - -
239B ASN* 3.5 3.2 - - - +
241B ILE* 3.6 14.3 - - + +
267B ASP* 4.4 1.0 - - - +
269B SER* 4.9 0.9 + - - -
401B XLF 2.8 27.5 + - - -
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Residues in contact with PRO 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE* 5.3 4.7 - - + -
71B SER 3.3 9.8 - - - +
72B ASN* 1.3 88.3 - - - +
74B PHE* 1.3 62.3 + - - +
76B ASN* 3.2 13.4 + - - +
77B GLN* 2.9 29.2 + - - +
241B ILE* 4.0 21.3 - - + -
269B SER* 3.9 14.8 - - - +
270B PHE* 3.6 36.6 - - + +
271B ILE* 4.0 21.1 - - + +
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASN* 2.9 14.3 + - - +
73B PRO* 1.3 79.3 - - - +
75B PHE* 1.3 71.2 + + - +
77B GLN* 3.3 3.8 + - - +
78B MET* 2.9 48.2 + - + +
141B PHE* 3.9 26.2 - + - -
267B ASP* 3.6 31.9 - - + +
269B SER* 3.7 10.6 - - - -
284B GLN* 3.6 39.0 - - + -
286B ILE* 3.6 28.0 - - + -
289B LEU* 4.4 1.3 - - + -
401B XLF 3.5 20.0 - - - +
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Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 3.9 16.5 - - + +
68B PRO* 3.5 34.8 - - + -
69B ASN* 3.6 29.2 - - + +
72B ASN* 2.8 17.3 + - + -
74B PHE* 1.3 83.2 - + - +
76B ASN* 1.3 62.6 + - - +
78B MET* 3.9 9.2 - - + +
79B ALA* 2.9 29.6 + - - +
123B SER* 3.8 13.9 - - - -
124B ARG* 3.5 34.8 - - - -
141B PHE* 3.9 20.4 - + - -
401B XLF 3.9 21.8 - - - -
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Residues in contact with ASN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASN* 4.7 0.8 - - - +
70A ILE* 3.4 40.7 + - + +
71A SER* 3.6 29.7 - - - +
76A ASN* 4.1 5.4 + - - -
70B ILE* 2.8 29.9 + - - +
71B SER 4.7 0.7 - - - +
72B ASN 3.2 7.5 + - - +
73B PRO* 3.2 21.4 + - + +
75B PHE* 1.3 76.9 - - - +
77B GLN* 1.3 64.4 + - + +
79B ALA* 3.3 3.0 + - - +
80B SER* 3.0 27.3 + - - -
270B PHE* 4.4 3.2 - - + -
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 6.0 1.6 - - - -
216A VAL* 4.0 27.8 - - + +
73B PRO 2.9 13.1 + - - +
74B PHE 3.8 2.9 - - - +
76B ASN* 1.3 76.3 - - + +
78B MET* 1.3 65.1 + - - +
80B SER* 3.2 7.7 + - - -
81B VAL* 3.0 29.7 + - + +
268B ASN 4.7 2.8 + - - -
269B SER* 3.2 17.8 - - - +
270B PHE* 2.8 50.5 + - + +
286B ILE* 3.8 21.0 - - + +
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Residues in contact with MET 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 5.6 1.8 - - + -
74B PHE* 2.9 38.1 + - + +
75B PHE* 3.9 12.8 - - + +
77B GLN* 1.3 76.3 - - - +
79B ALA* 1.3 57.4 + - - +
81B VAL* 3.2 1.4 + - - +
82B ILE* 2.8 59.8 + - + +
141B PHE* 4.1 33.9 - - - -
286B ILE* 3.7 26.6 - - + +
289B LEU* 4.0 19.5 - - + -
290B ALA* 4.8 3.4 - - + +
293B ILE* 4.3 10.8 - - - -
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 5.0 3.8 - - + -
97A ASN* 5.3 3.4 - - - +
65B LEU* 3.8 25.8 - - + -
67B VAL* 4.9 4.9 - - + -
75B PHE 2.9 18.2 + - - +
76B ASN* 3.7 6.7 - - - +
77B GLN 3.2 0.2 - - - -
78B MET* 1.3 76.3 - - - +
80B SER* 1.3 64.4 + - - +
82B ILE* 3.9 1.0 - - - +
83B GLU* 3.0 24.8 + - - +
93B LEU* 4.0 3.8 - - - +
95B LEU* 4.1 23.7 - - + +
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASN* 3.6 26.3 + - - -
71A SER* 5.7 1.0 - - - -
97A ASN* 4.0 10.5 + - - +
99A ASP* 5.9 1.3 - - - -
76B ASN 3.0 15.2 + - - -
77B GLN* 3.6 10.4 - - - -
79B ALA* 1.3 77.2 - - - +
81B VAL* 1.3 64.1 - - - +
83B GLU* 3.4 5.4 + - - +
84B GLU* 3.2 25.6 + - - +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLN* 3.0 18.2 + - + +
78B MET 4.1 0.4 - - - +
80B SER* 1.3 77.6 - - - +
82B ILE* 1.3 67.4 + - - +
84B GLU* 3.1 18.1 + - + +
85B TYR* 3.1 38.0 + - + -
286B ILE* 3.8 19.1 - - + -
287B GLU* 3.7 30.7 - - + +
290B ALA* 3.7 9.9 - - + -
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 4.0 25.1 - - + -
78B MET* 2.8 43.2 + - + +
79B ALA 3.9 3.4 - - - +
81B VAL* 1.3 75.5 - - - +
83B GLU* 1.3 58.6 + - - +
85B TYR* 3.3 1.9 + - - +
86B ALA* 2.8 27.7 + - - +
93B LEU* 4.0 15.3 - - + -
121B ILE* 3.8 26.0 - - + -
290B ALA* 3.7 24.5 - - + +
293B ILE* 4.2 17.0 - - + -
294B ILE* 3.9 15.4 - - + +
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASN* 4.0 28.0 + - - +
104A LYS* 5.5 9.1 - - - +
108A TYR* 2.6 40.3 + - - -
79B ALA 3.0 18.3 + - - +
80B SER* 3.5 8.1 - - - +
81B VAL 3.1 0.4 - - - -
82B ILE* 1.3 76.5 - - - +
84B GLU* 1.3 58.5 + - + +
86B ALA* 3.7 1.4 - - + +
87B LYS* 2.9 34.1 + - + +
91B TYR 4.7 1.9 - - - +
92B THR* 5.3 0.9 - - - +
93B LEU* 3.6 29.1 - - + +
95B LEU* 5.1 3.3 - - - +
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Residues in contact with GLU 84 (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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104A LYS* 4.4 15.5 + - - -
80B SER 3.2 15.2 + - - +
81B VAL* 3.1 13.5 + - + +
83B GLU* 1.3 78.5 - - - +
85B TYR* 1.3 66.4 + - + +
87B LYS* 3.3 29.2 + - - +
88B ASN* 3.1 31.8 + - - +
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Residues in contact with TYR 85 (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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81B VAL* 3.1 32.9 + - + -
82B ILE 4.0 1.8 - - - +
84B GLU* 1.3 79.9 - - + +
86B ALA* 1.3 66.3 + - - +
88B ASN* 3.3 32.3 + - + +
89B LYS* 3.4 13.3 + - - +
287B GLU* 2.6 46.5 + - - +
290B ALA* 3.8 4.9 - - + +
291B TYR* 3.7 45.8 - + + +
294B ILE* 3.7 24.5 - - + +
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Residues in contact with ALA 86 (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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63B ILE* 4.5 1.3 - - + -
82B ILE 2.8 17.2 + - - +
83B GLU* 3.7 4.7 - - - +
85B TYR* 1.3 75.7 - - - +
87B LYS* 1.3 63.4 + - - +
89B LYS* 2.9 15.1 + - - +
90B GLY 3.1 0.3 + - - -
91B TYR* 3.0 39.0 + - + +
93B LEU* 4.2 18.8 - - + -
294B ILE* 4.0 23.2 - - + +
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Residues in contact with LYS 87 (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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104A LYS* 4.2 24.7 - - + +
83B GLU* 2.9 21.8 + - + +
84B GLU* 3.5 30.2 + - - +
86B ALA* 1.3 77.8 - - - +
88B ASN* 1.3 67.0 + - - +
90B GLY* 3.0 13.7 + - - -
91B TYR 3.4 12.7 + - - +
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 3.1 18.4 + - - +
85B TYR* 3.4 30.0 - - + +
86B ALA 3.2 0.2 - - - -
87B LYS* 1.3 82.9 - - - +
89B LYS* 1.3 62.9 + - + +
90B GLY 3.8 0.2 + - - -
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Residues in contact with LYS 89 (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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61B LYS* 4.5 4.7 + - - -
85B TYR 3.6 12.6 - - - +
86B ALA 2.9 10.2 + - - +
88B ASN* 1.3 80.0 - - + +
90B GLY* 1.3 57.6 + - - +
91B TYR* 3.6 24.9 - - + -
294B ILE* 3.8 16.6 - - + -
295B GLU* 2.8 40.0 + - - -
298B ILE* 4.0 28.2 - - + +
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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
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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