Contacts of the strand formed by residues 1678 - 1683 (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 MET1678 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1253A ASP* 3.5 2.7 - - - -
1254A LEU* 2.9 27.9 + - - +
1255A PHE* 2.9 19.7 + - + +
1265A TYR* 3.3 45.1 - - + +
1266A ARG* 4.0 9.0 - - - -
1268A PRO* 4.7 1.8 - - - -
1282A ILE* 3.9 15.9 - - + -
1669A LEU* 4.1 14.6 - - + -
1670A TYR 3.6 4.3 - - - +
1671A GLU* 3.7 30.7 - - + +
1673A THR 3.8 19.3 - - - +
1675A SER* 4.2 1.8 - - - -
1676A GLU 4.0 8.1 - - - +
1677A GLU* 1.3 92.0 - - - +
1679A SER* 1.3 60.4 + - - +
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Residues in contact with SER1679 (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* 4.1 11.7 - - - +
1252A VAL 3.3 7.4 - - - -
1253A ASP* 3.9 12.5 + - - -
1649A LYS* 6.0 0.3 - - - -
1669A LEU* 3.2 5.5 - - - -
1670A TYR* 2.8 77.6 + - - -
1672A GLY* 5.0 4.0 + - - -
1677A GLU* 4.7 4.9 + - - +
1678A MET* 1.3 73.9 - - - +
1680A TYR* 1.3 58.6 + - - +
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Residues in contact with TYR1680 (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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1249A THR* 4.6 1.4 + - - -
1250A GLU 4.3 1.7 - - - +
1251A PRO* 3.6 0.5 - - - +
1252A VAL* 2.8 50.4 + - + +
1254A LEU* 4.2 17.0 - - + -
1270A LEU* 3.9 19.5 - - + -
1278A LEU* 3.7 16.5 - - + +
1307A GLY 4.2 1.0 + - - -
1308A GLY* 3.7 25.0 - - - -
1311A TRP* 4.2 23.6 - + - -
1661A LEU* 3.7 19.2 - - - +
1667A GLY* 3.8 5.0 - - - -
1668A LEU 3.2 23.6 - - - -
1669A LEU* 4.2 6.1 - - + -
1679A SER* 1.3 75.3 - - - +
1681A ILE* 1.3 83.1 + - - +
1682A GLU* 4.4 7.9 - - + +
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Residues in contact with ILE1681 (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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1248A LYS* 4.1 20.6 - - - -
1249A THR* 3.5 28.0 - - - +
1251A PRO* 3.6 24.2 - - + -
1648A VAL* 4.3 7.0 - - + +
1666A ILE 3.9 0.5 - - - +
1667A GLY* 3.4 3.1 - - - -
1668A LEU* 2.9 56.7 + - + +
1670A TYR* 4.1 16.8 - - + +
1679A SER 4.3 0.2 - - - -
1680A TYR* 1.3 87.1 - - - +
1682A GLU* 1.3 61.4 + - - +
1683A MET* 3.7 29.6 - - + -
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Residues in contact with GLU1682 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1247A VAL* 3.9 9.2 - - + +
1248A LYS* 3.3 4.2 - - - +
1249A THR* 2.9 42.0 + - + +
1307A GLY 4.0 8.0 - - - +
1308A GLY 5.9 0.2 - - - -
1309A LYS* 3.3 29.2 + - - +
1661A LEU* 3.5 29.8 - - + +
1663A ASN* 3.1 15.1 + - - -
1665A ASN* 2.8 30.6 + - + +
1666A ILE 3.3 4.0 - - - +
1680A TYR* 4.4 8.5 + - + +
1681A ILE* 1.3 75.4 - - - +
1683A MET* 1.3 65.1 + - - +
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Residues in contact with MET1683 (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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1247A VAL* 3.2 7.9 - - - +
1248A LYS* 4.1 9.4 - - + -
1620A VAL* 4.2 7.4 - - + -
1648A VAL* 3.7 29.6 - - - -
1665A ASN* 3.2 5.9 - - - +
1666A ILE* 2.8 57.4 + - + +
1668A LEU* 3.9 33.0 - - + -
1681A ILE* 3.7 13.5 - - + -
1682A GLU* 1.3 80.8 - - - +
1684A ASN* 1.3 63.2 + - - +
1687A TYR* 3.8 20.6 - - + -
1688A LEU* 3.9 18.2 - - + -
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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