Contacts of the strand formed by residues 1252 - 1255 (chain A) in PDB entry 2VK7
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 VAL1252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1250A GLU 3.9 7.6 - - - +
1251A PRO* 1.3 79.0 - - - +
1253A ASP* 1.3 62.3 + - - +
1254A LEU* 3.0 10.6 + - + +
1308A GLY 5.7 1.1 - - - +
1311A TRP* 5.0 9.9 - - + +
1679A SER* 3.3 3.0 - - - -
1680A TYR* 2.8 59.0 + - + +
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Residues in contact with ASP1253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1251A PRO* 5.3 2.9 - - - +
1252A VAL* 1.3 70.8 - - - +
1254A LEU* 1.3 65.4 + - - +
1255A PHE 3.2 12.0 + - - +
1256A HIS* 3.4 25.3 + - + +
1302A ARG* 4.4 2.9 + - - -
1677A GLU* 3.5 31.4 - - - +
1678A MET 3.5 5.4 - - - -
1679A SER* 3.9 10.4 + - - -
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Residues in contact with LEU1254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1252A VAL* 3.0 7.2 + - + -
1253A ASP* 1.3 73.0 - - - +
1255A PHE* 1.3 73.0 + - + +
1256A HIS* 4.7 0.4 + - - -
1259A PHE* 4.6 2.1 - - - -
1270A LEU* 5.5 0.2 - - + -
1280A ALA* 3.7 29.8 - - + -
1302A ARG* 2.7 47.0 + - - +
1311A TRP* 3.4 54.1 - - + +
1669A LEU* 3.9 23.6 - - + -
1678A MET 2.9 11.3 + - - +
1680A TYR* 4.2 13.7 - - + -
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Residues in contact with PHE1255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253A ASP 3.9 2.6 - - - -
1254A LEU* 1.3 96.4 - - + +
1256A HIS* 1.3 68.9 + - - +
1259A PHE* 3.9 14.4 - + - -
1265A TYR* 3.5 36.3 - + + -
1280A ALA* 3.9 27.6 - - + -
1282A ILE* 3.5 41.1 - - + -
1300A ALA* 4.5 8.7 - - + -
1301A VAL 4.6 0.4 - - - -
1302A ARG* 3.6 33.9 - - + -
1669A LEU* 4.3 6.7 - - + -
1676A GLU 4.2 1.1 - - - -
1677A GLU* 3.4 0.9 - - - -
1678A MET* 2.9 35.5 + - + +
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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