Contacts of the strand formed by residues 64 - 70 (chain C) in PDB entry 2V32
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 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C TRP* 3.5 18.4 - - + -
32C GLY 4.1 4.3 - - - +
33C VAL* 3.5 33.9 - - + +
59C PHE* 3.1 44.3 + - + +
60C LYS* 4.3 2.9 + - - +
62C ARG* 3.6 18.8 - - + +
63C GLY* 1.3 77.3 - - - +
65C LYS* 1.3 66.4 + - - +
66C LEU* 3.8 1.6 + - + +
132C ILE* 6.1 0.9 - - + -
160C ILE* 3.8 28.3 - - + -
164C GLN* 3.8 0.4 - - - +
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Residues in contact with LYS 65 (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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26C TRP* 3.4 39.3 + - + +
27C LEU* 3.0 34.4 + - + +
28C GLY* 4.8 2.4 - - - -
29C ASN 5.6 0.2 - - - +
30C SER* 3.6 20.8 - - - +
31C TRP 3.1 8.8 + - - +
32C GLY* 3.2 2.1 - - - -
33C VAL 2.7 32.6 + - - +
63C GLY 5.1 1.1 - - - +
64C VAL* 1.3 73.4 - - - +
66C LEU* 1.3 57.1 + - - +
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Residues in contact with LEU 66 (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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26C TRP* 3.4 5.7 - - - -
33C VAL* 3.5 19.7 - - + -
35C PHE* 4.3 11.0 - - + -
52C VAL* 3.7 30.3 - - + -
56C GLU* 4.6 15.0 - - + +
59C PHE* 3.7 52.7 - - + -
64C VAL 3.8 1.3 + - - +
65C LYS* 1.3 75.6 - - - +
67C ILE* 1.3 63.4 + - - +
95C PRO* 6.0 0.7 - - + +
96C TYR* 3.3 34.6 - - + +
97C PRO* 3.4 8.8 - - - +
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Residues in contact with ILE 67 (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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21C LEU* 3.9 25.4 - - + -
23C PHE* 4.0 9.0 - - + -
26C TRP* 3.5 31.9 - - + -
33C VAL 2.9 9.6 + - - +
34C LEU* 3.2 28.9 - - + +
35C PHE* 3.0 29.7 + - - -
66C LEU* 1.3 75.4 - - - +
68C ALA* 1.3 62.7 + - - +
96C TYR* 4.7 0.7 - - - -
97C PRO* 3.7 23.3 - - + +
99C ILE* 3.5 29.8 - - + -
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Residues in contact with ALA 68 (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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34C LEU* 4.7 0.2 - - - -
35C PHE* 3.1 34.2 - - + +
37C HIS* 4.8 1.8 - - + -
49C LEU* 4.2 7.2 - - + -
67C ILE* 1.3 75.4 - - - +
69C LEU* 1.3 63.6 + - - +
96C TYR* 3.9 13.7 - - + -
97C PRO 3.1 13.8 + - - +
98C ILE* 3.5 15.4 - - + -
99C ILE* 3.0 26.7 + - - +
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Residues in contact with LEU 69 (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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34C LEU* 4.2 16.6 - - + -
35C PHE 3.1 9.2 + - - +
36C SER* 3.1 7.8 - - - -
37C HIS* 2.9 32.4 + - - -
68C ALA* 1.3 77.5 - - - +
70C SER* 1.3 75.5 + - - +
98C ILE* 3.8 2.0 - - - +
99C ILE* 3.4 30.3 - - + +
101C ASP* 4.1 9.0 - - + -
106C LEU* 3.7 30.7 - - + -
110C LEU* 5.3 0.2 - - + -
112C MET* 3.7 30.5 - - + -
126C THR* 3.7 14.6 - - + -
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Residues in contact with SER 70 (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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37C HIS* 3.1 40.3 - - - -
38C PRO 4.3 1.6 - - - -
40C ASP* 3.1 2.6 + - - -
69C LEU* 1.3 82.6 - - - +
71C CYS* 1.3 58.4 + - - +
72C ASP* 2.7 30.1 + - - +
77C HIS* 3.1 16.6 + - - -
99C ILE 3.1 10.4 + - - +
100C ALA* 3.5 1.0 - - - -
101C ASP* 2.8 21.5 + - - +
126C THR* 4.2 0.9 - - - -
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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