Contacts of the strand formed by residues 1678 - 1683 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1253B ASP* 3.5 2.4 - - - -
1254B LEU* 2.9 27.4 + - - +
1255B PHE* 2.9 21.3 + - + +
1265B TYR* 3.3 44.9 - - + +
1266B ARG* 4.0 9.0 - - - -
1268B PRO* 4.8 1.3 - - - -
1282B ILE* 3.8 16.2 - - + -
1669B LEU* 4.1 15.3 - - + -
1670B TYR 3.7 4.0 - - - +
1671B GLU* 3.7 30.3 - - + +
1673B THR 3.7 19.3 - - - +
1675B SER* 4.2 2.0 - - - +
1676B GLU 4.0 8.1 - - - +
1677B GLU* 1.3 92.8 - - - +
1679B SER* 1.3 59.8 + - - +
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Residues in contact with SER1679 (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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1251B PRO* 4.1 12.7 - - - +
1252B VAL 3.2 7.4 - - - -
1253B ASP* 4.3 9.5 + - - -
1649B LYS* 6.0 0.3 - - - -
1669B LEU* 3.2 4.9 - - - -
1670B TYR* 2.8 76.3 + - - -
1672B GLY* 5.0 3.6 + - - -
1677B GLU* 4.1 5.6 + - - +
1678B MET* 1.3 73.8 - - - +
1680B TYR* 1.3 59.7 + - - +
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Residues in contact with TYR1680 (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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1249B THR* 4.6 1.6 + - - -
1250B GLU 4.3 1.2 - - - +
1251B PRO* 3.6 0.3 - - - +
1252B VAL* 2.8 51.9 + - + +
1254B LEU* 4.1 18.8 - - + -
1270B LEU* 4.0 16.2 - - + -
1278B LEU* 3.7 16.5 - - + +
1307B GLY 4.1 4.0 + - - -
1308B GLY* 3.7 22.9 - - - -
1311B TRP* 4.2 24.9 - + - -
1661B LEU* 3.8 18.2 - - - +
1667B GLY* 3.8 7.1 - - - -
1668B LEU 3.2 24.5 - - - -
1669B LEU* 4.3 4.7 - - + -
1678B MET 4.1 0.2 + - - -
1679B SER* 1.3 74.1 - - - +
1681B ILE* 1.3 85.4 + - - +
1682B GLU* 4.3 7.5 - - + +
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Residues in contact with ILE1681 (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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1248B LYS* 4.1 12.3 - - + -
1249B THR* 3.4 27.1 - - - +
1251B PRO* 3.6 24.2 - - + -
1648B VAL* 4.2 10.8 - - + +
1666B ILE 3.9 0.2 - - - +
1667B GLY* 3.3 3.8 - - - -
1668B LEU* 2.9 60.6 + - + +
1670B TYR* 4.1 16.2 - - + +
1680B TYR* 1.3 89.0 - - - +
1682B GLU* 1.3 62.7 + - - +
1683B MET* 3.9 29.6 - - + -
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Residues in contact with GLU1682 (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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1247B VAL* 4.0 6.0 - - + +
1248B LYS* 3.4 2.3 - - - -
1249B THR* 2.9 45.4 + - + +
1307B GLY 4.0 6.8 - - - +
1309B LYS* 3.5 29.4 + - - +
1661B LEU* 3.5 29.5 - - + +
1663B ASN* 3.0 15.9 + - - -
1665B ASN* 2.8 31.3 + - + +
1666B ILE 3.3 4.9 - - - +
1667B GLY* 4.4 0.2 - - - -
1680B TYR* 4.3 9.4 + - + +
1681B ILE* 1.3 77.2 - - - +
1683B MET* 1.3 64.4 + - - +
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Residues in contact with MET1683 (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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1247B VAL* 3.2 12.8 - - - +
1248B LYS* 4.3 3.6 - - + -
1620B VAL* 4.2 14.1 - - - -
1648B VAL* 3.0 35.9 - - + -
1665B ASN* 3.3 5.7 - - - +
1666B ILE* 2.9 50.7 + - + +
1668B LEU* 5.0 4.0 - - - -
1681B ILE* 3.9 22.7 - - + -
1682B GLU* 1.3 75.6 - - - +
1684B ASN* 1.3 61.7 + - - +
1687B TYR* 3.5 26.0 - - + -
1688B LEU* 3.7 26.7 - - + -
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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