Contacts of the strand formed by residues 1523 - 1527 (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 ARG1523 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1207A ALA* 4.5 9.5 - - - +
1211A LEU* 4.5 10.9 - - - +
1278A ILE 3.7 4.2 + - - -
1279A ALA* 3.5 25.1 - - - +
1280A HIS* 3.9 13.7 + - - +
1316A VAL* 5.1 7.0 - - + +
1320A TYR* 4.0 6.4 + - - +
1485A LEU* 3.4 15.9 - - + -
1486A PRO* 3.1 40.6 - - + +
1488A VAL* 3.2 35.4 - - + +
1518A LEU* 3.9 0.9 - - - +
1519A SER* 2.6 57.9 + - - +
1521A GLY 5.9 0.4 + - - -
1522A GLY* 1.3 82.6 - - - +
1524A LEU* 1.3 62.0 + - - +
1525A ILE* 3.4 28.7 - - - +
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Residues in contact with LEU1524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1447A ILE* 3.4 34.8 - - + -
1477A TYR* 4.1 17.7 - - + -
1482A TYR 3.4 24.7 - - - +
1483A GLY 5.3 0.4 - - - +
1485A LEU* 4.5 9.2 - - + +
1486A PRO 3.1 9.6 + - - +
1487A VAL* 3.6 9.3 - - + -
1488A VAL* 2.9 27.0 + - - -
1516A VAL* 4.8 4.0 - - + -
1517A ARG 3.2 18.6 - - - +
1518A LEU* 3.4 28.3 - - + -
1523A ARG* 1.3 78.8 - - - +
1525A ILE* 1.3 66.4 + - - +
1526A VAL* 3.6 3.8 - - - +
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Residues in contact with ILE1525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1277A ASN 3.8 0.4 - - - +
1278A ILE* 3.3 53.6 - - + +
1488A VAL* 3.5 17.5 - - + +
1490A ALA* 4.7 4.9 - - + -
1516A VAL* 3.3 12.0 - - - +
1517A ARG* 3.0 43.7 + - + +
1519A SER* 3.9 11.4 - - - +
1523A ARG* 3.4 22.1 + - - +
1524A LEU* 1.3 71.0 - - - +
1526A VAL* 1.3 81.9 + - - +
1527A PRO* 3.4 18.6 - - + -
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Residues in contact with VAL1526 (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* 4.4 9.2 - - + -
1487A VAL* 3.8 4.5 - - + -
1488A VAL 3.3 15.2 + - - +
1489A MET* 3.1 40.8 - - + -
1490A ALA* 3.1 20.3 + - - +
1513A VAL* 3.9 29.4 - - + -
1515A GLU 3.9 4.0 - - - -
1516A VAL* 4.2 9.2 - - + +
1524A LEU 3.6 8.5 - - - +
1525A ILE* 1.3 88.6 - - - +
1527A PRO* 1.4 65.7 - - - +
1528A ILE* 3.9 3.8 - - + +
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Residues in contact with PRO1527 (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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1278A ILE* 5.3 2.0 - - + -
1490A ALA* 3.2 17.5 - - + +
1513A VAL* 3.8 4.0 - - - -
1514A ARG 3.5 12.1 + - - -
1515A GLU* 3.3 50.9 + - + +
1516A VAL* 4.3 2.5 - - - -
1517A ARG* 4.5 13.5 - - + +
1525A ILE* 3.4 15.7 - - + -
1526A VAL* 1.4 89.1 - - - +
1528A ILE* 1.3 60.9 + - - +
1529A THR 4.5 9.4 - - - +
1531A ALA* 4.6 12.6 - - + +
1532A ILE* 5.1 3.1 - - + +
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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
------------------------------------------------------------
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