Contacts of the strand formed by residues 91 - 96 (chain A) in PDB entry 6W6Y
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 HIS 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A THR* 2.9 20.9 + - + +
34A VAL* 3.4 13.9 - - + -
35A VAL 3.1 22.9 + - - -
82A VAL* 4.0 21.0 - - + +
83A LEU 3.4 13.7 + - - +
84A SER* 5.1 1.4 - - - -
85A GLY* 3.5 5.4 - - - +
89A ALA* 3.4 5.7 - - - +
90A LYS* 1.3 119.6 + - + +
92A CYS* 1.3 61.8 + - - +
93A LEU 4.1 0.4 - - - -
119A HIS* 5.9 3.6 - + + -
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Residues in contact with CYS 92 (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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35A VAL* 3.2 19.1 - - + +
37A ASN* 3.7 20.0 - - - -
53A LEU* 5.0 0.9 - - - -
61A MET* 3.9 15.5 - - + -
81A CYS 3.5 2.9 - - - +
82A VAL* 3.5 2.6 - - - -
83A LEU 2.9 32.6 + - - -
84A SER 3.5 16.4 - - - +
85A GLY* 3.5 6.3 - - - +
91A HIS* 1.3 74.2 - - - +
93A LEU* 1.3 59.8 + - - +
94A HIS* 3.5 35.3 + - - +
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Residues in contact with LEU 93 (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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34A VAL* 3.9 17.3 - - + +
35A VAL 3.0 8.8 + - - +
36A VAL* 3.3 9.0 - - + +
37A ASN 2.9 23.6 + - - +
80A SER* 3.8 22.9 - - - +
81A CYS 3.7 3.8 - - - +
82A VAL* 3.6 27.8 - - + +
91A HIS 4.1 0.8 - - - -
92A CYS* 1.3 69.2 - - - +
94A HIS* 1.3 60.7 + - - +
95A VAL* 3.4 22.5 + - + -
115A ASN* 4.0 14.8 - - + +
116A PHE* 4.4 1.3 - - + -
118A GLN* 6.0 1.6 - - - +
119A HIS* 3.8 25.8 - - + +
122A LEU* 3.9 17.9 - - + -
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Residues in contact with HIS 94 (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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37A ASN* 3.0 34.3 + - - +
39A ALA* 3.9 3.6 - - + -
43A LEU* 3.8 21.8 - - + -
45A HIS* 3.6 22.9 - + - -
61A MET* 3.8 15.3 - - + +
64A GLU* 5.2 1.0 + - - -
65A SER* 4.1 2.8 + - - -
75A LEU* 4.2 2.7 - - + +
80A SER* 3.0 6.9 - - - -
81A CYS* 2.9 47.3 + - + +
83A LEU* 3.9 29.1 - - + +
84A SER 5.1 0.6 + - - -
92A CYS* 3.5 31.6 - - - +
93A LEU* 1.3 69.2 - - - +
95A VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 95 (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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36A VAL* 3.9 12.3 - - + -
37A ASN 3.0 12.0 + - - +
38A ALA* 3.8 3.5 - - - -
39A ALA* 2.9 22.3 + - - +
79A GLY 3.6 2.5 - - - -
80A SER* 3.9 6.3 - - - -
93A LEU* 3.6 35.2 - - + +
94A HIS* 1.3 78.9 - - - +
96A VAL* 1.3 64.6 + - - +
97A GLY 3.7 2.3 + - - -
112A ALA* 3.4 32.8 - - + +
115A ASN* 4.1 7.6 - - + +
116A PHE* 4.1 5.4 - - + -
127A LEU* 3.7 21.1 - - + +
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Residues in contact with VAL 96 (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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39A ALA* 3.5 15.0 - - + +
40A ASN* 3.8 23.8 - - - +
41A VAL* 3.9 22.2 - - + +
75A LEU* 3.7 35.4 - - + -
76A LYS 4.0 6.1 - - - +
77A VAL* 3.9 11.7 - - + -
78A GLY* 2.8 31.9 + - - -
79A GLY 2.9 13.1 + - - +
95A VAL* 1.3 72.3 - - - +
97A GLY* 1.3 70.8 + - - +
104A GLU* 5.5 0.4 - - - +
112A ALA* 3.7 4.5 - - - +
132A PHE* 5.2 0.7 - - + -
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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