Contacts of the strand formed by residues 95 - 101 (chain C) in PDB entry 2VK8
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 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C ALA 5.2 1.6 - - - +
58C ALA* 3.8 7.6 - - + -
59C ASP* 4.0 17.5 - - - +
68C SER* 3.4 22.7 - - - +
70C ILE* 3.8 28.0 - - + +
85C ILE* 4.1 12.8 - - + -
88C SER* 3.6 31.2 - - - +
93C VAL* 3.1 9.4 + - + +
94C GLY* 1.3 74.3 - - - +
96C LEU* 1.3 62.3 + - - +
97C HIS 3.6 1.0 + - - -
156C THR* 3.5 3.7 - - - +
162C PRO* 3.0 29.5 - - + +
163C VAL 3.1 4.2 + - - -
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Residues in contact with LEU 96 (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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10C LEU* 4.5 7.6 - - + -
14C LEU* 4.2 15.0 - - + -
67C MET* 4.4 3.4 - - + -
68C SER 2.9 18.6 + - - +
69C CYS* 3.2 6.4 - - - -
70C ILE* 2.9 27.4 + - - +
95C VAL* 1.3 72.0 - - - +
97C HIS* 1.3 59.3 + - - +
98C VAL* 3.7 20.3 + - + -
152C CYS* 3.9 24.2 - - + +
153C ILE* 3.9 25.1 - - + -
156C THR* 3.7 23.1 - - + +
163C VAL* 3.7 15.3 - - + +
165C LEU* 4.3 14.6 - - + -
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Residues in contact with HIS 97 (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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70C ILE* 3.5 18.2 - - + -
72C THR* 2.8 29.2 + - + +
78C GLU* 3.7 33.9 - - + -
81C ALA* 4.1 10.3 - - + +
82C LEU* 4.5 7.5 - - + +
85C ILE* 3.9 31.9 - - + +
95C VAL 3.6 1.4 + - - +
96C LEU* 1.3 70.3 - - - +
98C VAL* 1.3 71.6 + - - +
99C VAL* 3.7 6.9 + - + +
129C SER* 4.7 0.4 + - - -
162C PRO* 5.9 0.2 - - + -
163C VAL 2.8 15.6 + - - +
164C TYR* 3.5 17.3 - + + -
165C LEU 2.8 25.5 + - - -
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Residues in contact with VAL 98 (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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10C LEU* 4.4 9.4 - - + -
33C LEU* 4.0 17.5 - - + -
69C CYS* 3.8 22.4 - - - -
70C ILE 2.8 9.7 + - - +
71C ILE* 3.1 13.3 - - + +
72C THR 3.0 23.9 + - - -
96C LEU* 3.9 18.6 - - + -
97C HIS* 1.3 76.8 - - - +
99C VAL* 1.3 65.3 + - - +
165C LEU* 3.2 20.4 - - + +
167C LEU* 3.7 29.6 - - + -
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Residues in contact with VAL 99 (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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72C THR* 3.5 4.3 - - - +
73C THR 3.9 4.5 - - - -
74C PHE* 3.7 19.7 - - - +
78C GLU* 3.6 28.0 - - + +
97C HIS* 3.7 22.0 - - + +
98C VAL* 1.3 80.6 - - - +
100C GLY* 1.3 63.8 + - - +
101C VAL* 3.4 9.7 + - + +
164C TYR* 3.5 37.2 - - + +
165C LEU 2.9 11.3 + - - +
166C GLY* 3.5 1.7 - - - -
167C LEU* 2.8 28.1 + - - -
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Residues in contact with GLY 100 (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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29C PHE* 3.3 28.5 - - - +
30C ASN* 4.0 11.7 - - - +
33C LEU* 5.4 3.4 - - - -
71C ILE* 4.9 2.0 - - - +
72C THR 3.0 13.9 + - - -
73C THR 3.8 0.3 - - - -
74C PHE* 3.0 26.0 + - - +
98C VAL* 4.2 0.6 - - - +
99C VAL* 1.3 69.2 - - - +
101C VAL* 1.3 58.4 + - - -
167C LEU* 3.5 9.2 - - - -
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Residues in contact with VAL 101 (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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29C PHE* 4.1 4.8 - - - +
74C PHE* 3.7 18.6 - - + -
99C VAL* 3.6 22.7 - - + +
100C GLY* 1.3 77.7 - - - +
102C PRO* 1.4 81.5 - - + +
107C GLN* 3.9 7.9 - - - +
138C MET* 4.0 27.8 - - + -
164C TYR* 4.8 1.6 - - - +
166C GLY* 4.4 1.6 - - - -
167C LEU 3.0 8.7 + - - -
168C PRO* 3.4 33.4 - - + -
169C ALA* 2.9 24.8 + - - +
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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