Contacts of the strand formed by residues 1635 - 1642 (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 THR1635 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1607B LYS* 3.2 22.3 - - + +
1609B VAL* 3.7 29.4 - - + -
1629B LEU* 3.4 20.3 - - - +
1630B ASP 3.5 15.5 + - - -
1633B THR* 3.0 37.4 + - - +
1634B CYS* 1.3 74.3 - - - +
1636B LEU* 1.3 67.0 + - - +
1637B PHE* 4.0 19.4 + - + -
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Residues in contact with LEU1636 (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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1548B VAL* 5.5 3.1 - - + -
1567B PHE* 4.9 2.7 - - + -
1574B VAL* 3.8 48.7 - - + -
1606B TYR* 4.1 14.1 - - + -
1607B LYS 2.8 18.1 + - - +
1608B SER* 3.5 10.0 - - - +
1609B VAL* 2.7 31.2 + - - -
1626B LEU* 4.7 1.1 - - + -
1629B LEU* 3.5 25.1 - - + -
1634B CYS 4.3 0.9 - - - +
1635B THR* 1.3 75.1 - - - +
1637B PHE* 1.3 63.4 + - - +
1638B PHE* 3.5 27.3 - - + -
19C PHE* 4.3 17.0 - - + -
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Residues in contact with PHE1637 (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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1609B VAL* 3.4 24.9 - - + -
1626B LEU* 4.2 3.6 - - - +
1627B ILE* 3.4 33.1 + - + -
1628B SER 3.3 30.8 + - - +
1629B LEU* 4.2 0.6 - - - +
1630B ASP* 3.6 38.4 - - + -
1633B THR* 5.4 1.6 - - + -
1635B THR* 4.0 16.2 - - + -
1636B LEU* 1.3 70.3 - - - +
1638B PHE* 1.3 63.9 + - - +
1705B PRO* 4.7 17.9 - - + -
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Residues in contact with PHE1638 (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* 4.2 21.5 - - + -
1548B VAL* 4.2 17.5 - - + -
1550B MET* 4.6 11.7 - - - -
1565B ALA* 5.6 2.0 - - + -
1574B VAL* 5.6 1.1 - - + -
1608B SER* 4.1 9.0 - - - -
1609B VAL 3.2 8.6 + - - +
1610B ILE* 3.6 39.7 - - + -
1611B SER* 3.1 24.0 + - - -
1624B PRO* 5.2 1.8 - - + -
1625B MET 3.3 25.4 - - - +
1626B LEU* 3.8 26.2 - - + -
1627B ILE* 4.3 1.3 - - - -
1636B LEU* 3.5 43.1 - - + -
1637B PHE* 1.3 74.9 - - - +
1639B SER* 1.3 65.8 + - - +
1708B ALA* 4.8 0.9 - - - +
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Residues in contact with SER1639 (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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1610B ILE* 5.5 0.4 - - - -
1611B SER 3.4 6.5 - - - -
1613B VAL* 4.5 3.3 - - - +
1623B ARG 3.9 2.3 - - - +
1624B PRO* 3.8 1.0 - - - +
1625B MET* 3.1 32.6 + - - +
1627B ILE* 3.4 28.8 - - - +
1638B PHE* 1.3 79.6 + - - +
1640B TRP* 1.3 62.2 + - - +
1641B HIS* 4.1 22.1 + - - -
1700B PRO* 4.5 2.2 - - - +
1708B ALA* 3.8 18.4 - - - +
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Residues in contact with TRP1640 (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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1532B LEU* 3.7 24.5 - - + -
1538B PHE* 3.5 38.8 - + - -
1550B MET* 4.6 2.0 - - + -
1552B ILE* 3.7 26.9 - - + -
1610B ILE* 5.1 7.2 - - + -
1611B SER 3.0 9.0 + - - +
1612B PHE* 3.5 33.8 - + + -
1613B VAL 3.1 19.4 + - - +
1622B ASN 3.0 25.1 + - - -
1623B ARG* 3.6 15.7 - - + -
1624B PRO* 3.5 39.3 - - + -
1639B SER* 1.3 75.3 - - - +
1641B HIS* 1.3 61.6 + - - +
1642B THR* 3.2 30.1 + - + +
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Residues in contact with HIS1641 (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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1613B VAL* 3.3 43.2 - - + +
1614B CYS 4.2 9.4 - - - -
1615B ARG* 3.6 34.8 - - + +
1621B THR 4.8 1.6 + - - +
1622B ASN* 3.0 28.8 - - - +
1623B ARG 4.8 2.0 + - - -
1639B SER* 4.2 9.5 + - - -
1640B TRP* 1.3 71.8 + - - +
1642B THR* 1.3 61.7 + - - +
1697B PRO 4.7 4.9 - - - -
1698B LEU 3.2 21.5 + - - -
1699B ASN* 4.0 11.5 - - - -
1700B PRO* 3.4 39.2 - - + +
1709B GLY 6.0 0.2 - - - -
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Residues in contact with THR1642 (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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1529B LEU* 5.0 0.9 - - - +
1532B LEU* 4.8 5.8 - - + -
1612B PHE* 4.3 6.9 - - + -
1613B VAL 3.0 7.8 + - - +
1615B ARG 3.1 19.6 + - - -
1622B ASN* 4.9 5.2 - - + +
1640B TRP* 3.2 41.9 + - + +
1641B HIS* 1.3 72.8 - - - +
1643B PRO* 1.4 67.2 - - + +
1644B LEU* 3.0 26.4 - - + +
1645B ALA* 3.2 29.3 + - - +
1646B CYS* 3.6 1.9 - - - -
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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