Contacts of the strand formed by residues 1432 - 1436 (chain A) in PDB entry 1FNF
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 SER1432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1428A ALA* 4.4 0.4 - - - -
1429A THR* 3.1 43.2 + - - +
1431A THR* 1.3 83.2 - - - +
1433A LEU* 1.3 83.3 + - - +
1473A THR* 3.4 24.6 - - - +
1474A ILE 3.1 15.2 + - - -
1475A SER* 4.1 6.5 - - - -
1476A GLY 4.9 0.2 - - - -
1477A LEU* 3.9 3.6 - - - +
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Residues in contact with LEU1433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425A VAL* 3.8 12.3 - - + -
1427A ALA 3.7 3.4 - - - -
1428A ALA* 3.5 13.7 - - + +
1429A THR 5.3 0.7 - - - +
1432A SER* 1.3 89.6 + - - +
1434A LEU* 1.3 61.1 + - - +
1435A ILE* 3.8 9.3 + - + -
1473A THR* 3.4 2.3 - - - -
1474A ILE* 2.8 33.1 + - + +
1477A LEU* 3.5 22.2 - - + -
1483A TYR* 4.9 6.5 - - + -
1485A ILE* 3.4 28.7 - - + -
1507A TYR* 3.3 48.9 - - + -
1509A THR* 5.5 2.2 - - + +
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Residues in contact with LEU1434 (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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1425A VAL* 3.5 2.8 - - - -
1426A VAL* 2.7 51.5 + - + -
1427A ALA* 3.0 36.4 + - + -
1428A ALA* 4.7 0.2 - - - +
1433A LEU* 1.3 71.0 - - - +
1435A ILE* 1.3 58.7 + - - +
1471A THR* 5.3 11.2 - - + -
1472A ALA 3.3 12.1 - - - +
1473A THR* 3.3 29.4 - - + +
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Residues in contact with ILE1435 (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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1423A LEU* 4.1 12.1 - - + -
1424A GLU 3.2 10.5 - - - +
1425A VAL* 4.1 10.5 - - + -
1433A LEU* 4.4 4.7 - - + -
1434A LEU* 1.3 79.6 - - - +
1436A SER* 1.3 62.0 + - - +
1437A TRP* 3.8 21.1 - - + -
1449A ILE* 4.0 13.5 - - + -
1471A THR* 3.4 6.6 - - - +
1472A ALA* 2.7 47.3 + - + +
1474A ILE* 3.8 16.8 - - + -
1485A ILE* 3.7 47.8 - - + -
1487A VAL* 4.4 1.6 - - + -
1505A ILE* 5.3 0.4 - - + -
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Residues in contact with SER1436 (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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1422A ASP 3.5 2.2 - - - +
1423A LEU* 3.2 3.5 - - - +
1424A GLU* 2.8 34.5 + - - +
1426A VAL* 3.5 27.5 - - - +
1435A ILE* 1.3 76.6 - - - +
1437A TRP* 1.3 67.1 + - - +
1470A SER* 3.5 13.7 + - - -
1471A THR* 3.7 12.7 - - - +
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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