Contacts of the strand formed by residues 1624 - 1630 (chain B) 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 PRO1624 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1538B PHE* 4.1 21.5 - - + -
1539B THR 4.9 3.1 - - - +
1540B ALA* 3.9 25.2 - - + +
1541B ALA 4.9 0.9 + - - -
1550B MET* 4.2 23.6 - - - -
1610B ILE* 5.7 3.4 - - + -
1623B ARG* 1.4 93.8 - - + +
1625B MET* 1.3 61.6 + - - +
1638B PHE* 5.2 3.6 - - + -
1639B SER 3.8 7.4 - - - +
1640B TRP* 3.5 44.6 - - + -
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Residues in contact with MET1625 (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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1540B ALA* 5.1 1.6 - - - +
1541B ALA 5.8 1.6 - - - +
1621B THR* 5.4 5.8 - - - +
1623B ARG 3.8 9.4 - - - +
1624B PRO* 1.3 79.5 - - - +
1626B LEU* 1.3 67.4 + - - +
1627B ILE* 3.6 3.1 + - + +
1638B PHE* 3.3 18.7 - - - -
1639B SER 3.1 27.2 + - - +
1700B PRO* 3.7 46.7 - - + +
1701B MET 5.4 2.5 - - - +
1919B ILE* 4.1 35.2 - - + -
1923B ALA 3.5 23.6 - - - +
1924B LYS* 5.4 1.6 - - - -
1925B LEU* 5.4 7.4 - - + -
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Residues in contact with LEU1626 (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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1540B ALA* 5.2 2.5 - - + +
1541B ALA 4.3 18.4 + - - +
1542B TYR* 3.8 27.8 - - + -
1543B SER 5.5 0.2 - - - +
1548B VAL* 5.4 3.4 - - + -
1625B MET* 1.3 76.2 - - - +
1627B ILE* 1.3 68.6 + - - +
1628B SER* 4.5 8.7 - - - +
1629B LEU* 3.9 25.6 - - + -
1636B LEU* 4.7 1.3 - - + -
1637B PHE 4.2 6.5 - - - +
1638B PHE* 3.8 31.7 - - + -
1701B MET 4.9 1.6 - - - +
1702B HIS* 4.8 9.4 - - - -
1923B ALA* 5.6 5.0 - - + +
19C PHE* 4.1 17.9 - - + +
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Residues in contact with ILE1627 (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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1625B MET* 4.4 4.7 - - + +
1626B LEU* 1.3 78.3 - - - +
1628B SER* 1.3 64.9 + - - +
1637B PHE* 3.4 22.3 + - + +
1638B PHE 4.3 1.3 - - - -
1639B SER* 3.4 35.4 - - - +
1700B PRO* 3.6 33.7 - - + -
1701B MET 4.2 12.1 - - - +
1702B HIS* 4.1 5.4 + - - -
1703B ALA* 3.1 21.5 + - - -
1704B VAL 3.8 22.7 - - - +
1705B PRO* 3.8 16.8 - - + -
1706B CYS 4.9 4.0 - - - +
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Residues in contact with SER1628 (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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1626B LEU* 3.7 6.4 - - - +
1627B ILE* 1.3 84.2 - - - +
1629B LEU* 1.3 85.3 + - - +
1637B PHE* 3.3 26.1 + - - +
1703B ALA* 3.9 19.5 + - - +
1705B PRO* 3.8 27.3 - - - +
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Residues in contact with LEU1629 (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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1606B TYR* 5.5 5.4 - - + -
1626B LEU* 3.9 20.6 - - + -
1628B SER* 1.3 96.3 + - - +
1630B ASP* 1.3 64.6 + - - +
1631B LYS* 3.7 11.8 + - + +
1634B CYS* 5.5 2.0 - - - -
1635B THR 3.4 20.9 - - - +
1636B LEU* 3.5 30.1 - - + -
1637B PHE* 4.3 3.4 - - - -
1705B PRO* 5.6 2.1 - - - +
19C PHE* 3.5 34.3 - - + -
53C LEU* 5.9 6.5 - - + -
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Residues in contact with ASP1630 (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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1629B LEU* 1.3 73.2 - - - +
1631B LYS* 1.3 64.6 + - - +
1632B GLN* 3.4 21.0 + - - +
1633B THR* 3.3 29.9 + - + +
1634B CYS* 3.4 16.3 + - - -
1635B THR* 3.5 14.2 + - - +
1637B PHE* 3.6 24.4 - - + -
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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