Contacts of the strand formed by residues 1456 - 1463 (chain B) in PDB entry 2IUK
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 ALA1456 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435B TYR 4.8 0.4 - - - -
1436B GLN* 3.4 23.4 + - - +
1439B PHE* 3.9 18.2 - - + -
1440B ILE* 3.5 32.8 - - + +
1443B LEU* 4.5 1.6 - - + -
1455B TYR* 1.3 73.7 - - - +
1457B THR* 1.3 61.8 + - - +
1475B GLU 3.0 12.3 - - - +
1477B SER 2.8 22.1 + - - +
1515B ASN* 3.7 3.6 - - - -
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Residues in contact with THR1457 (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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1433B LEU 3.0 14.4 - - - +
1435B TYR* 3.4 18.2 + - - +
1455B TYR* 4.1 9.2 - - + -
1456B ALA* 1.3 76.7 - - - +
1458B ARG* 1.3 63.7 + - - +
1459B THR* 4.5 1.0 + - - -
1474B ILE* 4.6 0.2 - - - -
1475B GLU 3.2 3.8 - - - -
1476B LEU* 3.7 28.3 - - + -
1511B HIS 4.0 15.3 - - - +
1512B VAL* 3.4 31.7 - - + +
1515B ASN* 2.7 30.3 + - - +
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Residues in contact with ARG1458 (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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1391B PRO* 4.0 25.1 + - - +
1392B LYS 3.9 8.1 + - - -
1393B SER* 3.6 16.0 + - - -
1403B GLN 3.0 26.4 + - - -
1405B SER* 3.8 10.6 - - - +
1407B ILE* 4.8 5.5 - - + +
1432B ILE* 3.9 9.9 - - + -
1433B LEU 3.4 5.6 - - - -
1434B ASP* 3.3 28.8 + - - +
1436B GLN* 3.1 44.5 + - - +
1457B THR* 1.3 73.0 - - - +
1459B THR* 1.3 59.4 + - - +
1460B ILE 4.2 0.7 - - - -
1473B ALA 4.0 0.2 - - - +
1474B ILE* 3.3 4.0 - - - +
1475B GLU* 2.8 68.6 + - + +
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Residues in contact with THR1459 (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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1370B PHE* 3.8 29.8 - - + -
1432B ILE* 3.1 7.3 - - - +
1433B LEU* 3.0 42.6 + - + -
1457B THR 4.5 0.2 + - - -
1458B ARG* 1.3 72.0 + - - +
1460B ILE* 1.3 60.3 + - - +
1461B LEU* 3.9 19.1 + - + +
1471B PRO* 4.3 6.5 - - + -
1473B ALA 3.4 5.8 - - - +
1474B ILE* 3.8 9.4 - - + +
1512B VAL* 3.4 34.8 - - - +
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Residues in contact with ILE1460 (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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1386B LEU* 4.1 14.8 - - + -
1389B PHE* 4.5 2.5 - - + -
1391B PRO* 4.0 11.9 - - + -
1407B ILE* 3.6 30.5 - - + -
1412B LEU* 3.9 30.5 - - + -
1430B LEU* 3.7 25.4 - - + -
1431B PHE 3.5 7.9 - - - +
1432B ILE* 3.6 28.7 - - + -
1459B THR* 1.3 69.8 - - - +
1461B LEU* 1.3 61.7 + - - +
1471B PRO* 3.6 3.8 - - - +
1472B LEU* 3.0 29.2 + - + +
1473B ALA* 2.9 14.7 + - + +
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Residues in contact with LEU1461 (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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1370B PHE* 5.3 1.3 - - + -
1371B ALA* 4.0 30.1 - - + -
1374B VAL* 4.0 22.0 - - + -
1383B ILE* 3.6 31.9 - - + -
1430B LEU* 3.7 4.3 - - - -
1431B PHE* 2.8 42.7 + - + +
1433B LEU* 4.5 12.3 - - + +
1459B THR* 4.1 25.1 - - + +
1460B ILE* 1.3 73.3 - - - +
1462B PHE* 1.3 60.7 + - - +
1469B LEU* 4.1 17.3 - - + -
1470B LYS 3.6 3.4 - - - +
1471B PRO* 4.5 6.3 - - + -
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Residues in contact with PHE1462 (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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1416B MET* 3.6 34.1 - - + -
1419B VAL* 3.8 23.8 - - + -
1424B ALA* 3.7 20.6 - - + -
1429B ARG* 3.4 45.5 - - + -
1430B LEU* 3.5 15.0 - - + -
1460B ILE 4.2 0.8 + - - -
1461B LEU* 1.3 71.5 - - - +
1463B LEU* 1.3 61.8 + - - +
1464B LYS* 3.3 34.4 + - + -
1468B THR 3.2 2.3 - - - +
1469B LEU* 3.2 4.9 - - - -
1470B LYS* 2.8 43.2 + - + +
1472B LEU* 3.6 23.3 - - + +
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Residues in contact with LEU1463 (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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1428B GLN 4.5 6.5 - - - +
1429B ARG* 2.6 62.1 + - + +
1431B PHE* 3.9 16.2 - - + -
1461B LEU 3.8 1.2 + - - -
1462B PHE* 1.3 74.3 - - - +
1464B LYS* 1.3 57.0 + - - +
1467B GLY* 3.9 21.1 - - - -
1468B THR 3.3 13.9 - - - +
1469B LEU* 4.1 2.9 - - + +
1630B VAL 4.2 19.3 - - - +
1631B ILE* 3.7 31.9 - - + -
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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