Contacts of the strand formed by residues 1372 - 1375 (chain B) 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 ASN1372 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1337B MET* 4.0 4.8 - - - +
1340B GLY 3.1 10.3 + - - +
1341B GLU* 3.3 12.9 - - + +
1342B ILE 3.0 23.6 + - - +
1371B GLY* 1.3 82.3 + - - +
1373B LEU* 1.3 59.4 + - - +
1374B TYR* 3.2 37.5 + - + -
1391B LYS* 3.2 34.7 - - - +
1464B LEU* 4.3 4.7 - - - +
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Residues in contact with LEU1373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1333B VAL* 4.3 20.4 - - + +
1334B GLY* 5.9 0.2 - - - -
1337B MET* 4.4 2.9 - - + +
1342B ILE* 3.3 34.1 - - + +
1344B ILE* 4.5 7.6 - - + -
1360B ILE* 5.6 2.7 - - + -
1364B CYS* 4.9 2.2 - - + -
1365B LEU* 3.9 29.4 - - + -
1372B ASN* 1.3 73.4 - - - +
1374B TYR* 1.3 82.4 + - - +
1375B ALA* 4.4 7.6 - - + +
1383B PHE* 4.0 25.8 - - + -
1391B LYS 2.9 7.3 + - - -
1392B ALA* 3.1 10.8 - - + +
1393B VAL 2.9 25.3 + - - -
1394B ILE* 4.9 3.1 - - + -
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Residues in contact with TYR1374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341B GLU* 4.3 7.2 + - + -
1342B ILE 2.9 13.8 + - - +
1343B VAL* 3.3 8.1 - - + -
1344B ILE 2.8 31.5 + - - +
1372B ASN* 3.2 39.6 + - + -
1373B LEU* 1.3 80.2 - - - +
1375B ALA* 1.3 54.6 + - - +
1376B ASN 4.2 0.4 - - - -
1392B ALA* 5.7 1.1 - - - -
1393B VAL* 3.5 16.4 - - + -
1464B LEU* 3.9 16.9 - - + +
1467B ALA* 3.6 13.1 - - + +
1468B HIS* 3.5 45.3 - - + +
1471B HIS* 3.4 39.3 + + + -
1472B THR* 4.1 10.9 + - - +
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Residues in contact with ALA1375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1344B ILE* 3.5 5.4 - - + -
1359B ILE* 4.1 8.1 - - + -
1360B ILE* 3.6 31.9 - - + -
1373B LEU* 4.1 6.5 - - + -
1374B TYR* 1.3 72.5 - - - +
1376B ASN* 1.3 58.8 + - - +
1377B GLY 2.9 15.8 + - - +
1378B ARG 6.3 0.4 - - - -
1393B VAL 3.0 7.3 + - - -
1394B ILE* 3.6 27.4 - - + -
1395B GLU* 3.8 1.7 - - - +
1468B HIS* 3.4 12.6 - - - -
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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