Contacts of the helix formed by residues 1426 - 1440 (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 PHE1426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A COA 4.9 9.9 - - + -
1221A SER* 4.7 4.0 - - - -
1247A SER* 3.3 34.5 - - - -
1248A GLY* 4.1 7.6 - - - +
1252A THR* 4.3 10.1 - - + -
1255A LEU* 6.4 0.9 - - + -
1350A ILE* 4.3 7.2 - - + -
1354A GLU* 3.4 38.8 - - + -
1359A ILE* 3.7 26.0 - - + -
1422A ALA* 2.8 15.7 + - - +
1424A VAL 3.6 0.4 - - - -
1425A MET* 1.3 113.9 - - + +
1427A GLY* 1.3 64.9 + - - +
1429A PRO* 3.3 4.0 - - - +
1430A SER* 2.9 31.8 + - - +
1468A HIS* 3.9 10.3 - + - -
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Residues in contact with GLY1427 (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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1350A ILE* 4.0 24.0 - - - +
1354A GLU* 5.5 0.6 - - - +
1422A ALA 3.1 9.2 + - - -
1423A ASP* 3.8 7.6 - - - -
1426A PHE* 1.3 80.0 - - - +
1428A VAL* 1.3 61.8 + - - +
1430A SER* 3.7 2.1 - - - -
1431A VAL* 3.2 25.6 + - - +
1540A LYS* 4.3 14.3 - - - +
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Residues in contact with VAL1428 (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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1423A ASP* 2.8 24.6 + - + +
1424A VAL* 5.0 1.8 - - - -
1427A GLY* 1.3 68.6 - - - -
1429A PRO* 1.3 70.2 - - + +
1430A SER 3.2 0.2 + - - -
1431A VAL* 3.2 2.4 + - - +
1432A ILE* 3.0 49.3 + - + +
1540A LYS* 5.2 1.1 - - + +
1543A GLU* 4.0 23.6 - - + -
1544A VAL* 4.0 20.4 - - + +
1547A TRP* 3.7 36.3 - - + -
1548A THR* 5.2 0.9 - - - +
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Residues in contact with PRO1429 (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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1249A VAL* 3.7 12.1 - - + -
1251A LEU* 3.6 41.5 - - + +
1423A ASP 3.4 2.9 - - - +
1424A VAL 3.2 25.6 - - - +
1425A MET 3.6 11.9 - - - +
1426A PHE 3.3 10.8 - - - +
1428A VAL* 1.3 99.0 - - + +
1430A SER* 1.3 55.5 + - - +
1432A ILE* 3.7 3.6 - - + +
1433A VAL* 3.0 34.5 + - - +
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Residues in contact with SER1430 (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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1248A GLY* 4.6 6.2 + - - -
1249A VAL* 3.8 19.6 - - - +
1348A VAL* 3.9 20.5 - - - +
1349A GLY 4.6 1.9 + - - -
1350A ILE* 3.5 22.5 - - - +
1426A PHE* 2.9 24.3 + - - -
1427A GLY 3.7 4.3 - - - -
1429A PRO* 1.3 77.6 - - - +
1431A VAL* 1.3 57.1 + - - +
1433A VAL* 3.3 3.1 + - - +
1434A ALA* 2.9 29.1 + - - +
1446A MET* 4.0 6.7 - - - -
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Residues in contact with VAL1431 (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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1350A ILE* 5.9 0.2 - - + -
1427A GLY 3.2 16.1 + - - +
1428A VAL 3.9 0.2 - - - +
1430A SER* 1.3 76.0 - - - +
1432A ILE* 1.3 59.3 + - - +
1434A ALA* 3.3 1.6 + - - +
1435A ARG* 2.9 45.4 + - - +
1446A MET* 3.8 24.5 - - + -
1520A TYR* 3.5 19.5 - - - +
1539A LEU* 3.4 30.1 - - + +
1540A LYS* 3.9 9.2 - - + -
1544A VAL* 3.8 21.1 - - + -
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Residues in contact with ILE1432 (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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1251A LEU* 3.6 22.7 - - + -
1336A GLN* 4.0 3.8 - - - +
1428A VAL* 3.0 40.9 + - + +
1429A PRO* 3.7 4.0 - - + +
1431A VAL* 1.3 77.5 - - - +
1433A VAL* 1.3 63.1 + - - +
1435A ARG* 3.3 8.9 + - + +
1436A ASN* 3.0 42.3 + - - +
1544A VAL* 4.1 17.3 - - + -
1548A THR* 4.5 12.6 - - - +
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Residues in contact with VAL1433 (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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1228A SER* 4.5 7.0 - - - +
1249A VAL* 3.9 25.6 - - + -
1250A ALA* 4.9 1.6 - - + +
1251A LEU* 3.7 25.4 - - + +
1336A GLN* 3.8 15.0 + - - +
1346A TYR* 3.8 29.4 - - + +
1348A VAL* 4.7 2.7 - - + -
1429A PRO 3.0 21.0 + - - +
1430A SER 3.7 4.5 - - - +
1432A ILE* 1.3 75.3 - - - +
1434A ALA* 1.3 63.1 + - - +
1436A ASN* 3.4 2.3 + - - +
1437A HIS* 3.0 22.3 + - + +
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Residues in contact with ALA1434 (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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1348A VAL* 4.6 8.5 - - + -
1430A SER 2.9 17.7 + - - +
1431A VAL 3.6 2.2 - - - +
1433A VAL* 1.3 78.8 - - - +
1435A ARG* 1.3 57.2 + - - +
1437A HIS* 3.3 4.0 + - - +
1438A ARG* 2.9 29.1 + - - +
1444A THR* 3.7 16.7 - - + +
1446A MET* 3.5 36.1 - - + -
1520A TYR* 4.0 7.2 - - + -
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Residues in contact with ARG1435 (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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1431A VAL* 2.9 32.8 + - - +
1432A ILE* 3.3 8.7 + - + +
1434A ALA* 1.3 75.8 - - - +
1436A ASN* 1.3 58.8 + - - +
1438A ARG* 3.4 21.6 + - - +
1439A ASP* 2.9 38.2 + - - +
1520A TYR* 3.4 22.2 + - + +
1524A GLU* 2.9 30.6 + - - +
1539A LEU 4.9 0.2 + - - -
1541A ASP* 2.9 39.2 + - - +
1544A VAL* 3.4 27.6 - - - +
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Residues in contact with ASN1436 (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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1336A GLN* 3.5 55.2 + - + +
1337A ALA* 4.9 2.6 - - - +
1339A ARG* 3.3 22.8 + - - +
1432A ILE* 3.0 32.3 + - - +
1433A VAL 3.8 4.3 - - - +
1435A ARG* 1.3 75.0 - - - +
1437A HIS* 1.3 64.1 + - - +
1439A ASP* 4.5 2.7 + - - -
1440A ALA* 3.0 22.0 + - - +
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Residues in contact with HIS1437 (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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1231A VAL* 4.8 11.6 - - + +
1343A THR* 5.1 4.1 - - + -
1344A VAL* 2.8 35.2 + - - +
1346A TYR* 3.3 34.9 - + + +
1433A VAL* 3.0 18.3 + - + +
1434A ALA* 3.5 7.9 - - - +
1436A ASN* 1.3 73.5 - - - +
1438A ARG* 1.3 68.8 + - - +
1440A ALA* 2.9 22.7 + - + +
1441A GLY 3.4 4.2 + - - -
1442A ALA* 3.6 21.1 + - + +
1443A PRO 3.3 17.2 + - - -
1444A THR* 2.7 20.5 + - + +
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Residues in contact with ARG1438 (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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1434A ALA 2.9 17.0 + - - +
1435A ARG* 3.5 26.5 + - - +
1437A HIS* 1.3 77.3 - - - +
1439A ASP* 1.3 84.2 + - - +
1441A GLY* 2.9 22.9 + - - -
1442A ALA 4.2 3.5 - - - +
1444A THR* 3.3 11.8 + - - +
1519A GLU* 6.1 0.2 - - - +
1520A TYR* 3.4 24.3 - - + +
1521A ASN* 3.1 41.3 + - + -
1522A GLN* 3.4 25.1 + - - +
1524A GLU* 3.1 28.3 + - - +
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Residues in contact with ASP1439 (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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1339A ARG* 3.1 31.5 + - - +
1435A ARG* 2.9 20.9 + - - +
1436A ASN* 3.7 2.6 + - - -
1438A ARG* 1.3 104.4 + - - +
1440A ALA* 1.3 58.6 + - - +
1441A GLY* 3.2 1.6 + - - -
1522A GLN* 3.6 11.3 + - - -
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Residues in contact with ALA1440 (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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1338A GLU 4.6 8.1 - - - +
1339A ARG* 4.0 24.1 - - + +
1343A THR* 4.3 22.2 - - + +
1436A ASN 3.0 12.2 + - - +
1437A HIS* 2.9 18.3 + - + +
1439A ASP* 1.3 77.7 - - - +
1441A GLY* 1.3 58.8 + - - +
1442A ALA 3.7 1.2 + - - -
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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