Contacts of the strand formed by residues 88 - 97 (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 SER 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA* 3.6 1.9 - - - +
79B TRP* 2.9 30.6 + - - -
86B ALA* 3.1 12.8 + - - +
87B HIS* 1.3 80.1 - - - +
89B ALA* 1.3 62.0 + - - +
110B LEU* 3.8 9.9 - - - -
111B THR 3.2 14.8 - - - -
112B SER* 3.7 14.4 - - - -
61D ASP* 3.4 6.1 + - - +
72D ALA* 3.6 6.9 - - - +
3M HIS* 3.1 25.6 + - - -
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Residues in contact with ALA 89 (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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76B THR* 4.7 4.9 - - + -
77B VAL 3.2 12.8 - - - +
78B ALA* 4.0 9.0 - - + -
79B TRP* 3.9 1.3 - - - -
88B SER* 1.3 75.3 - - - +
90B THR* 1.3 63.6 - - - +
91B THR* 5.6 0.2 - - - -
110B LEU* 3.5 1.0 - - - +
111B THR* 2.9 30.7 + - - +
72D ALA* 3.7 3.1 - - + +
73D LEU* 3.8 39.7 - - - +
74D GLY 4.5 0.4 - - - +
93D SER* 3.8 5.8 + - - -
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Residues in contact with THR 90 (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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76B THR* 3.3 4.5 - - - +
77B VAL 2.9 31.3 + - - -
79B TRP* 2.8 20.4 + - - -
89B ALA* 1.3 73.1 - - - +
91B THR* 1.3 66.3 + - - +
92B TRP* 3.7 31.4 - - + -
108B TRP* 4.0 15.0 - - + -
109B LEU 3.2 13.9 - - - +
110B LEU* 3.2 12.1 - - - +
5M GLN* 2.8 31.4 + - - +
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Residues in contact with THR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TRP 3.2 6.1 - - - -
76B THR* 3.5 21.1 - - + +
89B ALA 5.6 0.4 - - - -
90B THR* 1.3 78.7 - - - +
92B TRP* 1.3 62.3 + - - +
93B SER 4.2 0.2 + - - -
107B GLN 4.2 0.2 - - - +
108B TRP* 3.2 3.6 - - - +
109B LEU* 3.0 30.4 + - - +
74D GLY* 3.8 8.7 - - - -
75D TRP 4.1 1.1 - - - +
91D THR* 3.4 26.8 + - - -
92D TRP 3.4 24.6 - - - +
93D SER* 3.4 21.5 + - - +
109D LEU* 4.9 0.5 - - - +
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Residues in contact with TRP 92 (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* 3.6 32.8 - + - -
74B GLY* 3.0 24.9 - - - -
75B TRP* 3.0 61.6 + + + -
77B VAL* 3.9 12.8 - - + -
79B TRP* 3.8 20.4 - + - -
90B THR* 3.7 34.1 - - + -
91B THR* 1.3 75.5 - - - +
93B SER* 1.3 59.7 + - - +
94B GLY 4.2 0.2 - - - -
106B THR* 3.3 26.5 - - - -
107B GLN 3.6 3.4 - - - -
108B TRP* 3.7 15.5 - + + -
128B ASP* 3.1 19.4 + - - -
130B PHE* 3.8 10.0 - + - -
91D THR* 3.4 2.9 - - - +
5M GLN* 4.0 13.9 - - + -
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Residues in contact with SER 93 (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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73B LEU 3.7 6.2 + - - -
91B THR 4.2 0.2 - - - -
92B TRP* 1.3 72.9 - - - +
94B GLY* 1.3 58.6 + - - +
106B THR* 3.4 2.8 - - - -
107B GLN* 3.0 29.9 + - - +
89D ALA 4.0 4.3 + - - -
91D THR* 3.4 24.9 - - - +
109D LEU* 3.3 32.7 + - - -
111D THR* 2.8 29.6 + - - -
123D THR* 5.5 0.2 - - - -
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Residues in contact with GLY 94 (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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72B ALA* 3.5 5.0 - - - -
73B LEU* 3.1 37.4 + - - +
93B SER* 1.3 77.5 + - - +
95B GLN* 1.3 63.5 + - - -
105B ASN 3.0 14.8 - - - -
106B THR* 4.0 5.4 - - - +
111D THR* 3.6 16.1 - - - +
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Residues in contact with GLN 95 (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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70B GLY* 3.4 13.1 - - - -
71B THR 3.2 9.6 - - - +
72B ALA* 4.6 0.4 - - - -
73B LEU* 4.4 1.7 - - - +
94B GLY* 1.3 78.1 - - - +
96B TYR* 1.3 63.9 + - - +
97B VAL* 3.9 11.7 + - + +
103B ARG 3.9 0.7 - - - +
104B ILE* 3.3 6.7 - - - -
105B ASN* 3.0 32.8 + - + +
111D THR* 3.7 6.7 - - + -
112D SER 3.2 21.3 - - - +
113D GLY* 3.4 4.2 - - - -
114D THR* 2.9 48.9 + - - +
119D ALA* 4.6 5.9 - - - +
122D SER* 3.5 14.0 + - - -
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Residues in contact with TYR 96 (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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13B ALA* 4.4 13.2 - - + -
16B GLY* 3.3 38.7 + - - -
17B ILE* 3.6 22.2 - - + -
21B TRP* 3.8 25.4 - + - -
70B GLY* 3.2 5.4 - - - -
71B THR* 2.8 47.2 + - - +
73B LEU* 3.8 22.2 - - + +
95B GLN* 1.3 74.3 - - - +
97B VAL* 1.3 60.8 + - - +
98B GLY* 3.5 27.2 - - - -
99B GLY 4.9 0.2 + - - -
102B ALA* 4.0 12.4 - - + +
103B ARG 3.6 3.6 - - - -
104B ILE* 4.1 7.2 - - + -
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLY 6.0 1.8 - - - +
69B SER 5.6 1.8 - - - +
70B GLY* 4.5 14.1 - - - +
95B GLN* 4.4 12.6 - - + +
96B TYR* 1.3 79.5 - - - +
98B GLY* 1.3 68.8 + - - +
101B GLU 4.4 2.1 - - - +
102B ALA* 3.2 3.6 - - - +
103B ARG* 2.9 40.7 + - + +
105B ASN* 4.4 19.5 - - - +
114D THR 6.0 0.2 - - - +
116D GLU* 3.8 23.6 - - - +
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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