Contacts of the helix formed by residues 75 - 86 (chain B) in PDB entry 1W7A
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 ALA 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PRO* 2.8 19.9 + - + +
74B HIS* 1.3 84.0 + - + +
76B VAL* 1.3 65.0 + - - +
77B GLU 3.2 2.9 - - - -
78B ASN* 2.9 23.1 + - + +
79B TYR* 3.1 32.9 - - + -
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Residues in contact with VAL 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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30B PHE* 4.2 7.4 - - + -
37B TYR* 3.2 43.1 - - + -
71B ILE* 3.9 20.9 - - + -
72B PRO 3.5 12.1 - - - +
73B TYR* 3.2 21.8 + - - +
74B HIS 3.7 0.4 - - - -
75B ALA* 1.3 77.4 - - - +
77B GLU* 1.3 61.3 + - - +
79B TYR* 3.3 1.6 + - - +
80B LEU* 2.8 46.0 + - + +
92B ILE* 4.7 3.4 - - + -
112B ARG* 5.7 0.4 - - - +
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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
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75B ALA 3.2 1.0 - - - -
76B VAL* 1.3 81.9 - - + +
78B ASN* 1.3 62.8 + - - +
80B LEU* 3.5 8.2 - - - +
81B ALA* 3.0 21.1 + - - +
112B ARG* 2.8 44.4 + - - -
121B ASP* 4.6 4.6 - - - +
123B ALA* 4.4 22.3 - - + +
124B LEU* 3.3 23.6 - - - +
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Residues in contact with ASN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA* 2.9 19.4 + - + +
77B GLU* 1.3 80.0 - - - +
79B TYR* 1.3 68.3 + - + +
81B ALA* 3.2 9.7 + - - +
82B LYS* 3.2 56.1 + - - +
123B ALA 6.0 0.2 - - - -
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Residues in contact with TYR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 5.1 1.8 - - + -
51B LEU* 3.6 40.8 - - + +
53B ILE* 4.5 13.1 - - + +
71B ILE* 3.7 49.8 - - + -
72B PRO* 4.5 9.2 - - + +
75B ALA* 3.1 39.7 + - + -
76B VAL 3.9 0.4 - - - +
78B ASN* 1.3 78.7 - - + +
80B LEU* 1.3 61.0 + - - +
82B LYS* 3.3 25.2 + - + +
83B LEU* 3.0 32.9 + - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 4.1 7.4 - - + -
76B VAL* 2.8 30.0 + - + +
77B GLU* 3.5 17.3 - - - +
78B ASN 3.2 0.2 - - - -
79B TYR* 1.3 74.9 - - - +
81B ALA* 1.3 54.7 + - - +
83B LEU* 3.3 3.8 + - - +
84B VAL* 2.8 39.3 + - - +
90B VAL* 3.5 39.5 - - + -
92B ILE* 4.0 11.9 - - + -
112B ARG* 3.4 38.8 - - - +
114B VAL* 4.0 11.9 - - + -
124B LEU* 3.8 11.0 - - + -
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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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77B GLU 3.0 13.4 + - - +
78B ASN* 3.4 12.3 - - - +
80B LEU* 1.3 75.8 - - - +
82B LYS* 1.3 58.9 + - + +
84B VAL* 3.8 5.1 - - - +
85B ASN* 2.8 30.3 + - - +
123B ALA 4.0 18.2 - - - +
124B LEU* 3.6 20.6 - - + +
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Residues in contact with LYS 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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51B LEU* 3.6 25.7 + - + +
78B ASN* 3.2 35.6 + - - +
79B TYR* 3.6 26.5 + - + +
80B LEU 3.2 0.2 - - - -
81B ALA* 1.3 75.1 - - + +
83B LEU* 1.3 66.3 + - - +
85B ASN* 3.1 7.3 + - - +
86B GLN* 3.1 35.9 + - - +
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Residues in contact with LEU 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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28B LEU* 3.7 18.6 - - + -
30B PHE* 3.5 27.6 - - + -
39B LEU* 5.7 0.2 - - + -
47B ALA* 5.4 4.0 - - + -
50B LEU* 4.3 24.7 - - + -
51B LEU* 3.8 28.5 - - + -
79B TYR 3.0 19.8 + - - +
80B LEU 3.7 3.1 - - - +
82B LYS* 1.3 75.7 - - - +
84B VAL* 1.3 63.2 + - - +
86B GLN* 3.0 13.0 + - - +
88B GLU* 3.0 27.8 + - + +
90B VAL* 3.4 32.3 - - + -
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Residues in contact with VAL 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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80B LEU 2.8 22.9 + - - +
81B ALA* 3.9 5.4 - - - +
83B LEU* 1.3 73.4 - - + +
85B ASN* 1.3 65.0 + - - +
87B GLY 3.0 11.6 + - - -
88B GLU 3.7 15.3 - - - +
90B VAL* 5.5 0.2 - - + -
114B VAL* 4.0 24.2 - - + -
115B THR 4.3 2.5 - - - -
116B PRO* 3.6 35.8 - - + +
119B ILE* 3.6 35.2 - - + -
124B LEU* 4.7 5.4 - - + +
131B ASN* 5.5 3.9 + - - +
176B ALA* 5.3 2.6 - - - +
194B ARG* 5.8 0.2 + - - -
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Residues in contact with ASN 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 ALA 2.8 20.9 + - - +
82B LYS* 3.1 8.5 + - - +
84B VAL* 1.3 78.8 - - - +
86B GLN* 1.3 62.2 + - - +
87B GLY 3.5 2.4 + - - -
126B GLN* 3.7 30.1 + - - +
129B GLN* 5.4 0.4 + - - -
131B ASN* 6.3 0.9 - - - +
194B ARG* 4.0 17.0 + - - -
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Residues in contact with GLN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.2 55.7 + - + +
51B LEU* 4.3 2.6 - - - +
82B LYS* 3.3 29.1 + - - +
83B LEU* 3.0 11.2 + - - +
85B ASN* 1.3 83.8 - - - +
87B GLY* 1.3 59.7 + - - +
88B GLU* 3.3 12.7 + - + +
194B ARG* 3.9 15.0 - - - +
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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