Contacts of the strand formed by residues 71 - 78 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLU* 5.7 1.2 + - - -
17D ILE* 4.2 10.5 - - + -
60D TYR* 4.0 17.3 - - + -
61D ASP 3.2 27.2 + - - +
69D SER 5.0 1.0 + - - -
70D GLY* 1.3 72.1 - - - -
72D ALA* 1.3 68.9 + - - +
73D LEU* 3.6 2.9 + - - +
95D GLN* 3.1 3.4 - - - -
96D TYR* 2.8 52.8 + - - +
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B HIS 4.0 9.1 + - - +
88B SER* 3.6 25.1 - - - +
89B ALA* 3.7 3.0 - - + +
111B THR 3.6 23.8 - - - +
112B SER 4.4 0.9 - - - -
113B GLY* 4.2 5.9 - - - +
60D TYR* 3.3 0.9 - - - +
61D ASP* 2.8 35.0 + - + +
70D GLY 3.9 3.6 + - - -
71D THR* 1.3 74.4 - - - +
73D LEU* 1.3 61.0 + - - +
94D GLY 3.5 8.3 - - - +
95D GLN* 4.3 2.9 - - - +
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ALA* 3.8 14.8 - - - +
111B THR* 5.1 0.2 - - - -
17D ILE* 4.0 27.6 - - + -
39D LEU* 4.3 8.3 - - + -
59D ARG 3.3 14.8 - - - +
60D TYR* 3.6 8.7 - - + +
71D THR 3.8 5.6 - - - +
72D ALA* 1.3 79.9 - - - +
74D GLY* 1.3 62.1 + - - +
75D TRP* 3.7 23.6 - - + -
93D SER* 3.7 2.9 + - - -
94D GLY 3.0 41.6 + - - +
96D TYR* 3.9 26.2 - - + +
104D ILE* 4.1 17.0 - - + -
106D THR* 5.0 0.4 - - + -
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Residues in contact with GLY 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B THR* 3.6 10.3 - - - +
91B THR* 3.8 10.8 - - - -
39D LEU* 3.9 2.9 - - - +
58D GLY* 3.4 0.3 - - - -
59D ARG 3.2 26.1 + - - +
73D LEU* 1.3 82.9 - - - +
75D TRP* 1.3 68.8 + - - +
92D TRP 2.9 16.2 - - - -
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Residues in contact with TRP 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B THR* 3.5 6.9 + - - -
29D PHE* 3.4 45.3 - + - -
39D LEU* 4.5 9.2 - - + -
43D TYR* 4.3 6.0 - + - -
56D LEU* 4.1 28.3 - - + -
57D THR 3.3 17.5 - - - +
58D GLY* 3.9 4.0 - - - -
73D LEU* 3.7 26.2 - - + -
74D GLY* 1.3 81.3 - - - +
76D THR* 1.3 65.8 + - - +
77D VAL* 4.3 0.4 - - + -
91D THR* 3.1 4.7 - - - -
92D TRP* 2.9 84.7 + + + +
104D ILE* 4.2 8.7 - - + -
106D THR* 4.0 7.6 - - + -
130D PHE* 3.9 23.8 - + - -
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Residues in contact with THR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLY* 4.4 1.7 - - - -
59B ARG* 3.9 23.9 - - + +
74B GLY* 3.3 47.4 - - - +
75B TRP* 3.4 11.1 + - - -
76B THR* 3.9 1.0 + - - -
56D LEU* 3.3 24.8 - - - +
57D THR 2.9 13.3 + - - -
75D TRP* 1.3 76.8 - - - +
77D VAL* 1.3 72.0 + - - +
89D ALA* 4.7 3.6 - - + -
90D THR 3.2 11.9 - - - +
91D THR* 3.4 9.3 - - + +
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Residues in contact with VAL 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ARG* 4.6 0.4 - - - -
43D TYR* 3.8 17.3 - - + -
54D TYR* 3.6 30.1 - - + -
55D VAL 3.9 6.7 - - - +
56D LEU* 3.6 20.6 - - + -
75D TRP* 4.3 1.6 - - + -
76D THR* 1.3 82.6 - - - +
78D ALA* 1.3 63.8 + - - +
79D TRP* 3.8 25.5 + - + -
89D ALA* 3.2 2.6 - - - +
90D THR 2.8 32.5 + - - -
92D TRP* 3.7 24.9 - - + -
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ARG* 3.7 28.3 + - + +
60B TYR 3.5 35.0 - - - +
61B ASP* 3.9 6.7 - - - +
54D TYR* 3.9 4.2 - - - +
55D VAL 4.5 2.9 + - - +
77D VAL* 1.3 79.5 - - - +
79D TRP* 1.3 57.7 + - - +
80D LYS* 2.9 18.8 + - + +
88D SER 3.7 6.3 - - - +
89D ALA* 4.0 5.6 - - + -
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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