Contacts of the strand formed by residues 1644 - 1652 (chain A) in PDB entry 5V7W
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 ARG1644 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1642A HIS 4.3 0.4 + - - -
1643A PHE* 1.3 72.6 - - - +
1645A ILE* 1.3 67.8 + - - +
1646A GLU* 3.7 4.3 + - - +
1799A PHE* 3.0 4.7 - - - +
1800A ARG* 2.7 75.0 + - + +
1801A LYS 4.8 8.6 + - - +
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Residues in contact with ILE1645 (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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1629A TYR* 3.2 25.7 + - - +
1633A ALA* 4.3 22.0 - - + -
1636A PHE* 3.7 38.4 - - + -
1637A ASN* 4.1 12.8 - - - +
1643A PHE 4.0 2.0 + - - +
1644A ARG* 1.3 81.4 + - - +
1646A GLU* 1.3 62.4 + - - +
1647A LYS 3.8 12.1 - - - +
1648A ILE* 4.0 21.5 - - + -
1797A ILE* 4.4 4.9 - - + -
1798A THR 3.8 7.6 - - - +
1799A PHE* 3.9 4.3 - - + -
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Residues in contact with GLU1646 (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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1621A GLU* 5.1 0.7 - - - +
1629A TYR* 5.5 0.6 + - - -
1644A ARG* 3.7 7.5 + - - +
1645A ILE* 1.3 73.4 - - - +
1647A LYS* 1.3 69.0 + - + +
1735A ARG* 3.1 30.5 + - + -
1798A THR* 2.7 26.4 + - + +
1799A PHE* 5.0 1.6 - - - -
1800A ARG* 3.0 40.3 + - + +
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Residues in contact with LYS1647 (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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1621A GLU* 3.6 33.7 - - - +
1622A LEU 5.7 0.7 - - - +
1629A TYR* 4.9 4.9 - - - -
1645A ILE* 3.6 4.6 - - - +
1646A GLU* 1.3 89.0 - - + +
1648A ILE* 1.3 67.1 + - - +
1649A GLU* 2.8 42.7 + - - +
1796A LEU* 3.7 1.3 - - - +
1797A ILE* 3.6 0.2 - - - -
1798A THR* 2.9 49.1 + - - +
1690B PRO* 5.6 10.5 + - - +
1691B HIS* 6.1 1.4 - - - +
1694B ARG* 4.5 11.0 - - - +
1695B ASN* 6.4 0.2 - - - +
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Residues in contact with ILE1648 (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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1621A GLU* 3.8 2.3 - - - +
1622A LEU* 2.9 45.0 + - + +
1629A TYR* 3.6 56.6 - - + +
1632A VAL* 4.2 14.8 - - + -
1633A ALA* 4.2 14.6 - - + +
1645A ILE* 4.0 14.1 - - + -
1647A LYS* 1.3 80.9 - - - +
1649A GLU* 1.3 66.3 + - - +
1795A TYR* 4.1 18.4 - - + -
1796A LEU 3.2 8.3 - - - +
1797A ILE* 4.1 12.8 - - + -
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Residues in contact with GLU1649 (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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1619A VAL* 3.2 24.1 - - + +
1620A VAL 3.2 7.4 - - - +
1621A GLU* 3.9 18.6 - - + -
1622A LEU* 4.5 0.7 - - - +
1647A LYS* 2.8 37.4 + - + +
1648A ILE* 1.3 80.0 - - - +
1650A ARG* 1.3 60.1 + - - +
1651A ILE* 3.8 1.1 + - + +
1795A TYR* 3.1 8.3 - - - -
1796A LEU* 2.7 62.9 + - + +
1798A THR* 4.6 1.7 + - - -
1617B PHE* 4.9 1.6 - - - -
1690B PRO* 6.0 2.0 - - - +
1694B ARG* 3.0 26.2 + - - -
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Residues in contact with ARG1650 (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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1618A CYS 3.8 0.9 - - - +
1619A VAL* 3.8 1.0 - - - -
1620A VAL* 2.8 54.3 + - + +
1622A LEU* 3.3 20.5 - - + +
1626A ASP* 5.4 0.2 + - - -
1628A GLU* 2.5 45.8 + - - -
1649A GLU* 1.3 72.3 - - - +
1651A ILE* 1.3 65.3 + - - +
1652A GLN* 3.2 37.6 + - + +
1794A GLU* 3.3 19.5 - - + +
1795A TYR* 4.0 14.1 - - + -
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Residues in contact with ILE1651 (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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1617A PHE* 4.7 6.5 - - + -
1618A CYS 3.8 4.7 - - - +
1619A VAL* 4.1 21.5 - - + -
1649A GLU 4.4 3.6 - - - +
1650A ARG* 1.3 74.0 - - - +
1652A GLN* 1.3 56.7 + - - +
1653A ASN* 4.8 4.7 - - + +
1693A ASN* 3.3 61.5 - - + +
1739A TYR* 4.2 7.6 - - + -
1792A TYR* 2.6 31.3 + - - +
1793A PRO* 3.3 27.6 - - + +
1794A GLU 2.7 13.8 + - - +
1796A LEU* 4.4 18.4 - - + +
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Residues in contact with GLN1652 (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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1617A PHE* 3.2 4.1 - - - -
1618A CYS* 2.9 50.3 + - + +
1620A VAL* 3.8 21.8 - - - +
1650A ARG* 3.2 44.7 + - + +
1651A ILE* 1.3 73.0 - - - +
1653A ASN* 1.3 59.5 + - - +
1654A PRO* 3.4 9.3 - - + +
1792A TYR* 3.6 1.8 - - - -
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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