Contacts of the strand formed by residues 1760 - 1766 (chain A) in PDB entry 2V5P
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 SER1760 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1712A VAL* 3.9 17.3 - - - +
1724A ILE 3.3 20.2 - - - -
1744A PHE* 2.8 45.6 + - - +
1759A THR* 1.3 75.5 + - - +
1761A LEU* 1.3 63.2 + - - +
1762A ILE* 4.9 0.5 - - - +
1784A ASP* 4.2 0.2 - - - -
1785A PHE* 3.5 12.2 - - - +
1787A PHE* 3.2 32.3 - - - -
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Residues in contact with LEU1761 (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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1732A ILE* 5.9 4.3 - - + -
1741A TYR* 5.0 9.9 - - + -
1742A LEU 3.7 8.5 - - - +
1743A ASN* 3.8 30.3 - - + +
1759A THR* 4.8 7.0 - - - +
1760A SER* 1.3 76.2 - - - +
1762A ILE* 1.3 64.0 + - - +
1784A ASP* 4.2 20.6 + - - +
1785A PHE 2.7 16.4 + - - +
1786A VAL* 3.4 9.3 - - + +
1787A PHE* 2.9 24.1 + - - +
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Residues in contact with ILE1762 (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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1692A ILE* 3.9 17.9 - - + -
1694A ILE* 3.8 18.4 - - + -
1712A VAL* 4.8 2.5 - - + -
1741A TYR* 3.4 7.0 - - - +
1742A LEU* 3.0 34.5 + - + +
1744A PHE* 3.5 30.7 - - + -
1760A SER* 4.9 0.9 - - - +
1761A LEU* 1.3 77.3 - - - +
1763A ALA* 1.3 63.6 + - - +
1764A PHE* 3.8 27.7 - - + -
1775A PRO* 5.2 2.7 - - + -
1787A PHE* 3.2 37.0 - - + +
1789A TRP* 4.3 11.7 - - + -
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Residues in contact with ALA1763 (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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1739A GLU* 4.9 5.2 - - - +
1741A TYR* 3.7 27.8 - - + -
1761A LEU 4.2 0.8 - - - -
1762A ILE* 1.3 73.6 - - - +
1764A PHE* 1.3 57.7 + - - +
1765A HIS* 6.0 2.0 - - + +
1786A VAL* 5.4 8.5 - - + +
1787A PHE 2.7 13.4 + - - +
1788A GLU* 3.5 13.1 - - + -
1789A TRP* 2.8 34.0 + - - +
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Residues in contact with PHE1764 (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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1663A LEU* 4.5 12.3 - - + -
1666A LEU* 4.5 3.4 - - + -
1694A ILE* 4.1 22.7 - - + -
1738A ASN 5.2 0.5 - - - +
1739A GLU* 3.8 24.4 - - - +
1740A ILE* 3.0 38.0 + - + +
1741A TYR* 4.7 0.4 - - - -
1742A LEU* 4.2 17.7 - - + -
1762A ILE* 3.8 27.8 - - + -
1763A ALA* 1.3 77.9 - - - +
1765A HIS* 1.3 66.7 + - - +
1789A TRP* 3.4 43.7 - + + -
1791A THR* 3.8 17.9 - - + -
1794A VAL* 3.7 27.1 - - + +
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Residues in contact with HIS1765 (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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1739A GLU* 4.6 20.5 + - + -
1763A ALA* 6.0 2.2 - - + +
1764A PHE* 1.3 79.5 - - - +
1766A CYS* 1.3 64.3 + - - +
1767A LYS* 3.9 0.7 - - + -
1788A GLU* 3.2 42.7 + - + +
1789A TRP 2.9 8.1 + - - +
1790A GLU* 3.7 35.3 + - + +
1791A THR* 3.1 20.0 + - - +
1794A VAL* 3.4 17.0 - - - +
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Residues in contact with CYS1766 (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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1765A HIS* 1.3 75.4 - - - +
1767A LYS* 1.3 59.5 + - - +
1768A ARG* 4.0 19.6 + - - -
1794A VAL 3.3 9.2 - - - +
1795A CYS* 2.0 51.1 - - - -
1796A PRO* 4.5 4.0 - - - -
2991A NAG 4.9 6.3 - - + -
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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