Contacts of the strand formed by residues 210 - 222 (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 GLY 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B TRP* 3.7 9.5 - - - -
45B VAL 3.1 13.0 - - - -
47B VAL* 3.8 5.2 - - - -
91B ALA* 3.8 5.6 - - - +
92B VAL* 3.1 25.0 + - - +
93B PRO* 3.8 14.4 - - - -
208B SER 3.8 2.6 + - - -
209B GLU* 1.3 80.2 - - - +
211B GLY* 1.3 61.0 + - - -
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 3.4 6.6 - - - -
45B VAL 2.9 33.2 + - - -
91B ALA 3.2 9.4 - - - -
92B VAL* 4.3 0.9 - - - -
93B PRO* 4.1 3.2 - - - +
98B MET* 3.5 19.5 - - - -
198B LEU* 3.6 8.3 - - - +
200B LEU* 4.3 4.9 - - - +
210B GLY* 1.3 73.3 - - - -
212B ARG* 1.3 62.0 + - - -
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Residues in contact with ARG 212 (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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32B ASP 4.9 1.6 + - - -
35B GLN* 5.5 4.8 - - - +
43B PHE 3.3 8.7 + - - +
44B TRP* 3.4 64.7 - - + +
89B ILE* 3.7 3.8 - - - +
90B GLU* 2.8 34.1 + - + +
91B ALA* 2.9 33.6 + - + +
98B MET* 4.3 0.5 - - - +
198B LEU* 3.7 2.5 - - - +
211B GLY* 1.3 71.4 - - - -
213B ALA* 1.3 65.1 + - - +
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Residues in contact with ALA 213 (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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41B ILE 3.8 0.7 - - - +
42B ARG* 3.5 1.9 - - - +
43B PHE* 2.8 34.0 + - + +
87B LEU* 4.6 1.1 - - + -
88B ARG 3.3 13.7 - - - +
89B ILE* 4.0 11.9 - - + -
90B GLU* 3.3 8.6 + - - +
198B LEU* 3.8 26.7 - - + -
212B ARG* 1.3 78.8 - - - +
214B THR* 1.3 60.2 + - - +
215B PHE* 4.5 13.7 - - + -
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Residues in contact with THR 214 (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* 4.3 20.9 - - + +
41B ILE 3.3 5.8 - - - +
42B ARG* 3.3 32.2 - - + -
87B LEU* 3.2 3.5 - - - -
88B ARG* 3.1 60.1 + - - +
90B GLU* 2.6 31.5 + - - -
213B ALA* 1.3 72.6 - - - +
215B PHE* 1.3 65.2 + - - +
216B SER 3.8 0.7 + - - -
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Residues in contact with PHE 215 (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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2B PRO* 4.5 1.7 - - - +
40B GLY* 3.2 2.4 - - - -
41B ILE* 2.7 49.2 + - + +
43B PHE* 3.4 32.1 - + - -
85B ALA* 3.9 13.5 - - + -
86B THR 3.3 4.7 - - - +
87B LEU* 3.6 32.5 - - + -
100B ILE 3.7 17.3 - - - -
160B TYR* 3.8 17.3 - + - -
196B ALA* 4.5 8.7 - - + -
197B GLY* 3.8 17.9 - - - -
213B ALA* 4.5 7.0 - - + -
214B THR* 1.3 76.6 - - - +
216B SER* 1.3 62.2 + - - +
217B GLU 3.3 19.1 - - - +
218B LEU* 4.2 13.5 - - + -
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Residues in contact with SER 216 (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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2B PRO* 4.4 10.8 - - - +
39B ASP 3.4 22.6 - - - +
40B GLY* 4.3 1.4 - - - -
86B THR* 2.8 35.1 + - - +
87B LEU* 4.8 0.5 - - - -
88B ARG* 5.0 8.7 - - - -
214B THR 3.8 2.4 + - - -
215B PHE* 1.3 72.8 - - - +
217B GLU* 1.3 58.8 + - - +
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Residues in contact with GLU 217 (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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2B PRO* 4.4 5.6 - - - -
84B GLU* 3.9 6.7 - - - +
85B ALA* 3.2 23.7 + - - +
86B THR* 2.5 55.6 + - - +
159B SER* 5.0 0.2 - - - -
161B ARG* 3.5 24.0 + - - -
215B PHE* 3.3 5.8 - - - -
216B SER* 1.3 81.1 - - - +
218B LEU* 1.3 69.3 + - - +
219B ARG* 3.8 33.7 + - + +
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Residues in contact with LEU 218 (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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2B PRO* 4.0 26.6 - - + +
3B ASP* 4.5 9.2 + - - +
4B LEU* 6.1 0.9 - - + -
7B TRP* 3.7 35.7 + - + +
41B ILE* 4.8 9.0 - - + -
43B PHE* 5.6 1.6 - - + -
62B LEU* 3.7 29.6 - - + -
83B LEU* 4.1 17.5 - - + -
84B GLU 3.2 10.5 - - - +
85B ALA* 4.5 2.0 - - + -
196B ALA* 4.2 12.1 - - + -
215B PHE* 4.2 19.1 - - + -
217B GLU* 1.3 80.5 - - - +
219B ARG* 1.3 72.5 + - - +
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Residues in contact with ARG 219 (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* 5.7 0.4 - - - -
82B TRP 3.8 0.3 - - - +
83B LEU* 3.3 4.3 - - - +
84B GLU* 2.8 63.3 + - + +
217B GLU* 3.8 26.8 + - + +
218B LEU* 1.3 86.0 - - - +
220B VAL* 1.3 67.5 + - - +
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Residues in contact with VAL 220 (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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6B THR* 4.8 11.2 - - - +
7B TRP* 3.2 43.9 - - + +
64B GLU* 3.4 20.4 - - + +
82B TRP 3.2 4.5 - - - +
83B LEU* 4.4 4.0 - - + -
194B PHE* 3.4 33.2 - - + -
219B ARG* 1.3 80.1 - - - +
221B SER* 1.3 68.2 + - - +
222B HIS* 3.8 7.2 - - + +
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Residues in contact with SER 221 (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 3.4 2.4 - - - +
81B ASN* 3.5 1.6 - - - -
82B TRP* 2.9 52.1 + - - +
84B GLU* 4.8 5.2 + - - -
220B VAL* 1.3 78.7 - - - +
222B HIS* 1.3 66.1 + - - +
223B GLN* 3.9 19.6 - - - +
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Residues in contact with HIS 222 (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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64B GLU* 2.5 29.5 + - - -
72B TYR* 3.5 23.2 + + - +
74B TRP* 3.3 39.1 - + - -
79B ALA* 4.1 8.1 - - + +
80B ASP 3.4 4.0 - - - -
81B ASN* 2.8 30.3 + - + +
194B PHE* 4.0 7.4 - + - -
220B VAL* 3.8 7.0 - - + +
221B SER* 1.3 75.7 + - - +
223B GLN* 1.3 69.3 + - - +
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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