Contacts of the strand formed by residues 1510 - 1513 (chain A) in PDB entry 1FP7
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 THR1510 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1461A ALA* 4.9 0.4 - - - -
1462A ASP* 4.7 4.7 + - + +
1463A GLY* 2.9 37.9 - - - +
1464A VAL* 3.7 4.5 - - - +
1465A ASN* 4.0 22.7 - - - +
1498A ASP* 3.5 11.1 - - - +
1509A PHE* 1.3 85.8 + - - +
1511A ILE* 1.3 68.8 + - - +
1512A THR* 3.9 2.8 + - - -
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Residues in contact with ILE1511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1451A ILE* 6.2 1.3 - - + -
1455A ALA* 3.9 25.6 - - + -
1459A TYR* 4.2 17.0 - - + -
1461A ALA* 4.2 6.9 - - + +
1463A GLY 3.1 6.3 + - - +
1464A VAL* 3.4 16.6 - - + -
1465A ASN* 2.7 32.8 + - - +
1489A MET* 6.1 1.8 - - - -
1491A LYS* 5.1 2.2 - - + -
1497A SER* 4.1 4.3 - - - -
1498A ASP* 3.8 22.7 - - + +
1509A PHE* 3.8 21.3 - - + -
1510A THR* 1.3 75.1 - - - +
1512A THR* 1.3 59.8 + - - +
1513A VAL 4.0 0.9 - - - +
1528A ILE* 3.6 33.7 - - + -
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Residues in contact with THR1512 (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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1465A ASN* 3.0 33.0 + - + +
1467A THR* 5.2 4.7 - - + -
1498A ASP* 3.6 13.8 + - - +
1510A THR 4.9 2.4 + - - -
1511A ILE* 1.3 78.0 + - - +
1513A VAL* 1.3 58.3 + - - +
1514A ARG* 2.9 51.8 + - + +
1528A ILE* 3.0 19.2 - - - +
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Residues in contact with VAL1513 (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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1451A ILE* 5.2 2.2 - - + -
1464A VAL* 3.6 13.2 - - + -
1465A ASN 2.7 21.1 + - - +
1466A TYR* 3.2 30.7 - - + -
1467A THR* 3.4 17.5 + - - +
1470A ALA* 3.6 6.4 - - + +
1511A ILE* 4.5 1.0 - - + +
1512A THR* 1.3 71.8 - - - +
1514A ARG* 1.3 62.3 + - - +
1515A GLU 3.5 21.5 - - - +
1516A VAL* 3.8 17.3 - - + -
1526A VAL* 3.9 16.8 - - + -
1527A PRO 3.8 7.9 - - - +
1528A ILE* 4.2 8.7 - - + -
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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