Contacts of the helix formed by residues 1309 - 1320 (chain A) in PDB entry 4GG7
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 PRO1309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1178A VAL* 4.6 4.0 - - + -
1182A ILE* 3.9 20.6 - - + -
1277A MET* 3.8 11.9 - - + -
1304A GLN* 3.9 0.2 + - - -
1307A TYR 3.4 10.1 - - - +
1308A CYS* 1.3 89.3 - - + +
1310A ASP* 1.3 65.8 + - - +
1311A PRO* 3.8 12.6 - - + -
1312A LEU* 3.0 28.2 + - + +
1313A TYR 3.1 9.5 + - - -
1340A ILE* 5.0 5.8 - - + -
1344A PHE* 4.8 20.6 - - + -
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Residues in contact with ASP1310 (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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1304A GLN* 2.9 29.7 + - - +
1308A CYS 3.4 0.8 + - - -
1309A PRO* 1.3 70.3 - - - +
1311A PRO* 1.4 69.6 - - + +
1313A TYR* 3.3 3.8 + - - +
1314A GLU* 3.1 30.4 + - - +
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Residues in contact with PRO1311 (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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1309A PRO* 3.3 13.2 - - + -
1310A ASP* 1.4 94.1 - - + +
1312A LEU* 1.3 61.8 + - - +
1314A GLU* 3.2 16.7 + - + +
1315A VAL* 3.1 23.4 + - - +
1340A ILE* 3.9 25.5 - - + +
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Residues in contact with LEU1312 (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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1182A ILE* 3.8 34.5 - - + -
1273A LEU* 4.0 26.0 - - + -
1277A MET* 3.8 25.1 - - + -
1308A CYS* 4.1 4.9 - - - -
1309A PRO* 3.0 20.2 + - + +
1311A PRO* 1.3 79.3 - - - +
1313A TYR* 1.3 62.8 + - - +
1315A VAL* 3.1 9.6 + - + +
1316A MET* 3.0 27.2 + - + +
1337A ILE* 4.2 26.0 - - + -
1340A ILE* 3.9 16.1 - - + +
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Residues in contact with TYR1313 (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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1301A ARG* 5.1 0.9 - - - +
1302A LEU 2.7 26.6 + - - -
1303A LEU* 3.6 6.5 - - - +
1304A GLN* 3.4 66.7 + - + +
1305A PRO* 4.6 0.9 - - + -
1308A CYS* 3.7 8.2 - - - -
1309A PRO 3.1 5.3 + - - -
1310A ASP 3.7 7.9 - - - +
1312A LEU* 1.3 73.9 - - - +
1314A GLU* 1.3 67.8 + - + +
1316A MET* 2.9 21.6 + - - +
1317A LEU* 2.9 60.0 + - + +
1320A TRP* 4.4 8.1 - + - -
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Residues in contact with GLU1314 (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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1310A ASP* 3.1 21.3 + - - +
1311A PRO* 3.2 17.4 + - - +
1313A TYR* 1.3 77.5 - - + +
1315A VAL* 1.3 63.4 + - + +
1317A LEU* 3.2 14.6 + - + +
1318A LYS* 3.0 39.5 + - - +
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Residues in contact with VAL1315 (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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1273A LEU* 4.1 18.8 - - + -
1311A PRO 3.1 13.1 + - - +
1312A LEU* 3.2 11.4 - - + +
1314A GLU* 1.3 76.8 - - + +
1316A MET* 1.3 61.3 + - - +
1318A LYS* 3.4 12.4 + - + +
1319A CYS* 3.2 21.4 + - - -
1333A LEU* 3.6 28.0 - - + +
1336A ARG* 4.4 25.1 - - + +
1337A ILE* 4.3 9.6 - - + -
1340A ILE* 4.3 17.7 - - + -
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Residues in contact with MET1316 (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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1270A GLY* 4.2 4.5 - - - +
1273A LEU* 3.7 27.4 - - + +
1274A TRP* 3.6 46.7 - - - +
1277A MET* 3.8 10.1 - - + -
1305A PRO* 4.7 2.0 - - + -
1308A CYS* 3.6 27.4 - - + -
1312A LEU* 3.0 19.3 + - + +
1313A TYR* 2.9 25.8 + - + +
1315A VAL* 1.3 74.8 - - - +
1317A LEU* 1.3 63.9 + - - +
1319A CYS* 3.0 20.4 + - - +
1320A TRP* 3.3 35.8 + - + -
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Residues in contact with LEU1317 (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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1301A ARG* 4.5 13.0 - - + -
1313A TYR* 2.9 57.4 + - + +
1314A GLU* 3.2 15.0 + - + +
1316A MET* 1.3 78.4 - - - +
1318A LYS* 1.3 61.4 + - - +
1320A TRP* 3.1 30.2 + - + +
1321A HIS* 3.6 8.7 + - - +
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Residues in contact with LYS1318 (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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1314A GLU* 3.0 30.2 + - - +
1315A VAL* 3.5 15.3 - - + +
1316A MET 3.2 0.2 - - - -
1317A LEU* 1.3 77.0 - - + +
1319A CYS* 1.3 62.1 + - - +
1320A TRP 3.1 1.0 + - - -
1321A HIS* 3.3 16.5 + - - +
1326A MET 4.9 0.6 - - - +
1327A ARG* 3.6 11.8 - - - +
1328A PRO* 3.6 27.2 - - + +
1332A GLU* 5.2 3.1 - - - +
1336A ARG* 3.5 40.8 - - - +
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Residues in contact with CYS1319 (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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1266A VAL* 3.3 36.8 - - - +
1267A TRP* 3.3 13.7 - - - +
1269A PHE* 4.3 3.8 - - - -
1270A GLY* 3.9 20.9 - - - -
1273A LEU* 5.5 0.4 - - - -
1315A VAL* 3.2 17.9 + - - -
1316A MET 3.0 11.1 + - - +
1318A LYS* 1.3 78.2 - - - +
1320A TRP* 1.3 59.5 + - + +
1321A HIS 3.5 0.2 - - - -
1327A ARG* 3.2 21.1 + - - -
1328A PRO* 4.3 1.6 - - - -
1333A LEU* 3.8 27.8 - - - -
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Residues in contact with TRP1320 (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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1267A TRP* 3.1 53.1 + + + -
1270A GLY* 3.3 29.1 - - - -
1271A VAL* 3.5 7.7 - - + +
1274A TRP* 4.4 2.7 - + + -
1284A TYR* 5.6 2.9 - - - -
1301A ARG* 2.8 60.4 + - + +
1302A LEU* 3.7 55.0 - - + -
1313A TYR* 4.4 2.0 - + - -
1316A MET* 3.3 38.8 - - + -
1317A LEU* 3.1 23.1 + - + +
1318A LYS 3.1 1.4 - - - -
1319A CYS* 1.3 83.2 - - + +
1321A HIS* 1.3 61.4 + - - +
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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