Contacts of the strand formed by residues 81 - 91 (chain B) in PDB entry 1VAV
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 ASN 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B TRP* 3.2 38.9 - - + +
75B ARG 4.7 1.6 - - - +
76B TYR* 3.2 11.1 + - - +
78B ARG* 5.6 1.0 - - - +
79B ALA* 3.0 22.3 + - - +
80B ASP* 1.3 71.1 - - - +
82B TRP* 1.3 65.7 + - - +
163B GLY* 2.9 24.9 - - - -
164B VAL* 3.0 41.8 + - + +
194B PHE* 3.9 2.5 - - + -
221B SER 3.5 4.3 - - - -
222B HIS* 2.8 28.3 + - + +
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Residues in contact with TRP 82 (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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80B ASP* 4.2 25.5 - - + +
81B ASN* 1.3 79.0 + - - +
83B LEU* 1.3 63.8 + - - +
84B GLU* 4.3 11.7 - - - +
161B ARG* 4.6 20.0 - - + -
162B ILE 3.8 17.3 - - - -
163B GLY* 4.1 11.0 - - - -
165B SER* 5.8 8.8 - - - +
171B SER* 3.7 34.8 - - - -
173B SER* 5.9 0.4 - - - -
194B PHE* 3.4 8.9 - - - -
219B ARG 4.3 0.7 - - - -
220B VAL* 3.2 5.4 - - - -
221B SER* 2.9 51.8 + - - +
223B GLN* 6.5 0.9 - - + -
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Residues in contact with LEU 83 (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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7B TRP* 4.6 2.9 - - + -
82B TRP* 1.3 76.3 - - - +
84B GLU* 1.3 72.5 + - - +
160B TYR* 3.3 32.5 - - + +
161B ARG* 3.2 4.9 - - - +
162B ILE* 2.9 55.2 + - + +
194B PHE* 3.5 40.8 - - + -
195B LYS 3.8 19.5 - - - +
196B ALA* 4.7 0.2 - - + -
218B LEU* 4.1 11.4 - - + -
219B ARG 3.3 4.0 - - - -
220B VAL* 4.4 10.3 - - + +
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Residues in contact with GLU 84 (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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82B TRP* 4.5 16.2 - - + +
83B LEU* 1.3 75.8 - - - +
85B ALA* 1.3 61.0 + - - +
160B TYR 3.3 4.5 - - - -
161B ARG* 3.1 50.3 + - + +
217B GLU* 3.9 10.6 - - - +
218B LEU* 3.2 4.9 + - - +
219B ARG* 2.8 65.8 + - + +
221B SER* 4.8 4.5 + - - -
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Residues in contact with ALA 85 (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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84B GLU* 1.3 78.1 - - - +
86B THR* 1.3 58.6 + - - +
87B LEU* 4.6 1.3 - - - -
159B SER* 3.0 7.6 - - - -
160B TYR* 2.8 56.6 + - + +
161B ARG* 4.0 1.1 + - - +
215B PHE* 3.9 19.1 - - + -
217B GLU* 3.2 24.8 - - - +
218B LEU* 4.2 5.4 - - + -
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Residues in contact with THR 86 (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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85B ALA* 1.3 72.8 + - - +
87B LEU* 1.3 68.1 + - - +
157B PRO* 4.8 14.6 - - + -
158B PHE 3.3 13.9 - - - +
159B SER* 4.0 8.1 - - - -
215B PHE* 3.3 2.9 - - - -
216B SER* 2.8 43.2 + - - +
217B GLU* 2.5 34.8 + - - +
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Residues in contact with LEU 87 (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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85B ALA 4.6 0.2 - - - -
86B THR* 1.3 83.7 - - - +
88B ARG* 1.3 62.2 + - - +
89B ILE* 4.1 18.2 - - + -
100B ILE* 4.3 11.9 - - + -
157B PRO* 3.2 4.0 - - - +
158B PHE* 2.8 79.6 + - + +
160B TYR* 3.7 22.0 - - + -
213B ALA* 4.6 2.7 - - + -
214B THR 3.2 15.0 - - - +
215B PHE* 3.6 37.5 - - + -
216B SER* 4.4 1.3 - - - +
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Residues in contact with ARG 88 (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 ASP* 4.1 24.7 + - - +
42B ARG* 5.5 4.2 - - - +
87B LEU* 1.3 77.1 - - - +
89B ILE* 1.3 63.9 + - - +
90B GLU* 3.4 23.0 + - + +
155B GLY* 3.8 22.2 - - - +
156B GLN 3.9 19.1 - - - +
157B PRO* 3.9 12.9 - - + +
158B PHE* 4.4 2.0 - - - -
213B ALA* 3.3 5.2 - - - +
214B THR* 3.1 63.5 + - - +
216B SER* 5.0 7.5 - - - -
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Residues in contact with ILE 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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87B LEU* 4.1 15.9 - - + -
88B ARG* 1.3 74.2 - - - +
90B GLU* 1.3 61.1 + - - +
91B ALA 3.8 3.4 - - - +
92B VAL* 3.7 10.5 - - + -
98B MET* 3.6 31.4 - - + -
100B ILE* 4.2 13.0 - - + -
121B TYR* 3.7 38.6 - - + +
152B ILE* 5.9 0.2 - - + -
153B PRO 5.5 0.6 + - - +
154B LEU* 3.4 24.3 - - + +
155B GLY* 2.8 30.5 + - - +
156B GLN 4.8 1.6 + - - -
158B PHE* 4.0 8.0 - - + -
212B ARG 3.7 1.6 - - - +
213B ALA* 4.0 17.3 - - + -
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Residues in contact with GLU 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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42B ARG* 4.9 7.1 + - - +
88B ARG* 3.4 26.2 + - + +
89B ILE* 1.3 76.0 - - - +
91B ALA* 1.3 65.5 + - - +
154B LEU* 4.2 13.2 - - - +
155B GLY* 4.9 4.3 - - - +
212B ARG* 2.8 21.9 + - + +
213B ALA* 3.3 19.1 + - - -
214B THR* 2.6 37.3 + - - -
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Residues in contact with ALA 91 (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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44B TRP* 5.9 0.9 - - + -
89B ILE* 3.6 2.0 - - - +
90B GLU* 1.3 83.4 - - - +
92B VAL* 1.3 70.7 + - - +
98B MET* 3.4 3.3 - - - +
154B LEU* 4.4 7.9 - - - -
210B GLY 3.8 7.0 - - - +
211B GLY* 3.2 2.4 - - - -
212B ARG* 2.9 50.1 + - + +
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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