Contacts of the strand formed by residues 1689 - 1693 (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 HIS1689 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1559A LEU* 3.8 6.3 - - - +
1560A HIS* 2.7 64.4 + + - -
1562A ASP* 3.2 19.1 - - + -
1614A TRP* 3.7 21.1 - + + -
1615A HIS 3.2 11.9 - - - +
1616A ILE* 4.0 17.0 - - + -
1683A ILE* 3.6 19.8 - - + +
1687A ALA 2.9 22.2 + - - +
1688A PRO* 1.3 74.9 - - - +
1690A GLN* 1.3 61.3 + - - +
1691A VAL* 4.8 1.8 - - + -
2721A MN 2.0 36.3 + - - -
2722A OGA 3.2 9.3 + - - -
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Residues in contact with GLN1690 (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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1557A THR 3.5 8.1 - - - +
1558A ASN 4.1 0.4 - - - -
1559A LEU* 3.6 27.2 - - + +
1560A HIS* 5.2 0.7 - - - -
1613A LEU 4.1 0.2 - - - +
1614A TRP* 3.4 5.7 - - - +
1615A HIS* 3.0 67.8 + - + +
1653A TYR* 3.5 25.5 - - + -
1654A LEU* 2.7 58.0 + - - +
1689A HIS* 1.3 73.4 - - - +
1691A VAL* 1.3 66.8 + - - +
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Residues in contact with VAL1691 (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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1555A GLY* 3.7 2.1 - - - -
1556A THR* 2.9 22.3 + - - -
1557A THR* 2.9 18.9 + - - +
1560A HIS* 5.9 0.2 - - + -
1612A ALA* 3.9 13.5 - - + -
1613A LEU 3.6 3.8 - - - +
1614A TRP* 3.6 34.8 - - + +
1653A TYR* 4.3 1.7 - - - -
1689A HIS* 4.8 1.3 - - + -
1690A GLN* 1.3 82.6 - - - +
1692A HIS* 1.3 64.1 + - - +
1693A ASN* 3.8 19.1 - - - +
1699A LYS* 3.8 13.2 - - - +
2722A OGA 3.5 34.8 - - - +
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Residues in contact with HIS1692 (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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1546A LEU* 3.0 32.5 + - + +
1551A ASP 3.4 20.9 - - - -
1552A ARG* 4.1 9.1 + - - -
1554A VAL 2.7 27.3 + - - -
1556A THR* 3.5 3.4 - - - +
1589A THR* 3.8 24.8 - - + +
1612A ALA* 4.3 0.7 - - - -
1613A LEU* 2.8 45.4 + - + +
1653A TYR* 3.3 27.6 + - + +
1691A VAL* 1.3 74.3 - - - +
1693A ASN* 1.3 69.4 + - - +
1694A LEU* 3.5 4.8 + - + +
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Residues in contact with ASN1693 (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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1543A ALA* 3.2 37.6 + - - +
1544A TYR 3.5 11.9 + - - +
1546A LEU* 3.0 22.9 + - - +
1556A THR* 2.7 26.7 + - - +
1611A GLY 3.9 4.0 - - - -
1612A ALA* 3.6 6.8 - - - +
1691A VAL* 3.8 2.3 - - - +
1692A HIS* 1.3 81.7 - - - +
1694A LEU* 1.3 59.0 + - - +
1695A TYR 3.5 10.5 - - - +
1697A CYS* 3.5 20.1 - - - +
1699A LYS* 3.0 25.0 + - - +
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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