Contacts of the helix formed by residues 1425 - 1431 (chain A) in PDB entry 5IYB
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 GLY1425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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882A SER* 5.5 0.4 + - - -
883A ILE* 4.9 3.8 - - - +
1424A THR* 1.3 78.7 - - - +
1426A PRO* 1.3 76.2 - - - +
1427A LEU 3.2 2.5 - - - -
1428A MET* 3.2 9.8 + - - +
1429A LYS* 3.1 18.2 + - - +
1448A SER 5.1 0.4 - - - -
1449A ASP* 3.3 14.4 - - - -
1450A PRO* 4.4 11.6 - - - +
1456A GLU* 5.2 4.2 + - - -
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Residues in contact with PRO1426 (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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23A PHE* 3.8 29.8 - - + -
1424A THR 3.8 1.5 - - - +
1425A GLY* 1.3 84.3 - - - +
1427A LEU* 1.3 59.1 + - - +
1429A LYS* 3.6 15.7 - - + +
1430A CYS* 2.8 33.1 + - - +
1438A VAL* 4.3 7.5 - - + +
1439A LEU* 4.5 4.2 - - + +
1442A ALA* 3.6 28.0 - - + -
1447A GLU* 4.4 13.7 - - + +
1448A SER 4.1 6.5 - - - +
1449A ASP* 3.6 19.5 - - + +
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Residues in contact with LEU1427 (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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21A VAL* 5.0 9.4 - - + -
23A PHE* 4.7 14.8 - - + -
1425A GLY 3.2 0.6 - - - -
1426A PRO* 1.3 80.0 - - - +
1428A MET* 1.3 63.3 + - - +
1430A CYS* 3.1 26.0 - - - -
1431A SER* 3.8 1.7 + - - -
1439A LEU* 4.9 4.0 - - + -
1449A ASP* 3.3 28.9 - - + +
1451A MET* 4.1 7.4 - - - -
1456A GLU* 3.7 28.9 - - + +
1459A MET* 3.5 43.4 - - + +
1460A LEU* 5.3 5.4 - - + -
1158B LEU* 5.2 4.7 - - + -
1159B PHE* 5.3 12.6 - - + -
1162B LEU* 6.4 0.7 - - + -
1167B ILE* 6.2 0.9 - - + -
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Residues in contact with MET1428 (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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866A LYS* 5.0 5.6 - - - +
869A GLU* 3.2 38.6 - - - +
870A SER* 4.2 14.6 - - - +
882A SER* 3.7 15.7 - - - +
1424A THR* 3.5 38.8 - - + +
1425A GLY 3.2 8.5 + - - +
1427A LEU* 1.3 78.0 - - - +
1429A LYS* 1.3 62.9 + - + +
1431A SER* 3.0 23.5 + - - -
1432A PHE* 3.8 5.4 + - - +
1454A VAL 5.7 1.3 - - - -
1455A SER* 4.6 6.5 - - - -
1456A GLU* 3.6 32.7 - - - +
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Residues in contact with LYS1429 (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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138A LYS* 5.9 3.4 - - - +
1419A VAL 5.0 1.1 - - - +
1420A ASN* 3.2 57.2 + - - +
1421A ARG 5.4 1.2 - - - -
1422A GLN 3.5 21.1 + - - +
1423A ASP* 5.0 2.2 - - - +
1424A THR* 3.2 37.4 + - - +
1425A GLY 3.1 6.7 + - - +
1426A PRO* 3.2 18.2 + - - +
1428A MET* 1.3 77.1 - - + +
1430A CYS* 1.3 61.5 + - - +
1432A PHE* 3.4 10.9 + - - +
1433A GLU 4.2 2.4 + - - -
1435A THR 4.7 0.7 + - - -
1438A VAL* 3.9 20.0 - - + +
1447A GLU* 5.9 3.8 - - - +
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Residues in contact with CYS1430 (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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350A VAL* 4.4 7.1 - - - +
1426A PRO 2.8 18.3 + - - +
1427A LEU* 3.1 36.8 - - - -
1428A MET 3.3 0.2 - - - -
1429A LYS* 1.3 69.9 - - - +
1431A SER* 1.3 56.1 + - - +
1432A PHE 3.1 8.0 + - - -
1435A THR* 3.1 46.1 + - + +
1438A VAL* 4.4 3.9 - - + +
1439A LEU* 3.5 42.8 - - + -
1459A MET* 4.2 10.1 - - - -
1158B LEU* 5.6 0.4 - - - -
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Residues in contact with SER1431 (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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350A VAL* 3.6 19.8 - - - +
351A ARG* 5.2 5.0 - - - +
355A MET* 3.4 29.4 - - - +
862A ARG* 3.5 17.2 + - - -
866A LYS* 3.4 20.4 + - - -
1427A LEU 4.1 8.1 + - - -
1428A MET* 3.0 19.1 + - - +
1430A CYS* 1.3 78.5 - - - +
1432A PHE* 1.3 59.2 + - - +
1435A THR* 5.4 0.2 - - - -
1455A SER* 4.4 3.1 - - - -
1459A MET* 4.4 2.2 - - - -
1088B GLU* 5.0 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