Contacts of the helix formed by residues 1524 - 1532 (chain X) in PDB entry 2IWL
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 CYS1524 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1418X PHE* 3.9 0.2 - - - -
1473X LEU* 3.7 26.9 - - - -
1476X ILE* 5.5 3.6 - - + -
1477X PHE* 4.1 10.8 - - + -
1520X ASP 3.3 17.9 + - - +
1521X VAL 3.1 18.4 + - - -
1522X ALA 3.6 0.4 - - - -
1523X GLU* 1.3 82.5 - - - +
1525X ASP* 1.3 66.2 + - - +
1526X LEU* 3.9 12.6 - - - -
1527X VAL* 3.2 8.9 + - - +
1528X CYS* 3.1 21.5 + - - +
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Residues in contact with ASP1525 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1415X THR* 4.4 12.1 + - - +
1416X TYR 3.1 9.8 - - - +
1417X SER* 2.9 33.7 - - - -
1418X PHE 4.6 0.3 + - - -
1523X GLU 4.6 3.5 - - - +
1524X CYS* 1.3 74.2 - - - +
1526X LEU* 1.3 57.4 + - - +
1528X CYS* 4.2 1.8 - - - -
1529X THR* 2.7 39.1 + - - -
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Residues in contact with LEU1526 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409X LEU* 3.8 38.1 - - + +
1469X LEU* 3.9 11.3 - - + +
1472X LYS* 3.7 35.4 - - + -
1473X LEU* 3.8 13.7 - - + +
1476X ILE* 3.8 29.6 - - + -
1524X CYS* 3.3 8.7 - - - -
1525X ASP* 1.3 77.3 - - - +
1527X VAL* 1.3 56.6 + - - +
1529X THR* 3.2 6.4 + - - -
1530X PHE* 2.8 29.5 + - - +
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Residues in contact with VAL1527 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1418X PHE* 4.0 4.7 - - + -
1424X ILE* 5.2 0.7 - - + -
1469X LEU* 4.4 5.2 - - + -
1473X LEU* 4.2 16.2 - - + -
1514X LEU* 3.8 29.4 - - + -
1515X MET* 5.4 2.9 - - - -
1521X VAL 3.6 18.8 - - - +
1522X ALA 3.6 20.6 - - - +
1524X CYS* 3.2 15.2 + - - +
1526X LEU* 1.3 75.3 - - - +
1528X CYS* 1.3 69.2 + - - +
1530X PHE* 3.1 15.2 + - - +
1531X PHE* 3.2 41.6 + - + -
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Residues in contact with CYS1528 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1416X TYR* 3.6 6.7 - - - +
1417X SER* 3.2 37.0 - - - -
1418X PHE* 3.3 37.2 - - + +
1421X ASP* 3.8 24.0 - - - +
1450X ARG* 5.2 0.7 + - - -
1524X CYS 3.1 9.5 + - - +
1525X ASP 3.7 8.1 - - - +
1527X VAL* 1.3 77.7 - - - +
1529X THR* 1.3 57.0 + - - +
1531X PHE* 3.0 19.6 + - - +
1532X HIS* 3.1 10.4 + - - +
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Residues in contact with THR1529 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409X LEU* 3.8 17.3 - - + -
1411X PHE* 5.2 1.2 - - - -
1412X SER* 3.5 34.9 - - - +
1414X LYS 4.0 8.7 - - - +
1415X THR* 3.7 7.4 - - - -
1416X TYR* 2.9 26.2 + - + +
1461X ARG* 4.8 0.7 + - - -
1525X ASP 2.7 26.4 + - - -
1526X LEU* 3.6 5.4 - - - -
1528X CYS* 1.3 71.6 - - - +
1530X PHE* 1.3 66.5 + - - +
1532X HIS* 3.0 24.1 + - - +
1534X LEU* 6.0 0.2 - - - +
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Residues in contact with PHE1530 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409X LEU* 3.8 6.7 - - + +
1411X PHE* 3.6 23.6 - + - -
1446X VAL* 5.1 1.3 - - + -
1459X VAL* 4.8 0.3 - - - +
1461X ARG* 3.0 58.8 + - + -
1465X GLU 3.3 25.8 - - - -
1466X PHE* 3.7 41.1 - + - -
1469X LEU* 3.8 33.9 - - + -
1511X LEU* 4.8 0.9 - - + -
1526X LEU 2.8 13.3 + - - +
1527X VAL 3.4 9.6 - - - +
1529X THR* 1.3 75.3 - - - +
1531X PHE* 1.3 86.9 + + - +
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Residues in contact with PHE1531 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1418X PHE* 4.5 1.1 - + - -
1424X ILE* 3.4 28.3 - - + -
1427X VAL* 4.0 21.5 - - + -
1446X VAL* 4.2 12.1 - - + -
1448X ILE* 3.9 22.2 - - + +
1450X ARG* 3.6 24.3 + - - +
1459X VAL* 3.8 15.5 - - + +
1461X ARG* 4.2 1.8 - - - +
1469X LEU* 5.9 0.7 - - + -
1511X LEU* 4.0 23.8 - - + -
1514X LEU* 5.2 3.8 - - + -
1515X MET* 4.9 6.3 - - - -
1527X VAL* 3.2 41.2 + - + -
1528X CYS 3.0 8.4 + - - +
1530X PHE* 1.3 101.5 - + - +
1532X HIS* 1.3 62.2 + - - +
1533X PRO* 3.4 4.0 - - - +
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Residues in contact with HIS1532 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1412X SER* 5.6 1.3 - - - +
1416X TYR* 3.3 58.5 + + + -
1421X ASP* 2.5 44.5 + - - +
1450X ARG* 4.7 0.2 - - - +
1461X ARG* 2.9 17.9 + - - -
1528X CYS 3.1 5.5 + - - +
1529X THR* 3.0 15.1 + - + +
1531X PHE* 1.3 76.1 - - - +
1533X PRO* 1.3 98.7 + - + +
1534X LEU* 3.4 9.6 + - + +
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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