Contacts of the strand formed by residues 1410 - 1415 (chain A) in PDB entry 2Y23
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 ILE1410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1362A GLU* 5.4 3.1 - - - +
1377A LYS* 5.2 5.4 - - + -
1378A CYS 3.6 14.6 - - - +
1379A LYS* 4.2 22.2 - - + +
1404A HIS* 3.6 35.6 + - + +
1409A GLY* 1.3 76.6 - - - +
1411A CYS* 1.3 64.6 + - - +
1412A THR* 3.8 23.8 - - + -
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Residues in contact with CYS1411 (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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1376A LEU 3.5 0.3 - - - +
1377A LYS* 3.4 5.2 - - - -
1378A CYS* 3.2 49.0 + - - -
1380A VAL* 4.3 20.4 - - + -
1389A ILE* 4.3 24.7 - - - -
1391A TRP* 4.1 11.1 - - + -
1401A ASP* 3.9 19.5 - - - -
1404A HIS* 5.4 5.4 - - - -
1409A GLY 4.0 1.0 + - - -
1410A ILE* 1.3 75.5 - - - +
1412A THR* 1.3 63.1 + - - +
1428A VAL* 5.8 1.6 - - + -
1430A LEU* 6.2 0.2 - - - -
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Residues in contact with THR1412 (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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1375A LEU* 3.6 34.6 - - + +
1376A LEU 2.9 13.9 - - - +
1377A LYS* 4.2 6.5 - - + -
1391A TRP* 3.7 9.8 + - - -
1401A ASP* 4.8 5.7 + - - +
1404A HIS* 5.6 3.5 + - + -
1410A ILE* 3.8 21.7 - - + -
1411A CYS* 1.3 80.5 - - - +
1413A LEU* 1.3 63.1 + - - +
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Residues in contact with LEU1413 (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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1375A LEU* 3.5 5.2 - - - +
1376A LEU* 2.8 39.3 + - + +
1391A TRP* 3.6 50.5 - - + +
1398A ILE* 4.8 19.1 - - + -
1399A SER* 3.9 27.8 - - - +
1412A THR* 1.3 79.0 - - - +
1414A LEU* 1.3 69.6 + - - +
1415A ILE* 4.0 5.2 + - + -
1426A TYR* 5.1 11.7 - - + -
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Residues in contact with LEU1414 (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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1369A THR* 4.3 12.8 - - + -
1373A ASN* 3.7 35.0 - - + +
1374A VAL 3.7 9.4 - - - +
1375A LEU* 3.8 19.5 - - + +
1412A THR* 4.4 0.4 + - - -
1413A LEU* 1.3 80.8 - - - +
1415A ILE* 1.3 65.4 - - - +
1416A THR* 4.0 12.7 + - - +
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Residues in contact with ILE1415 (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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1373A ASN* 3.3 6.7 - - - +
1374A VAL* 2.7 46.0 + - + +
1376A LEU* 4.0 28.0 - - + -
1413A LEU* 4.9 9.2 - - + +
1414A LEU* 1.3 75.7 - - - +
1416A THR* 1.3 63.1 + - - +
1418A PHE* 4.1 10.0 + - + -
1422A ASP* 3.4 40.2 - - + +
1426A TYR* 4.0 33.9 - - + +
1443A LEU* 4.4 10.5 - - + -
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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