Contacts of the strand formed by residues 18 - 26 (chain B) in PDB entry 6VVT
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 ARG 18 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 2.7 55.3 + - + +
15B ALA* 2.7 26.8 + - + +
17B ASN* 1.3 81.2 - - - +
19B SER* 1.3 61.2 + - - +
173B LYS* 5.3 13.7 - - - +
195B ASP* 2.9 32.5 + - - +
196B VAL 3.7 11.4 - - - +
197B GLU* 3.6 39.1 + - + +
204B PRO* 4.3 1.4 - - - +
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLU 3.4 13.5 - - - -
13B THR* 3.4 22.4 + - - +
14B VAL* 3.8 2.0 - - - +
15B ALA 4.3 0.2 + - - -
16B GLU 6.0 0.2 - - - -
18B ARG* 1.3 78.4 + - - +
20B ARG* 1.3 59.5 + - - +
21B PHE* 3.8 10.7 - - - -
195B ASP* 4.2 4.5 - - - -
196B VAL* 3.2 36.6 + - - +
204B PRO* 4.0 24.4 - - - +
205B ARG* 4.1 12.1 + - - -
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 3.5 2.1 - - - +
12B GLU* 2.9 72.2 + - + +
14B VAL* 3.9 12.6 - - + +
19B SER* 1.3 74.1 - - - +
21B PHE* 1.3 64.6 + - - +
22B VAL* 4.2 15.5 - - + +
193B ILE* 3.5 32.9 - - + +
194B ILE 3.2 12.3 - - - +
195B ASP* 4.0 14.4 - - + +
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Residues in contact with PHE 21 (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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9B LEU* 4.3 13.7 - - + -
10B SER 3.2 7.6 - - - +
11B GLU* 3.3 35.0 - - + -
19B SER* 3.8 9.6 - - - -
20B ARG* 1.3 72.6 - - - +
22B VAL* 1.3 70.6 + - - +
23B ILE* 5.8 0.9 - - + -
192B LEU 3.6 0.6 - - - +
193B ILE* 3.4 2.9 - - - +
194B ILE* 2.9 54.3 + - + +
196B VAL* 3.3 28.5 - - + -
204B PRO* 3.9 32.1 - - + -
205B ARG* 4.2 17.0 - - + -
208B LEU* 3.9 28.7 - - + -
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 3.5 2.3 + - - +
9B LEU* 3.5 2.8 - - - +
10B SER* 2.8 60.8 + - - +
12B GLU* 6.6 0.2 - - + -
20B ARG* 4.2 22.7 - - + +
21B PHE* 1.3 78.7 - - - +
23B ILE* 1.3 64.5 + - - +
24B GLU* 4.3 8.9 + - + +
191B LYS* 4.9 7.0 - - + -
192B LEU 3.1 5.2 - - - -
193B ILE* 3.2 30.5 - - + -
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Residues in contact with ILE 23 (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 PRO* 4.1 8.5 - - + -
8B THR 3.0 11.4 - - - +
9B LEU* 3.8 22.2 - - + -
21B PHE* 5.8 0.9 - - + -
22B VAL* 1.3 77.2 - - - +
24B GLU* 1.3 65.8 + - - +
25B PRO* 4.4 0.4 - - - +
26B LEU* 3.6 29.5 - - + +
34B LEU* 5.0 8.1 - - + -
38B LEU* 6.4 2.2 - - + -
190B ASP 4.2 2.1 - - - +
191B LYS* 3.6 6.3 - - - +
192B LEU* 3.0 55.4 + - + +
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Residues in contact with GLU 24 (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 PRO* 3.3 0.4 - - - +
8B THR* 2.7 48.8 + - - +
22B VAL* 4.2 8.3 - - + +
23B ILE* 1.3 73.0 - - - +
25B PRO* 1.3 67.7 - - + +
181B THR* 2.7 36.5 + - - +
182B ARG* 6.3 0.2 - - + -
191B LYS* 2.9 39.4 + - + +
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Residues in contact with PRO 25 (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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5B GLN* 4.4 15.5 - - + +
6B ARG 3.9 15.0 - - - +
7B PRO* 3.2 18.8 - - + +
24B GLU* 1.3 92.4 - - + +
26B LEU* 1.3 63.6 + - - +
27B GLU* 5.7 0.9 - - - +
181B THR* 4.9 0.7 - - - +
182B ARG* 3.8 33.9 - - + +
189B PHE* 3.8 25.2 - - + -
190B ASP 3.7 6.5 - - - +
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Residues in contact with LEU 26 (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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218A LEU* 5.1 9.4 - - + -
7B PRO* 3.9 11.2 - - + -
23B ILE* 3.6 31.2 - - + +
25B PRO* 1.3 78.0 - - - +
27B GLU* 1.3 61.9 + - - +
30B PHE* 3.9 30.7 - - + +
31B GLY* 3.9 10.8 - - - -
34B LEU* 4.2 22.7 - - + -
189B PHE* 3.0 11.4 - - - -
190B ASP* 2.8 45.4 + - + +
192B LEU* 4.1 19.7 - - + +
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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