Contacts of the strand formed by residues 1446 - 1453 (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 TYR1446 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1444A VAL* 3.1 7.7 - - - +
1445A ARG* 1.3 110.1 - - + +
1447A TYR* 1.3 62.0 + - - +
1448A ARG* 4.9 3.4 - - + -
1464A THR* 3.7 32.8 - - + -
1465A VAL 3.0 19.7 - - - +
1466A PRO* 4.2 2.5 - - + -
1467A GLY* 3.5 7.4 - - - +
1490A VAL* 2.8 66.6 + - + +
1497A PRO* 3.7 15.6 - - - +
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Residues in contact with TYR1447 (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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1420A PRO* 4.0 14.4 - - + -
1437A TRP* 3.3 37.0 - + + -
1439A ALA* 3.0 31.5 - - - +
1440A PRO* 4.1 3.1 - - + -
1444A VAL* 3.6 22.2 - - + +
1446A TYR* 1.3 76.6 - - - +
1448A ARG* 1.3 60.0 + - - +
1449A ILE* 3.8 6.1 - - + +
1464A THR* 3.1 8.0 - - - -
1465A VAL* 2.8 32.5 + - + +
1466A PRO 3.7 7.2 - - - -
1467A GLY* 3.4 26.6 + - - -
1469A LYS 3.5 23.6 - - - -
1470A SER* 5.0 0.6 - - - -
1487A VAL* 4.0 13.0 - - + -
1488A TYR 3.1 15.3 - - - +
1489A ALA* 3.9 9.9 - - + -
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Residues in contact with ARG1448 (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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1446A TYR* 4.3 6.5 + - + -
1447A TYR* 1.3 73.8 - - - +
1449A ILE* 1.3 63.0 + - - +
1450A THR* 3.8 11.4 - - + +
1460A VAL* 5.3 3.6 - - - +
1462A GLU* 2.9 45.7 + - - +
1463A PHE 3.7 5.8 - - - +
1464A THR* 4.6 3.4 - - + +
1487A VAL* 3.3 1.7 - - - -
1488A TYR* 2.8 87.2 + - + +
1490A VAL* 4.4 14.1 - - + +
1499A SER* 5.4 3.6 + - - -
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Residues in contact with ILE1449 (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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1435A ILE* 4.0 22.9 - - + -
1437A TRP* 4.3 4.9 - - + -
1447A TYR* 3.8 17.5 - - + +
1448A ARG* 1.3 78.2 - - - +
1450A THR* 1.3 66.8 + - - +
1462A GLU* 2.9 26.7 - - - +
1463A PHE* 3.0 44.5 + - + +
1465A VAL* 3.2 37.5 - - + -
1472A ALA* 4.7 0.4 - - + -
1474A ILE* 4.1 8.7 - - + -
1485A ILE* 4.1 4.3 - - + -
1486A THR 3.2 9.2 - - - +
1487A VAL* 4.0 16.4 - - + -
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Residues in contact with THR1450 (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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1448A ARG* 3.8 20.4 - - - +
1449A ILE* 1.3 74.6 - - - +
1451A TYR* 1.3 63.4 + - - +
1460A VAL* 3.8 21.3 - - + +
1461A GLN 3.1 7.9 - - - -
1462A GLU* 3.4 33.0 - - + +
1484A THR 3.7 0.6 - - - +
1485A ILE* 3.4 4.7 - - - +
1486A THR* 2.8 54.2 + - - +
1488A TYR* 4.1 9.3 + - + +
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Residues in contact with TYR1451 (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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1450A THR* 1.3 78.6 - - - +
1452A GLY* 1.3 60.1 + - - +
1460A VAL* 3.6 5.1 - - - -
1461A GLN* 2.9 85.1 + - + +
1462A GLU 4.7 0.2 - - - -
1463A PHE* 4.0 26.2 - + - -
1474A ILE* 3.6 38.6 - - + -
1475A SER 4.3 8.5 + - - -
1477A LEU* 3.8 22.0 - - + -
1483A TYR* 4.6 13.2 - + + -
1484A THR 3.2 9.2 - - - +
1485A ILE* 4.5 7.0 - - + -
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Residues in contact with GLY1452 (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 TYR* 1.3 78.2 - - - +
1453A GLU* 1.3 61.8 + - - +
1458A SER 6.0 0.7 - - - -
1459A PRO 5.5 1.6 - - - -
1460A VAL* 4.6 15.1 - - - +
1461A GLN* 6.0 0.4 - - - -
1483A TYR* 3.7 10.4 - - - -
1484A THR* 2.8 34.8 + - - +
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Residues in contact with GLU1453 (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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1452A GLY* 1.3 70.9 - - - -
1454A THR* 1.3 67.7 + - - +
1455A GLY 3.2 0.7 + - - -
1456A GLY* 2.8 39.5 + - - -
1457A ASN 4.6 0.5 + - - -
1480A GLY 5.0 1.0 - - - +
1481A VAL* 3.1 34.7 - - + +
1482A ASP* 3.1 16.2 - - + +
1483A TYR* 3.7 8.8 - - + -
1484A THR* 5.4 0.2 - - - -
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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