Contacts of the helix formed by residues 74 - 86 (chain B) in PDB entry 3W1Y
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 THR 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A MET* 4.3 4.7 - - - +
72B THR 4.5 5.4 - - - +
73B ALA* 1.3 77.1 - - - +
75B VAL* 1.3 64.1 + - - +
76B MET* 3.8 5.4 + - - +
77B GLU* 3.1 36.0 + - - +
78B PHE* 3.0 23.7 + - - +
105B ASN 3.5 9.6 + - - -
106B SER* 3.5 22.4 - - - +
107B ALA 3.3 11.4 - - - +
108B CYS* 4.5 3.8 - - + -
109B LEU* 3.9 4.7 - - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 1.3 71.2 - - - +
76B MET* 1.3 51.9 + - - +
78B PHE* 3.3 9.0 + - + +
79B MET* 2.8 52.8 + - + +
96B VAL* 4.0 14.1 - - + -
98B ILE* 4.8 1.6 - - + -
103B PRO* 3.8 27.6 - - + +
104B PRO 3.4 25.4 - - - +
105B ASN 3.5 0.2 + - - -
107B ALA 3.0 16.4 + - - +
109B LEU* 4.1 13.4 - - + +
112B ILE* 3.7 26.2 - - + -
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Residues in contact with MET 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 4.9 7.4 - - + +
76A MET* 3.6 30.1 - - + -
105A ASN* 3.7 30.5 - - + +
106A SER* 3.8 21.5 - - - -
74B THR* 3.9 4.9 - - - +
75B VAL* 1.3 73.5 - - - +
77B GLU* 1.3 65.9 + - - +
79B MET* 3.2 23.6 + - - +
80B MET* 3.0 35.2 + - - +
105B ASN* 2.9 38.6 + - + +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A MET* 4.0 22.6 - - - +
80A MET* 3.4 30.8 - - + +
83A ARG* 5.7 5.2 + - - -
69B LEU* 5.5 0.4 - - - -
72B THR 4.2 2.4 - - - +
73B ALA* 3.7 18.5 - - + +
74B THR* 3.1 42.7 + - - +
76B MET* 1.3 75.4 - - - +
78B PHE* 1.3 57.9 + - - +
80B MET 3.1 1.6 + - - -
81B ALA* 2.8 28.2 + - - +
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.9 22.7 - - + -
35B CYS* 4.2 17.3 - - - -
67B PHE* 4.3 9.9 - + - -
69B LEU* 3.2 41.8 - - + +
74B THR 3.0 13.6 + - - +
75B VAL* 3.5 9.0 - - - +
77B GLU* 1.3 74.8 - - - +
79B MET* 1.3 58.0 + - - +
81B ALA* 3.4 4.3 + - + +
82B LEU* 2.9 45.1 + - + +
96B VAL* 4.2 19.3 - - + -
98B ILE* 6.5 0.7 - - + -
109B LEU* 3.7 22.2 - - + -
125B VAL* 3.8 27.6 - - + -
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Residues in contact with MET 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 2.8 31.1 + - + +
76B MET* 3.2 36.5 + - - +
78B PHE* 1.3 73.1 - - - +
80B MET* 1.3 62.6 + - - +
82B LEU* 3.6 7.9 + - - +
83B ARG* 3.0 26.0 + - - +
94B VAL* 4.0 31.5 - - + +
95B PHE* 4.6 1.3 - - - -
96B VAL* 4.0 34.5 - - + -
105B ASN* 2.8 32.1 - - - +
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Residues in contact with MET 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 3.8 15.3 - - - -
76A MET* 4.0 19.3 - - + -
77A GLU* 2.9 51.1 - - + +
80A MET* 3.6 16.2 - - - -
76B MET* 3.0 27.8 + - - +
77B GLU 3.6 7.2 - - - +
79B MET* 1.3 77.0 - - - +
81B ALA* 1.3 66.9 + - - +
83B ARG* 3.3 35.2 + - + +
84B GLN* 3.3 18.9 + - - +
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Residues in contact with ALA 81 (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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80A MET* 4.3 10.8 - - + +
69B LEU* 5.4 7.0 - - + -
77B GLU 2.8 16.8 + - - +
78B PHE* 3.7 10.5 - - + +
80B MET* 1.3 76.8 - - - +
82B LEU* 1.3 60.4 + - - +
83B ARG 3.3 0.2 + - - -
84B GLN* 3.4 13.2 + - - +
85B ARG* 3.1 23.0 + - - +
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Residues in contact with LEU 82 (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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35B CYS* 4.2 11.4 - - - -
67B PHE* 3.7 37.9 - - + -
78B PHE* 2.9 30.4 + - + +
79B MET* 3.7 4.9 - - - +
81B ALA* 1.3 75.8 - - - +
83B ARG* 1.3 64.0 + - - +
85B ARG* 3.4 18.7 - - + +
86B LEU* 3.4 23.0 + - + +
94B VAL* 3.5 27.6 - - + -
96B VAL* 4.1 11.0 - - + -
127B TYR* 3.9 24.7 - - + -
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Residues in contact with ARG 83 (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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77A GLU* 3.8 11.2 + - - +
79B MET 3.0 15.2 + - - +
80B MET* 3.4 34.1 - - + +
81B ALA 3.2 0.4 - - - -
82B LEU* 1.3 74.6 - - - +
84B GLN* 1.3 64.9 + - - +
86B LEU* 3.0 26.7 + - - +
88B LEU* 3.5 39.5 + - + +
89B GLU 3.0 36.0 + - - -
90B GLU* 3.5 21.2 + - - +
91B GLY 4.3 0.6 - - - +
92B GLN 2.9 18.2 + - - +
93B ALA* 4.8 4.7 - - - +
94B VAL* 3.8 13.9 - - + +
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Residues in contact with GLN 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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77A GLU* 5.5 8.7 - - + +
84A GLN* 4.5 18.0 + - - +
80B MET 3.3 11.5 + - - +
81B ALA* 3.6 12.1 - - - +
83B ARG* 1.3 77.4 - - - +
85B ARG* 1.3 65.7 + - - +
86B LEU 2.8 15.7 + - - +
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 4.0 31.1 - - + -
81B ALA 3.1 10.5 + - - +
82B LEU* 3.4 18.6 - - + +
84B GLN* 1.3 78.1 - - - +
86B LEU* 1.3 63.5 + - + +
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Residues in contact with LEU 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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65B ASN* 6.1 2.9 - - - +
82B LEU* 3.4 22.2 + - + +
83B ARG 3.0 12.9 + - - +
84B GLN* 2.9 13.1 - - - +
85B ARG* 1.3 82.9 - - + +
87B LEU* 1.3 59.0 + - - +
88B LEU* 2.8 34.6 + - + -
94B VAL* 4.6 9.4 - - + -
127B TYR* 4.0 37.7 - - + +
129B VAL* 5.1 4.3 - - + -
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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
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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