Contacts of the strand formed by residues 71 - 78 (chain B) in PDB entry 1VWJ
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 THR 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA 4.2 11.8 + - - +
17B ILE* 4.4 9.4 - - + -
60B TYR* 4.2 14.8 - - + -
61B ASP 3.2 27.1 - - - +
62B SER* 5.1 0.2 - - - -
63B ALA* 4.8 12.1 + - - +
65B ALA* 5.6 2.1 - - - +
69B SER 5.2 0.7 + - - -
70B GLY* 1.3 73.5 - - - -
72B ALA* 1.3 69.0 + - - +
73B LEU* 3.7 1.4 + - - +
95B GLN* 3.2 3.5 - - - -
96B TYR* 2.8 55.5 + - - +
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Residues in contact with ALA 72 (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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60B TYR* 3.4 1.7 - - - +
61B ASP* 2.9 31.1 + - + +
70B GLY 4.0 2.8 + - - -
71B THR* 1.3 76.1 - - - +
73B LEU* 1.3 60.0 + - - +
94B GLY 3.5 10.1 - - - +
95B GLN* 4.3 2.2 - - - +
87D HIS 4.1 7.8 + - - +
88D SER* 3.6 37.0 - - - +
89D ALA* 3.8 3.6 - - + +
111D THR* 3.7 11.7 - - - +
112D SER 4.4 0.9 - - - -
113D GLY* 4.2 7.4 - - - +
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Residues in contact with LEU 73 (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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17B ILE* 4.1 20.6 - - + -
39B LEU* 4.3 9.6 - - + -
59B ARG 3.2 14.8 - - - +
60B TYR* 3.7 9.4 - - + +
71B THR 3.9 6.1 - - - +
72B ALA* 1.3 77.8 - - - +
74B GLY* 1.3 60.7 + - - +
75B TRP* 3.7 26.0 - - + -
93B SER* 3.7 2.6 + - - -
94B GLY 3.1 41.5 + - - +
96B TYR* 3.8 27.8 - - + +
104B ILE* 4.1 22.7 - - + -
89D ALA* 3.9 13.4 - - - +
111D THR* 5.4 0.3 - - - -
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Residues in contact with GLY 74 (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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39B LEU* 4.0 2.1 - - - +
58B GLY* 3.1 1.9 - - - -
59B ARG 3.0 28.6 + - - +
73B LEU* 1.3 79.4 - - - +
75B TRP* 1.3 67.1 + - - +
92B TRP 3.0 15.3 - - - -
76D THR* 3.3 18.3 + - - +
91D THR* 3.8 5.4 - - - -
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Residues in contact with TRP 75 (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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29B PHE* 3.5 44.8 - + - -
39B LEU* 4.4 8.1 - - + -
43B TYR* 4.2 4.6 - + - -
56B LEU* 4.1 26.5 - - + -
57B THR 3.2 17.0 - - - +
58B GLY* 3.9 3.8 - - - -
73B LEU* 3.7 26.7 - - + -
74B GLY* 1.3 80.0 - - - +
76B THR* 1.3 65.9 + - - +
77B VAL* 4.3 0.7 - - + -
91B THR* 3.2 5.2 - - - -
92B TRP* 3.0 79.8 + + + -
104B ILE* 4.3 7.2 - - + -
106B THR* 3.9 10.3 - - + -
130B PHE* 3.9 31.9 - + - -
76D THR* 3.4 6.1 + - - -
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Residues in contact with THR 76 (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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56B LEU* 3.2 24.4 - - - +
57B THR 3.0 11.7 + - - -
75B TRP* 1.3 79.0 - - - +
77B VAL* 1.3 71.5 + - - +
89B ALA* 4.7 3.8 - - + -
90B THR 3.3 13.2 - - - +
91B THR* 3.5 13.6 - - + +
57D THR 4.8 0.2 + - - -
58D GLY* 4.5 3.0 - - - -
59D ARG* 3.9 25.7 - - + +
74D GLY* 3.7 30.1 - - - +
75D TRP* 3.5 20.1 + - - -
76D THR* 3.9 1.0 + - - -
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Residues in contact with VAL 77 (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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43B TYR* 3.8 20.2 - - + -
54B TYR* 3.7 28.9 - - + -
55B VAL 3.9 7.2 - - - +
56B LEU* 3.6 20.4 - - + -
75B TRP* 4.3 1.3 - - + -
76B THR* 1.3 81.2 - - - +
78B ALA* 1.3 66.2 + - - +
79B TRP* 3.7 25.7 + - + -
89B ALA* 3.2 1.9 - - - +
90B THR 2.9 31.4 + - - -
92B TRP* 3.9 21.8 - - + -
59D ARG* 4.7 0.2 - - - -
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Residues in contact with ALA 78 (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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54B TYR* 4.0 3.6 - - - +
55B VAL 4.5 3.3 + - - +
77B VAL* 1.3 80.0 - - - +
79B TRP* 1.3 58.8 + - - +
80B LYS* 2.9 19.0 + - + +
88B SER 3.6 8.7 - - - +
89B ALA* 4.0 6.1 - - + +
59D ARG* 3.8 25.7 + - + +
60D TYR* 3.5 33.9 - - - +
61D ASP* 4.1 5.4 - - - +
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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