Contacts of the strand formed by residues 86 - 91 (chain C) in PDB entry 6XHU
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C TYR* 5.0 5.6 - - + -
38C CYS 3.4 13.9 - - - +
40C ARG* 4.3 4.3 - - - -
82C MET* 3.6 4.2 - - - +
83C GLN* 2.8 56.8 + - + +
85C CYS* 1.3 82.0 - - - +
87C LEU* 1.3 64.2 + - - +
88C LYS* 4.7 6.5 - - + -
162C MET* 4.1 17.9 - - + -
164C HIS* 4.2 2.2 - - - +
175C THR* 4.1 12.6 - - - +
176C ASP 4.5 2.7 - - - +
177C LEU* 4.2 12.3 - - + +
178C GLU 4.2 3.8 - - - -
179C GLY* 3.7 24.5 - - - +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C VAL 3.5 1.4 - - - +
37C TYR* 3.5 5.7 - - - -
38C CYS* 2.8 40.7 + - - +
40C ARG* 4.0 15.7 - - + +
42C VAL* 3.8 20.6 - - + -
43C ILE* 3.8 12.1 - - + -
58C LEU* 4.1 24.9 - - + -
66C PHE* 3.8 29.8 - - + -
80C HIS* 5.1 2.2 - - + -
81C SER 3.4 25.1 - - - +
82C MET* 4.1 5.4 - - + -
86C VAL* 1.3 74.7 - - - +
88C LYS* 1.3 63.2 - - - +
89C LEU* 4.0 13.5 - - + -
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C VAL* 3.9 12.6 - - + -
36C VAL 3.5 4.0 - - - -
37C TYR* 3.5 36.4 + - + +
80C HIS* 3.3 4.0 - - - +
81C SER* 2.8 53.6 + - - +
83C GLN* 3.0 41.5 + - + +
86C VAL* 4.7 2.7 - - + -
87C LEU* 1.3 75.2 - - - +
89C LEU* 1.3 61.8 + - - +
90C LYS 4.0 0.9 + - - -
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL* 4.1 21.1 - - + -
35C VAL* 3.4 3.0 - - - -
36C VAL* 2.8 50.3 + - + +
38C CYS* 4.6 7.2 - - - -
66C PHE* 4.1 34.5 - - + -
68C VAL* 3.9 24.5 - - + -
77C VAL* 4.4 13.0 - - + -
79C GLY 3.5 4.0 - - - +
80C HIS* 3.8 23.8 - - + -
87C LEU* 4.4 15.5 - - + -
88C LYS* 1.3 73.6 - - - +
90C LYS* 1.3 63.9 + - - +
91C VAL* 3.6 3.4 + - + +
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Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASP* 2.8 45.8 + - - +
35C VAL* 3.9 15.9 - - + +
77C VAL* 3.4 4.5 - - - -
78C ILE* 2.6 42.5 + - + -
79C GLY* 2.7 26.0 + - - +
88C LYS 4.0 1.8 + - - -
89C LEU* 1.3 72.4 - - - +
91C VAL* 1.3 63.3 + - - +
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TRP* 3.8 13.5 - - + +
34C ASP* 3.0 34.6 + - - +
35C VAL 4.3 0.4 - - - +
36C VAL* 4.2 15.3 - - + -
68C VAL* 4.8 3.4 - - + -
75C LEU* 4.1 23.3 - - + -
76C ARG 3.1 12.8 - - - +
77C VAL* 4.3 15.3 - - + -
78C ILE* 4.1 4.8 - - - +
89C LEU* 4.0 7.6 - - + +
90C LYS* 1.3 84.0 - - - +
92C ASP* 1.3 63.3 + - - +
93C THR 3.4 21.7 + - - +
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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