Contacts of the helix formed by residues 74 - 84 (chain A) in PDB entry 3WAP
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LEU* 1.3 73.5 - - - +
75A MET* 1.3 62.4 + - - +
76A THR* 2.9 11.6 + - - -
77A GLN* 2.5 61.7 + - + +
78A PHE* 2.9 18.7 + - - +
106A MET 4.0 9.4 - - - -
107A SER* 4.5 9.9 - - - +
108A ALA 3.5 11.0 - - - +
109A THR* 4.6 1.0 - - - +
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Residues in contact with MET 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU 3.3 3.2 + - - -
74A THR* 1.3 70.3 - - - +
76A THR* 1.3 53.7 + - - +
78A PHE* 3.4 5.3 - - - +
79A LEU* 2.4 40.2 + - + +
96A LEU* 3.6 48.5 - - + +
98A VAL* 5.1 4.0 - - + -
104A VAL* 4.3 12.1 - - + -
105A SER 3.9 13.2 - - - +
106A MET* 3.7 31.9 + - + -
108A ALA* 3.6 10.6 + - + +
110A MET* 3.9 20.9 - - + +
113A ILE* 4.7 12.8 - - + -
126A MET* 4.1 16.8 - - - -
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 2.9 9.7 + - - -
75A MET* 1.3 78.1 - - - +
77A GLN* 1.3 67.5 + - + +
79A LEU* 3.1 9.6 + - + +
80A SER* 2.8 21.7 + - - -
106A MET* 2.7 35.9 + - - +
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Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.3 28.0 - - + +
74A THR* 2.5 59.1 + - + +
76A THR* 1.3 72.4 - - + +
78A PHE* 1.3 57.2 + - - +
80A SER* 2.6 29.4 + - - -
81A ILE* 2.9 20.1 + - + +
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Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 4.0 17.0 - - + -
50A VAL* 3.8 22.4 - - + -
67A PHE* 4.3 20.9 - + + -
69A VAL* 4.1 24.0 - - + -
73A LEU* 4.7 3.7 - - + +
74A THR 2.9 9.1 + - - +
75A MET* 3.4 5.4 - - - +
77A GLN* 1.3 75.3 - - - +
79A LEU* 1.3 65.0 + - - +
81A ILE* 3.1 19.1 + - + +
82A ILE* 2.8 50.9 + - + +
96A LEU* 4.0 11.4 - - + -
110A MET* 3.3 33.0 - - + -
126A MET* 3.9 15.7 - - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A MET* 2.4 27.4 + - + +
76A THR* 3.3 8.5 - - + +
78A PHE* 1.3 73.3 - - - +
80A SER* 1.3 67.1 + - - +
82A ILE* 2.7 20.4 + - - +
83A ARG* 2.8 30.2 + - + +
94A PHE* 3.4 48.5 - - + +
95A TYR* 5.5 0.2 - - - -
96A LEU* 4.3 26.2 - - + +
106A MET* 4.7 19.1 - - + -
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A THR* 2.8 12.3 + - - -
77A GLN* 2.6 18.3 + - - -
79A LEU* 1.3 72.4 - - - +
81A ILE* 1.3 52.5 + - - -
83A ARG* 2.9 11.3 + - - +
84A SER* 2.6 37.7 + - - -
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PHE* 5.5 0.9 - - - -
69A VAL* 5.5 1.6 - - + -
73A LEU* 4.1 19.7 - - + -
77A GLN* 2.9 19.7 + - + +
78A PHE* 3.6 25.4 - - + +
80A SER* 1.3 73.2 + - - +
82A ILE* 1.3 60.4 + - - +
84A SER* 3.6 13.3 + - - +
85A ARG* 3.5 24.8 - - + +
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Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 4.2 16.2 - - + -
62A LEU* 4.3 13.5 - - + +
67A PHE* 4.7 13.9 - - + -
78A PHE* 2.8 62.0 + - + +
79A LEU* 2.7 8.1 + - - +
81A ILE* 1.3 77.2 - - - +
83A ARG* 1.3 67.4 + - - +
84A SER 2.9 1.6 - - - -
85A ARG* 2.9 18.8 + - - +
86A MET* 3.4 21.1 - - + +
94A PHE* 3.7 21.8 - - + -
96A LEU* 4.1 13.9 - - + -
128A TYR* 5.5 1.3 - - + -
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 2.8 29.1 + - + +
80A SER* 3.6 9.6 - - - +
82A ILE* 1.3 73.7 - - - +
84A SER* 1.3 61.5 + - - +
86A MET* 3.3 23.8 + - + +
89A ARG* 3.5 26.2 + - + +
90A ALA* 3.5 33.1 + - + +
92A GLU 3.0 22.1 + - - -
93A ALA* 3.2 28.1 - - - +
94A PHE* 3.5 35.5 + - + +
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER* 2.6 22.6 + - - -
81A ILE* 3.6 22.8 + - - +
82A ILE 2.9 0.6 - - - -
83A ARG* 1.3 74.4 - - - +
85A ARG* 1.3 62.3 + - - +
86A MET 3.4 5.7 + - - +
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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