Contacts of the helix formed by residues 1372 - 1386 (chain G) in PDB entry 4Z94
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 ASP1372 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1210G ILE* 3.3 24.2 - - - +
1370G ARG 4.5 2.2 - - - +
1371G ALA* 1.3 75.9 - - - +
1373G ASP* 1.3 66.7 + - - +
1374G HIS* 3.0 36.9 + - - +
1375G VAL* 3.0 12.9 + - - +
1376G ALA* 3.0 19.2 + - - +
1398G HIS* 4.5 10.8 - - + +
1399G ILE* 4.0 16.5 - - - +
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Residues in contact with ASP1373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372G ASP* 1.3 73.8 - - - +
1374G HIS* 1.3 60.4 + - + +
1376G ALA* 4.0 4.7 - - - -
1377G PHE* 2.6 60.0 + - + -
1398G HIS 4.8 1.2 + - - +
1399G ILE* 3.7 1.0 - - - +
1400G THR* 2.9 46.5 + - - +
1402G LYS* 4.7 1.6 - - - +
1403G GLY* 2.9 28.3 + - - -
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Residues in contact with HIS1374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210G ILE* 4.4 6.3 - - + -
1214G LYS* 4.2 30.6 + - + +
1372G ASP* 3.0 21.9 + - - +
1373G ASP* 1.3 80.5 - - + +
1375G VAL* 1.3 62.3 + - - +
1377G PHE* 3.2 22.5 + + - +
1378G ALA* 2.9 24.1 + - - +
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Residues in contact with VAL1375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210G ILE* 3.8 21.5 - - + +
1213G LEU* 4.1 30.1 - - + +
1214G LYS* 4.4 7.6 - - + +
1217G ALA* 6.3 0.2 - - + -
1366G LEU* 4.3 7.4 - - + -
1371G ALA* 4.0 20.9 - - + -
1372G ASP* 3.2 30.1 - - - +
1374G HIS* 1.3 77.6 - - - +
1376G ALA* 1.3 55.8 + - - +
1378G ALA* 3.4 3.0 + - - +
1379G ILE* 2.9 51.8 + - + +
1399G ILE* 5.9 0.9 - - + -
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Residues in contact with ALA1376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372G ASP 3.0 9.0 + - - +
1373G ASP* 3.1 7.2 + - - +
1375G VAL* 1.3 74.7 - - - +
1377G PHE* 1.3 59.5 + - - +
1379G ILE* 3.4 8.8 + - - +
1380G ALA* 2.9 28.6 + - - +
1399G ILE* 3.7 23.7 - - + +
1403G GLY* 3.5 30.5 - - - +
1407G ILE* 3.6 15.5 - - + +
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Residues in contact with PHE1377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1373G ASP* 2.6 46.4 + - + -
1374G HIS* 3.4 26.5 - + - +
1376G ALA* 1.3 70.7 - - - +
1378G ALA* 1.3 65.9 + - - +
1380G ALA* 2.9 9.2 + - - +
1381G ILE* 2.9 28.4 + - + +
1402G LYS* 3.6 60.1 - - + -
1403G GLY* 4.2 1.3 - - - -
1406G ALA* 3.9 12.8 - - + -
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Residues in contact with ALA1378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1214G LYS* 4.1 25.4 - - + +
1217G ALA* 3.7 19.7 - - + +
1218G GLU 5.5 0.2 - - - +
1374G HIS 2.9 12.9 + - - +
1375G VAL 3.5 8.5 - - - +
1377G PHE* 1.3 75.0 - - - +
1379G ILE* 1.3 58.5 + - - +
1381G ILE* 3.1 12.0 + - - +
1382G MET* 2.9 28.4 + - - +
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Residues in contact with ILE1379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217G ALA* 4.2 11.7 - - + -
1229G PHE* 4.9 6.1 - - + -
1366G LEU* 4.5 9.4 - - + -
1375G VAL* 2.9 38.5 + - + +
1376G ALA* 3.5 8.7 - - - +
1378G ALA* 1.3 76.1 - - - +
1380G ALA* 1.3 63.8 + - - +
1382G MET* 3.2 16.7 + - + +
1383G LEU* 3.0 41.7 + - + +
1392G LEU* 3.7 22.2 - - + -
1394G LEU* 3.8 28.5 - - + -
1407G ILE* 4.3 7.6 - - + -
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Residues in contact with ALA1380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376G ALA 2.9 12.8 + - - +
1377G PHE* 2.9 10.6 + - - +
1379G ILE* 1.3 73.8 - - - +
1381G ILE* 1.3 68.1 + - + +
1383G LEU* 3.1 11.3 + - - -
1384G LYS* 3.4 10.4 + - - +
1406G ALA* 3.5 38.4 - - + +
1407G ILE* 3.8 5.8 - - - +
1410G ALA* 3.3 24.6 - - + +
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Residues in contact with ILE1381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221G LYS* 4.2 25.6 - - - +
1377G PHE* 2.9 21.2 + - + +
1378G ALA* 3.4 8.7 - - - +
1380G ALA* 1.3 75.9 - - + +
1382G MET* 1.3 64.1 + - - +
1383G LEU 3.2 0.7 + - - -
1384G LYS* 3.2 44.5 + - + +
1385G ALA* 3.8 2.8 + - - +
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Residues in contact with MET1382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217G ALA* 3.5 27.8 - - + +
1220G LEU* 4.0 15.9 - - + -
1221G LYS* 4.1 25.7 - - + +
1229G PHE* 4.5 10.3 - - + -
1378G ALA 2.9 13.2 + - - +
1379G ILE* 3.3 28.0 - - + +
1381G ILE* 1.3 76.0 - - - +
1383G LEU* 1.3 65.2 + - + +
1385G ALA* 3.2 6.1 + - - +
1386G ASN* 2.8 50.4 + - - +
1389G ILE* 3.4 29.4 - - + -
1392G LEU* 4.8 3.1 - - + -
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Residues in contact with LEU1383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1379G ILE* 3.0 38.2 + - + +
1380G ALA* 3.1 8.2 + - - +
1382G MET* 1.3 88.7 - - + +
1384G LYS* 1.3 65.5 + - - +
1386G ASN* 3.7 8.4 - - + +
1389G ILE* 5.5 4.7 - - + +
1392G LEU* 4.6 7.6 - - + -
1407G ILE* 4.0 24.0 - - + +
1410G ALA* 4.3 7.4 - - + -
1411G LEU* 4.6 9.9 - - + -
1414G ASN* 3.0 52.7 + - + +
1417G LEU* 4.2 24.0 - - + -
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Residues in contact with LYS1384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1380G ALA* 3.7 13.3 - - - +
1381G ILE* 3.2 50.0 + - + +
1383G LEU* 1.3 79.3 - - - +
1385G ALA* 1.3 60.2 + - + +
1386G ASN 4.9 0.9 - - - +
1387G LYS* 5.7 0.7 - - - +
1406G ALA 5.8 0.2 + - - -
1410G ALA* 4.3 17.9 - - + +
1413G GLN* 3.4 62.2 + - + +
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Residues in contact with ALA1385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221G LYS* 4.0 29.0 - - + +
1222G GLU* 4.8 11.8 - - - +
1381G ILE 3.8 2.1 + - - +
1382G MET 3.2 7.4 + - - +
1384G LYS* 1.3 81.3 - - + +
1386G ASN* 1.3 64.0 + - - +
1387G LYS* 3.3 18.2 + - - +
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Residues in contact with ASN1386 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220G LEU 3.0 22.2 + - - -
1221G LYS 3.6 11.4 + - - +
1223G ASN* 3.9 4.6 + - - +
1382G MET* 2.8 34.2 + - - +
1383G LEU* 3.7 4.6 - - + +
1384G LYS 3.7 0.9 - - - +
1385G ALA* 1.3 72.1 - - - +
1387G LYS* 1.3 59.8 + - - +
1388G THR* 2.8 27.9 + - - +
1389G ILE* 3.0 40.1 + - - +
1414G ASN* 3.4 24.3 + - - +
1416G THR* 3.5 1.9 + - - -
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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