Contacts of the strand formed by residues 64 - 70 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B TRP* 3.6 9.9 - - + -
32B GLY* 4.2 4.7 - - - +
33B VAL* 3.4 39.5 - - + +
59B PHE* 3.1 41.3 + - + +
60B LYS* 4.2 4.1 + - - +
62B ARG* 3.5 26.9 - - + +
63B GLY* 1.3 76.5 - - - +
65B LYS* 1.3 63.9 + - - +
66B LEU* 3.8 2.4 + - - +
132B ILE* 5.8 0.4 - - + -
160B ILE* 4.0 17.3 - - + -
164B GLN* 3.8 13.5 - - - +
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Residues in contact with LYS 65 (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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25B ASP 5.3 0.4 + - - -
26B TRP* 3.0 54.9 + - + +
27B LEU* 3.1 24.5 + - + +
28B GLY* 4.9 1.4 - - - -
30B SER* 3.4 20.0 - - - +
31B TRP 3.0 11.4 + - - +
32B GLY* 3.2 2.9 - - - -
33B VAL 2.8 30.7 + - - +
63B GLY 3.9 0.6 + - - -
64B VAL* 1.3 70.4 - - - +
66B LEU* 1.3 56.7 + - - +
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Residues in contact with LEU 66 (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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26B TRP* 3.5 12.5 - - - -
33B VAL* 3.4 20.0 - - + -
35B PHE* 4.1 11.0 - - + -
52B VAL* 3.6 26.7 - - + -
56B GLU* 4.4 12.6 - - + +
59B PHE* 3.5 60.3 - - + -
64B VAL 3.8 0.8 + - - +
65B LYS* 1.3 73.0 - - - +
67B ILE* 1.3 62.8 + - - +
95B PRO* 5.6 1.3 - - + +
96B TYR* 3.4 32.5 - - + +
97B PRO* 3.6 1.6 - - - +
153B PHE* 5.9 1.1 - - + -
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Residues in contact with ILE 67 (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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21B LEU* 4.2 12.8 - - + -
23B PHE* 4.1 8.5 - - + -
26B TRP* 3.5 35.4 - - + -
32B GLY* 6.4 0.2 - - - -
33B VAL 2.9 16.5 + - - +
34B LEU* 3.3 21.5 - - + +
35B PHE* 2.9 30.1 + - - -
66B LEU* 1.3 76.4 - - - +
68B ALA* 1.3 64.4 + - - +
96B TYR* 4.6 0.9 - - - -
97B PRO* 3.7 32.5 - - + +
99B ILE* 3.5 33.4 - - + -
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Residues in contact with ALA 68 (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 LEU* 4.8 0.2 - - - -
35B PHE* 3.2 33.2 - - + +
37B HIS* 4.9 2.2 - - - +
49B LEU* 4.3 7.6 - - + -
67B ILE* 1.3 77.9 - - - +
69B LEU* 1.3 63.4 + - - +
96B TYR* 4.0 12.5 - - + -
97B PRO 3.0 14.3 + - - +
98B ILE* 3.3 13.1 - - + -
99B ILE* 2.8 25.7 + - - +
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Residues in contact with LEU 69 (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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12B PHE* 5.3 0.4 - - + -
34B LEU* 4.2 16.8 - - + -
35B PHE 2.8 13.6 + - - +
36B SER* 3.1 9.1 - - - -
37B HIS* 3.0 32.3 + - - -
68B ALA* 1.3 79.1 - - - +
70B SER* 1.3 69.1 + - - +
98B ILE* 4.3 0.4 - - - -
99B ILE* 3.6 40.6 - - + -
101B ASP* 4.1 7.0 - - + -
106B LEU* 3.8 20.2 - - + -
110B LEU* 5.4 0.2 - - + -
112B MET* 3.5 33.4 - - + -
126B THR* 3.7 15.7 - - + -
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Residues in contact with SER 70 (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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37B HIS* 3.3 40.0 - - - -
38B PRO 4.3 3.4 - - - -
40B ASP* 3.3 2.3 + - - -
69B LEU* 1.3 80.9 - - - +
71B CYS* 1.3 60.4 + - - +
72B ASP* 2.9 29.6 + - - +
77B HIS* 3.2 12.2 + - - -
99B ILE 3.3 9.6 + - - +
100B ALA* 3.7 0.7 - - - -
101B ASP* 2.8 23.9 + - - +
126B THR* 4.3 1.3 - - - -
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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