Contacts of the helix formed by residues 1370 - 1380 (chain C) in PDB entry 3B13
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 ARG1370 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1341C ASP* 4.6 4.3 - - - +
1343C PHE* 3.8 5.6 - - - -
1368C TYR 3.6 9.8 + - - +
1369C GLU* 1.3 79.4 - - - +
1371C ARG* 1.3 67.4 + - - +
1372C GLU* 3.0 45.1 + - - +
1373C ASP* 3.0 22.3 + - - +
1374C PHE* 3.1 9.7 + - - +
23D TYR* 2.2 65.6 + - - +
24D THR* 4.4 3.8 + - - +
26D ASN* 3.5 32.2 - - - +
44D VAL* 4.7 15.7 - - + +
166D LYS* 4.4 17.1 - - - +
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Residues in contact with ARG1371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1343C PHE* 3.3 23.5 - - + -
1370C ARG* 1.3 69.5 - - - +
1372C GLU* 1.3 62.4 + - - +
1374C PHE* 3.9 1.3 - - - -
1375C GLN* 2.8 43.5 + - - +
1408C CYS* 3.5 41.5 + - - -
1409C PHE* 3.5 12.5 - - - +
1410C THR* 3.3 19.6 + - - +
26D ASN* 2.8 44.1 + - - +
27D ALA 3.0 25.2 + - - -
28D PHE* 3.7 17.8 - - - +
29D PRO* 3.8 10.7 - - - +
162D GLN* 4.1 6.9 + - - -
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Residues in contact with GLU1372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1370C ARG* 3.0 42.4 + - - +
1371C ARG* 1.3 81.2 + - + +
1373C ASP* 1.3 58.6 + - - +
1375C GLN* 4.2 3.4 - - - +
1376C MET* 3.0 38.5 + - + +
26D ASN* 3.4 12.6 + - - +
162D GLN* 4.3 11.9 - - - +
165D LEU* 5.9 2.3 - - - +
166D LYS* 4.0 25.9 + - + +
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Residues in contact with ASP1373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1368C TYR 4.6 5.7 - - - +
1369C GLU* 4.3 14.2 - - + +
1370C ARG* 3.0 24.8 + - - +
1372C GLU* 1.3 74.9 - - - +
1374C PHE* 1.3 67.3 + - - +
1376C MET* 3.3 14.5 + - - +
1377C GLN* 3.1 22.9 + - - +
166D LYS* 3.3 28.8 + - - -
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Residues in contact with PHE1374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1343C PHE* 3.5 42.6 - + + -
1345C VAL* 4.0 9.9 - - + -
1363C TYR* 3.5 47.6 - + + -
1369C GLU* 3.5 34.2 + - - -
1370C ARG 3.1 7.6 + - - +
1371C ARG 3.7 5.6 - - - +
1373C ASP* 1.3 81.2 - - - +
1375C GLN* 1.3 57.8 + - - +
1377C GLN* 3.2 4.0 + - - +
1378C LEU* 2.9 41.0 + - + +
1408C CYS* 4.0 18.8 - - - -
1480C ARG* 4.1 12.6 - - - -
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Residues in contact with GLN1375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371C ARG* 2.8 31.3 + - - +
1372C GLU* 4.2 3.8 - - - +
1374C PHE* 1.3 73.8 - - - +
1376C MET* 1.3 67.2 + - - +
1378C LEU* 2.9 8.9 + - + +
1379C MET* 2.9 42.3 + - + +
1387C LYS* 3.5 42.8 - - - +
1388C MET 5.4 1.8 + - - -
1406C ILE* 4.7 4.8 + - - +
1408C CYS* 3.9 43.9 + - + +
28D PHE* 5.8 1.2 - - - -
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Residues in contact with MET1376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372C GLU* 3.0 27.2 + - + +
1373C ASP* 3.4 12.8 - - - +
1375C GLN* 1.3 80.8 - - - +
1377C GLN* 1.3 63.2 + - - +
1378C LEU 3.2 0.2 + - - -
1379C MET* 3.3 11.0 + - - +
1380C THR* 3.4 20.9 + - + +
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Residues in contact with GLN1377 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1366C LYS* 5.9 5.0 - - - -
1369C GLU* 5.7 2.4 - - - +
1373C ASP 3.1 10.0 + - - +
1374C PHE* 3.9 6.7 - - - +
1376C MET* 1.3 80.0 - - - +
1378C LEU* 1.3 59.3 - - - +
1380C THR* 2.7 26.9 + - - +
1381C GLN* 3.8 13.8 + - - +
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Residues in contact with LEU1378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198C ASP* 4.3 17.5 - - - +
1345C VAL* 4.1 26.7 - - + -
1347C TYR* 3.9 17.9 - - - +
1363C TYR* 4.3 11.2 - - + +
1374C PHE* 2.9 30.2 + - + +
1375C GLN* 2.9 13.6 + - + +
1377C GLN* 1.3 77.7 - - - +
1379C MET* 1.3 63.3 + - + +
1380C THR 3.1 0.4 - - - -
1381C GLN* 2.9 28.8 + - + +
1382C PHE* 3.5 14.7 - - + -
1406C ILE* 4.2 22.4 - - + -
1408C CYS* 5.2 4.0 - - + -
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Residues in contact with MET1379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375C GLN* 2.9 40.3 + - + +
1376C MET* 3.3 4.9 + - - +
1378C LEU* 1.3 76.1 - - - +
1380C THR* 1.3 60.8 + - + +
1381C GLN 3.2 0.2 - - - -
1382C PHE* 3.3 25.9 - - - +
1383C PRO* 3.8 3.8 - - - +
1385C ALA* 3.7 37.2 - - + +
1386C GLU 3.9 4.0 - - - +
1387C LYS* 3.8 27.1 - - + -
1406C ILE* 3.7 30.3 - - - -
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Residues in contact with THR1380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376C MET* 3.4 20.9 - - + +
1377C GLN* 2.7 27.8 + - - +
1379C MET* 1.3 78.1 - - - +
1381C GLN* 1.3 61.7 + - - +
1382C PHE 3.1 4.3 + - - -
1383C PRO* 3.7 16.6 - - - +
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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