Contacts of the helix formed by residues 1385 - 1390 (chain A) in PDB entry 2H7C
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 SER1385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1306A LEU* 4.2 4.1 - - - +
1366A TYR* 2.5 39.5 + - - -
1381A LEU 2.8 23.1 + - - -
1382A LEU* 3.4 14.5 - - - -
1383A TRP 3.0 0.6 - - - -
1384A LYS* 1.3 75.1 - - - +
1386A TYR* 1.3 63.1 + - - -
1387A PRO* 3.3 4.0 - - - -
1388A LEU* 2.8 16.4 + - - -
1389A VAL* 3.0 21.8 + - - +
1417A PHE* 4.9 0.2 - - - -
1421A ILE* 4.6 6.4 - - - +
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Residues in contact with TYR1386 (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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1312A PRO* 3.9 9.2 - - + -
1313A ARG* 3.5 45.2 - - + +
1382A LEU 3.6 3.3 + - - -
1383A TRP* 3.0 30.7 + + - +
1385A SER* 1.3 77.2 - - - +
1387A PRO* 1.3 68.9 - - + +
1389A VAL* 4.4 1.3 - - - -
1390A CYS* 2.6 66.8 + - - +
1391A ILE 3.5 32.1 - - - +
1392A ALA* 4.0 6.1 - - - +
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Residues in contact with PRO1387 (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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1253A SER* 5.4 0.3 + - - -
1254A VAL* 3.5 21.9 + - - +
1306A LEU* 4.6 11.9 - - + -
1307A ASP 6.1 0.2 - - - +
1312A PRO 3.5 11.9 - - - +
1315A SER* 3.7 24.7 - - - +
1317A PRO* 3.6 30.7 - - + +
1384A LYS 3.4 12.6 - - - +
1385A SER 3.3 2.7 - - - -
1386A TYR* 1.3 99.6 - - + +
1388A LEU* 1.3 61.9 + - + +
1390A CYS* 5.0 1.6 + - - +
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Residues in contact with LEU1388 (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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1A COA 4.6 6.1 - - - -
1253A SER* 4.1 12.1 + - - -
1254A VAL* 3.5 35.9 + - + +
1306A LEU* 5.3 2.0 - - + -
1317A PRO* 4.8 2.9 - - + -
1355A PHE* 4.1 16.2 - - + -
1364A MET* 3.8 39.7 - - + -
1366A TYR* 3.2 29.8 - - + +
1385A SER* 2.8 10.8 + - - +
1387A PRO* 1.3 85.6 - - + +
1389A VAL* 1.3 62.1 + - + +
1390A CYS 3.7 0.2 - - - -
1421A ILE* 5.1 1.3 - - + -
1424A VAL* 5.3 0.3 - - - +
1425A MET* 3.8 30.0 - - - +
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Residues in contact with VAL1389 (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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1253A SER* 4.9 3.8 + - - -
1382A LEU* 4.1 17.5 - - + +
1385A SER* 3.0 23.5 + - - +
1386A TYR 4.4 0.2 - - - +
1388A LEU* 1.3 80.4 - - + +
1390A CYS* 1.3 74.0 + - - +
1391A ILE* 3.4 28.1 + - + +
1421A ILE* 4.1 32.1 - - + -
1424A VAL* 3.6 42.1 - - + +
1425A MET* 4.3 2.2 - - + -
1551A PHE* 4.4 3.5 - - - -
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Residues in contact with CYS1390 (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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1253A SER* 4.7 12.8 - - - +
1386A TYR* 2.6 55.4 + - + +
1387A PRO 5.5 1.6 - - - +
1388A LEU 5.4 0.4 - - - -
1389A VAL* 1.3 76.2 - - - +
1391A ILE* 1.3 60.8 + - - +
1392A ALA 3.9 1.7 + - - -
1551A PHE* 4.2 9.5 - - - -
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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