Contacts of the strand formed by residues 1406 - 1412 (chain A) in PDB entry 1OFD
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 THR1406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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993A ARG 3.0 24.7 + - - +
994A SER* 3.9 20.8 - - - -
995A LYS* 4.0 14.8 + - - +
1000A LEU* 4.8 8.7 - - + -
1386A ARG* 3.1 25.1 + - - +
1387A ASN 2.8 8.3 + - - -
1388A SER* 3.3 5.1 + - - -
1404A TYR 3.5 4.7 + - - +
1405A MET* 1.3 76.0 - - - +
1407A GLY* 1.3 57.1 + - - +
1423A GLY 5.6 0.2 - - - +
1425A THR* 3.7 22.2 - - + -
1426A GLY* 3.4 23.0 - - - +
1427A GLY 3.7 0.7 + - - -
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Residues in contact with GLY1407 (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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995A LYS* 5.7 0.9 - - - -
1387A ASN* 3.1 21.0 + - - +
1388A SER 3.1 18.9 + - - +
1405A MET* 3.3 10.9 - - - +
1406A THR* 1.3 79.2 - - - +
1408A GLY* 1.3 63.2 + - - -
1426A GLY 3.6 3.0 + - - -
1427A GLY* 3.5 13.7 - - - -
1499A GLU* 5.1 0.9 - - - -
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Residues in contact with GLY1408 (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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1388A SER 3.5 4.0 + - - -
1389A VAL* 3.8 20.1 - - - +
1390A GLY 3.4 12.3 - - - -
1391A LYS* 4.9 3.6 - - - -
1405A MET* 3.8 2.9 - - - -
1407A GLY* 1.3 74.1 - - - -
1409A VAL* 1.3 69.1 + - - +
1427A GLY* 3.3 2.9 - - - -
1428A LEU 3.1 23.0 + - - -
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Residues in contact with VAL1409 (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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1390A GLY 3.2 5.7 + - - -
1391A LYS* 3.2 37.4 - - + +
1392A ALA 3.1 24.0 + - - +
1405A MET* 4.1 0.4 - - - +
1408A GLY* 1.3 80.1 - - - +
1410A ILE* 1.3 65.1 + - - +
1411A VAL* 4.8 0.2 - - + -
1428A LEU* 3.3 10.5 - - + +
1430A TYR* 3.8 29.2 - - + -
1460A GLN* 3.5 23.8 - - + +
1464A LEU* 3.7 25.2 - - + +
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Residues in contact with ILE1410 (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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1365A LEU* 4.2 3.6 - - + -
1383A PHE* 4.0 17.7 - - + -
1384A ALA* 3.7 21.8 - - + -
1387A ASN* 3.9 11.4 - - - +
1390A GLY 4.1 2.0 - - - +
1392A ALA* 3.7 23.3 - - + +
1402A CYS* 3.9 20.2 - - - -
1405A MET* 3.7 25.8 - - + -
1409A VAL* 1.3 84.8 - - - +
1411A VAL* 1.3 61.8 + - - +
1412A VAL* 3.9 21.1 - - + -
1428A LEU 3.0 6.7 + - - -
1429A ALA* 3.1 8.5 - - + +
1430A TYR* 2.7 32.4 + - - +
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Residues in contact with VAL1411 (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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1392A ALA 2.9 11.8 + - - +
1393A VAL* 3.3 16.0 - - + -
1394A ILE* 3.0 26.7 + - - +
1409A VAL* 4.8 0.2 - - + -
1410A ILE* 1.3 77.9 - - - +
1412A VAL* 1.3 65.7 + - - +
1413A LEU* 3.8 23.8 - - + -
1430A TYR* 3.4 15.7 - - + +
1461A LEU* 3.6 34.3 - - + -
1464A LEU* 4.1 31.9 - - + -
1465A ILE* 4.3 3.4 - - + -
1491A PHE* 4.7 1.1 - - + -
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Residues in contact with VAL1412 (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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1394A ILE* 3.4 18.6 - - + -
1396A GLY* 3.6 35.7 - - - +
1401A CYS* 4.1 5.6 - - - -
1410A ILE* 3.9 16.2 - - + -
1411A VAL* 1.3 76.9 - - - +
1413A LEU* 1.3 60.5 + - - +
1414A GLY 3.3 13.7 + - - +
1416A VAL* 3.9 13.9 - - + -
1430A TYR 2.9 9.8 + - - +
1431A PHE* 3.6 30.0 - - + -
1432A LEU* 3.0 26.5 + - - +
1491A PHE* 4.6 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