Contacts of the strand formed by residues 1426 - 1432 (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 GLY1426 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995B LYS* 3.8 4.3 - - - -
1405B MET* 3.2 21.4 + - - +
1406B THR 3.2 22.7 - - - -
1407B GLY 3.6 3.3 + - - -
1424B MET* 3.9 6.1 - - - +
1425B THR* 1.3 81.9 - - - +
1427B GLY* 1.3 66.7 + - - +
1496B PRO* 3.6 4.1 - - - +
1498B SER* 3.5 10.8 - - - -
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Residues in contact with GLY1427 (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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1405B MET* 4.0 3.1 - - - -
1407B GLY* 3.6 15.2 - - - -
1408B GLY 3.3 15.3 - - - -
1424B MET* 5.0 1.4 - - - +
1426B GLY* 1.3 72.2 - - - -
1428B LEU* 1.3 62.9 + - - -
1496B PRO* 3.1 26.5 - - - +
1499B GLU* 2.7 23.9 + - - +
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Residues in contact with LEU1428 (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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1405B MET* 3.4 6.2 - - - +
1408B GLY 3.1 7.3 + - - +
1409B VAL* 3.2 13.0 - - + +
1410B ILE 3.1 21.1 + - - -
1424B MET* 5.6 0.7 - - - -
1427B GLY* 1.3 80.5 - - - +
1429B ALA* 1.3 61.6 + - - +
1430B TYR* 4.5 10.8 - - + -
1460B GLN* 3.8 9.9 - - - +
1493B GLN* 4.0 15.3 - - + +
1494B ALA 3.5 16.8 - - - +
1495B VAL* 4.0 19.3 - - + -
1499B GLU* 3.9 22.9 - - + +
1502B SER* 4.2 9.2 - - - +
1504B GLU* 3.6 33.0 - - + -
1505B ALA* 4.5 2.7 - - + +
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Residues in contact with ALA1429 (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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1402B CYS* 3.8 24.0 - - - -
1405B MET* 4.7 1.8 - - + -
1410B ILE* 3.1 11.0 - - + +
1424B MET* 4.8 3.8 - - + +
1428B LEU* 1.3 76.6 - - - +
1430B TYR* 1.3 64.7 + - - +
1431B PHE* 3.5 24.7 - - + -
1492B TRP 3.9 0.3 - - - +
1493B GLN* 3.5 4.2 - - - +
1494B ALA* 2.8 43.4 + - + +
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Residues in contact with TYR1430 (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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1409B VAL* 3.9 17.5 - - + -
1410B ILE 2.8 17.3 + - - +
1411B VAL* 3.5 9.1 - - + -
1412B VAL* 2.8 27.4 + - - +
1428B LEU* 4.2 8.6 - - + +
1429B ALA* 1.3 74.3 - - - +
1431B PHE* 1.3 65.6 + - - +
1432B LEU 4.2 0.2 - - - -
1452B ILE* 3.7 28.5 - - + -
1457B GLY* 3.5 27.9 + - - -
1460B GLN* 2.7 32.8 + - + -
1461B LEU* 3.8 29.6 - - + -
1491B PHE* 4.4 4.5 - - + -
1492B TRP 3.5 2.7 - - - -
1493B GLN* 3.0 38.9 + - + -
1504B GLU* 4.1 1.6 - - - +
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Residues in contact with PHE1431 (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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1401B CYS* 3.9 16.8 - - - -
1402B CYS* 4.3 4.9 - - - -
1412B VAL* 3.6 34.5 - - + +
1414B GLY 5.5 0.9 - - - +
1416B VAL* 3.9 20.4 - - + -
1420B VAL* 3.5 30.5 - - + -
1424B MET* 6.0 0.2 - - + -
1429B ALA* 3.5 31.9 - - + -
1430B TYR* 1.3 75.0 - - - +
1432B LEU* 1.3 62.8 + - - +
1433B ASP* 3.4 6.7 + - - +
1438B LEU* 3.6 28.7 - - + -
1449B LEU* 5.0 2.2 - - + -
1491B PHE* 3.3 4.8 - - - -
1492B TRP* 2.8 42.1 + - - +
1494B ALA* 4.0 14.6 - - + -
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Residues in contact with LEU1432 (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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1412B VAL 3.0 15.9 + - - +
1413B LEU* 3.9 20.9 - - - +
1414B GLY* 4.0 18.3 - - - +
1415B PRO 4.8 0.2 - - - -
1431B PHE* 1.3 71.0 - - - +
1433B ASP* 1.3 72.1 + - - +
1434B GLU* 3.9 35.5 + - + +
1476B LYS* 4.0 4.9 - - - -
1480B ILE* 4.0 24.0 - - + -
1487B TYR* 4.1 14.1 - - + +
1490B LYS* 4.0 19.3 - - + +
1491B PHE* 3.5 32.1 - - + -
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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
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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