Contacts of the strand formed by residues 1563 - 1571 (chain A) in PDB entry 5V7T
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 ARG1563 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1562A PHE* 1.3 72.0 - - - +
1564A ILE* 1.3 75.0 + - - +
1565A GLU* 3.4 12.2 + - + +
1718A PHE* 3.1 5.7 - - - -
1719A ARG* 2.7 86.5 + - + +
1720A LYS 4.5 5.6 - - - +
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Residues in contact with ILE1564 (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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1548A TYR* 3.6 23.7 + - + +
1552A ALA* 4.0 29.2 - - + -
1555A PHE* 3.8 38.1 - - + -
1556A ASN* 4.0 12.3 - - - +
1562A PHE 4.1 2.6 + - - +
1563A ARG* 1.3 82.4 + - - +
1565A GLU* 1.3 63.7 + - - +
1566A LYS 3.9 9.6 - - - +
1567A ILE* 3.8 24.2 - - + -
1716A ILE* 4.2 6.5 - - + -
1717A THR 3.9 2.7 - - - +
1718A PHE* 3.8 4.5 - - - -
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Residues in contact with GLU1565 (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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1540A GLU* 5.2 0.7 - - - +
1548A TYR* 5.7 0.4 - - - -
1563A ARG* 3.4 12.9 + - - +
1564A ILE* 1.3 74.9 - - - +
1566A LYS* 1.3 65.6 + - + +
1654A ARG* 3.2 41.0 + - - +
1717A THR* 2.8 23.0 + - + +
1718A PHE* 4.6 2.7 - - - -
1719A ARG* 2.8 44.6 + - + +
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Residues in contact with LYS1566 (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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1540A GLU* 3.7 35.9 - - + +
1548A TYR* 5.1 4.5 - - - -
1564A ILE* 3.9 3.3 - - - +
1565A GLU* 1.3 84.7 - - - +
1567A ILE* 1.3 69.3 + - - +
1568A GLU* 3.0 40.8 + - + -
1654A ARG* 6.4 0.7 - - - +
1715A LEU* 5.8 0.6 - - - +
1717A THR* 2.9 53.3 + - - +
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Residues in contact with ILE1567 (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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1540A GLU* 3.7 4.2 - - - +
1541A LEU* 2.9 44.0 + - + +
1548A TYR* 3.6 41.1 - - + +
1551A VAL* 4.1 20.9 - - + -
1552A ALA* 4.0 29.2 - - + +
1564A ILE* 3.8 15.0 - - + -
1566A LYS* 1.3 82.0 - - - +
1568A GLU* 1.3 68.4 + - - +
1714A TYR* 4.4 5.4 - - + -
1715A LEU 3.3 10.8 - - - +
1716A ILE* 4.2 12.1 - - + -
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Residues in contact with GLU1568 (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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1538A VAL* 3.3 32.9 - - + +
1539A VAL 3.2 7.2 - - - +
1540A GLU* 3.7 23.6 + - + +
1541A LEU* 4.7 0.7 - - - -
1566A LYS* 3.0 36.7 + - + +
1567A ILE* 1.3 78.3 - - - +
1569A ARG* 1.3 61.3 + - - +
1570A ILE* 4.8 0.9 - - + -
1714A TYR* 3.1 9.6 - - - +
1715A LEU* 2.8 58.6 + - + +
1717A THR* 4.4 2.8 + - - -
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Residues in contact with ARG1569 (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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1537A CYS 3.8 0.3 - - - +
1538A VAL* 3.7 3.1 - - - -
1539A VAL* 2.8 36.6 + - + +
1541A LEU* 4.1 17.9 - - + +
1545A ASP* 5.5 0.2 + - - -
1547A GLU* 2.9 42.9 + - - -
1568A GLU* 1.3 72.4 - - - +
1570A ILE* 1.3 71.5 + - - +
1571A GLN* 3.4 37.0 + - + +
1713A GLU* 3.3 22.0 - - + +
1714A TYR* 3.7 15.5 - - + -
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Residues in contact with ILE1570 (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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1536A PHE* 4.6 5.6 - - + -
1537A CYS 3.8 5.4 - - - +
1538A VAL* 4.2 16.2 - - + -
1568A GLU 4.6 0.9 - - - +
1569A ARG* 1.3 79.7 - - - +
1571A GLN* 1.3 58.1 + - - +
1572A ASN* 4.8 1.3 - - + -
1612A ASN* 3.5 62.1 - - + +
1658A TYR* 4.2 7.2 - - + -
1711A TYR* 2.6 34.5 + - - +
1712A PRO* 3.1 29.8 - - + +
1713A GLU 2.7 13.1 + - - +
1715A LEU* 4.4 20.0 - - + +
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Residues in contact with GLN1571 (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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1536A PHE* 3.1 4.5 - - - -
1537A CYS* 2.9 46.8 + - + +
1539A VAL* 3.3 37.1 - - - +
1569A ARG* 3.4 43.1 + - - +
1570A ILE* 1.3 72.8 - - - +
1572A ASN* 1.3 60.7 + - - +
1573A PRO* 3.4 9.7 - - + +
1711A TYR* 3.7 1.3 - - - -
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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