Contacts of the strand formed by residues 86 - 91 (chain B) in PDB entry 6Y2G
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 VAL 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B TYR* 4.4 11.9 - - + -
38B CYS 3.5 9.4 - - - +
40B ARG* 4.3 4.3 - - - -
82B MET* 3.7 2.8 - - - +
83B GLN* 2.8 42.3 + - + +
84B ASN 3.3 0.2 - - - -
85B CYS* 1.3 80.9 - - - +
87B LEU* 1.3 72.3 + - - +
88B LYS* 4.3 12.8 - - + -
162B MET* 4.1 16.4 - - + -
164B HIS* 4.7 1.3 - - - +
175B THR* 4.0 11.9 - - - +
176B ASP 4.3 1.6 - - - +
177B LEU* 4.2 17.5 - - - +
178B GLU 5.2 0.2 - - - -
179B GLY* 3.6 23.6 - - - +
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Residues in contact with LEU 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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36B VAL 3.6 1.2 - - - +
37B TYR* 3.5 5.5 - - - -
38B CYS* 2.9 44.6 + - - +
40B ARG* 4.0 13.0 - - + +
42B VAL* 4.0 17.9 - - + -
43B ILE* 4.4 5.2 - - + -
58B LEU* 3.9 27.1 - - + -
66B PHE* 3.7 30.5 - - + -
80B HIS* 5.3 0.7 - - + -
81B SER 3.7 18.4 - - - +
82B MET* 4.3 13.5 - - + -
86B VAL* 1.3 73.9 - - - +
88B LYS* 1.3 60.6 + - - +
89B LEU* 3.8 19.7 - - + -
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Residues in contact with LYS 88 (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 VAL* 3.9 10.8 - - + -
36B VAL 3.5 4.7 - - - -
37B TYR* 3.5 35.2 - - + +
80B HIS* 3.4 4.0 - - - +
81B SER* 2.8 54.8 + - - +
83B GLN* 3.4 34.4 + - + +
86B VAL* 4.3 8.5 - - + +
87B LEU* 1.3 72.5 - - - +
89B LEU* 1.3 62.0 - - - +
90B LYS 3.8 1.8 + - - -
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Residues in contact with LEU 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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20B VAL* 4.1 28.9 - - + -
35B VAL* 3.5 2.9 - - - +
36B VAL* 2.8 49.3 + - + +
38B CYS* 4.7 6.3 - - - -
66B PHE* 3.8 34.3 - - + -
68B VAL* 4.2 10.8 - - + -
77B VAL* 4.2 13.7 - - + -
79B GLY 3.7 1.8 - - - -
80B HIS* 3.8 24.0 - - + -
87B LEU* 3.8 24.7 - - + -
88B LYS* 1.3 71.9 - - - +
90B LYS* 1.4 62.5 + - - +
91B VAL* 3.7 4.4 + - + +
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Residues in contact with LYS 90 (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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34B ASP* 3.2 44.3 + - - +
35B VAL* 4.2 12.7 - - + +
77B VAL* 3.2 11.6 - - - +
78B ILE* 2.9 44.0 + - + -
79B GLY* 3.0 24.8 + - - +
88B LYS 3.8 3.6 + - - -
89B LEU* 1.4 70.2 - - - +
91B VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 91 (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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31B TRP* 3.9 13.5 - - + +
34B ASP* 2.9 42.0 + - - +
35B VAL 4.2 0.7 - - - +
36B VAL* 4.1 16.4 - - + -
68B VAL* 4.9 1.8 - - + -
75B LEU* 4.2 17.7 - - + -
76B ARG 3.2 17.3 - - - +
77B VAL* 4.3 10.1 - - + +
78B ILE* 3.7 15.5 - - - +
89B LEU* 3.9 9.9 - - + +
90B LYS* 1.3 80.1 - - - +
92B ASP* 1.3 67.8 + - - +
93B THR 3.6 17.0 + - - +
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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