Contacts of the strand formed by residues 1696 - 1704 (chain A) in PDB entry 4C8D
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 SER1696 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1466A PHE* 2.7 52.4 + - - -
1472A ARG* 3.4 13.2 + - - -
1543A ALA 3.6 8.1 - - - -
1544A TYR* 3.6 8.0 - - - -
1545A GLY 3.9 2.6 + - - +
1573A VAL* 3.3 5.4 - - - +
1574A GLY 2.6 44.8 + - - -
1576A PRO* 4.0 3.6 - - - +
1695A TYR* 1.3 71.1 - - - +
1697A CYS* 1.3 59.0 + - - +
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Residues in contact with CYS1697 (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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1466A PHE* 3.5 8.2 - - - -
1541A TYR 3.4 1.0 - - - +
1542A ASN* 3.4 7.3 - - - -
1543A ALA 3.0 28.9 + - - -
1570A MET* 3.6 22.0 - - - -
1572A TYR 3.6 2.9 - - - -
1573A VAL* 5.0 0.2 - - - -
1611A GLY* 3.2 41.3 - - - -
1693A ASN* 3.5 22.0 - - - +
1695A TYR 3.5 9.2 - - - -
1696A SER* 1.3 74.1 - - - +
1698A ILE* 1.3 59.3 + - - +
1699A LYS* 3.9 10.3 - - + +
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Residues in contact with ILE1698 (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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1429A TRP 3.9 10.8 - - - +
1431A PRO* 4.2 5.8 - - + -
1434A PHE* 3.9 14.8 - - + -
1463A TRP* 3.6 28.0 - - + -
1466A PHE* 3.6 17.3 - - + -
1540A MET* 3.6 18.6 - - + -
1542A ASN* 3.3 17.0 - - - +
1570A MET* 3.7 2.9 - - - +
1571A VAL* 2.9 42.2 + - + +
1572A TYR* 2.9 42.7 + - + +
1697A CYS* 1.3 69.9 - - - +
1699A LYS* 1.3 60.5 + - - +
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Residues in contact with LYS1699 (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 MET* 3.2 6.9 - - - +
1541A TYR* 2.8 49.3 + - + +
1542A ASN* 4.2 0.5 - - - +
1568A ASN* 3.4 30.1 - - - +
1569A VAL 3.2 4.5 - - - +
1570A MET* 3.8 16.4 - - - -
1612A ALA* 3.8 19.5 - - - -
1614A TRP* 4.5 0.7 - - + +
1675A GLN* 3.6 18.6 - - - +
1691A VAL* 3.8 4.1 - - - +
1693A ASN* 3.0 27.8 + - - +
1697A CYS* 4.1 4.6 - - + +
1698A ILE* 1.3 75.5 - - - +
1700A VAL* 1.3 65.3 + - - +
1701A ALA 4.3 0.2 - - - -
2722A OGA 2.6 35.3 + - - +
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Residues in contact with VAL1700 (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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1429A TRP* 3.7 26.2 - - + -
1494A PHE* 4.2 21.3 - - + -
1505A LEU* 3.5 35.8 - - + +
1509A LEU* 5.9 0.2 - - - +
1538A PRO* 4.7 2.9 - - + -
1539A LYS 3.4 9.9 - - - +
1540A MET* 4.0 10.8 - - + -
1568A ASN* 4.5 0.4 - - - -
1569A VAL* 2.9 37.0 + - - +
1571A VAL* 4.0 17.5 - - + -
1699A LYS* 1.3 79.0 - - - +
1701A ALA* 1.3 63.4 + - - +
1702A GLU 4.4 0.2 + - - -
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Residues in contact with ALA1701 (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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1505A LEU* 5.3 0.7 - - - -
1538A PRO* 3.2 6.8 - - - +
1539A LYS* 2.8 37.6 + - + +
1541A TYR* 3.8 27.1 - - + +
1566A ALA* 5.0 6.3 - - + -
1567A VAL 3.0 12.1 - - - +
1568A ASN* 4.0 13.2 - - + -
1699A LYS 4.3 0.2 - - - -
1700A VAL* 1.3 75.0 - - - +
1702A GLU* 1.3 61.6 + - - +
1703A ASP* 4.2 5.1 + - - +
2722A OGA 4.2 3.8 - - - +
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Residues in contact with GLU1702 (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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1502A PHE* 5.9 0.3 - - - -
1505A LEU* 5.1 4.5 - - + +
1506A MET* 4.1 16.4 - - - +
1509A LEU* 4.0 23.1 - - + +
1515A THR 3.5 24.6 - - - +
1517A ARG* 4.5 15.4 + - - +
1538A PRO* 3.3 35.6 - - - +
1566A ALA* 3.2 1.4 - - - -
1567A VAL* 2.8 45.2 + - + +
1700A VAL 4.4 0.4 + - - -
1701A ALA* 1.3 74.1 - - - +
1703A ASP* 1.3 76.4 + - - +
1704A PHE* 3.7 2.1 - - - -
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Residues in contact with ASP1703 (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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1515A THR 4.5 0.7 - - - +
1522A ASN* 4.6 3.1 + - - -
1524A ALA* 5.3 2.1 - - - +
1538A PRO* 5.6 1.2 - - - +
1539A LYS* 6.0 1.6 - - - +
1562A ASP* 5.9 4.7 - - - +
1563A VAL* 6.2 0.3 - - - +
1564A SER* 3.3 21.4 + - - +
1565A ASP 3.3 5.6 - - - -
1566A ALA* 3.5 14.8 - - - +
1701A ALA* 4.2 5.9 + - - +
1702A GLU* 1.3 95.3 + - - +
1704A PHE* 1.3 64.6 + - - +
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Residues in contact with PHE1704 (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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1405A PHE* 5.3 1.1 - + - -
1409A TRP* 3.9 17.7 - + - -
1514A TYR* 3.3 38.1 - + + +
1515A THR* 4.1 21.8 - - + -
1522A ASN* 3.4 15.3 - - - +
1524A ALA* 4.6 3.8 - - - -
1564A SER* 3.5 1.9 - - - -
1565A ASP* 2.9 55.9 + - + +
1566A ALA 3.5 25.4 - - - -
1567A VAL 3.8 2.2 - - - -
1682A PHE* 3.9 18.8 - + - -
1702A GLU 3.7 11.7 - - - -
1703A ASP* 1.3 75.1 - - - +
1705A VAL* 1.3 72.1 + - - +
1706A SER* 4.0 14.1 - - - -
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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