Contacts of the helix formed by residues 1254 - 1264 (chain N) in PDB entry 4G7Z
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 GLN1254 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1238N MET* 5.3 0.2 - - - -
1253N THR* 1.3 74.5 - - - +
1255N GLY* 1.3 65.0 + - - +
1257N PRO* 3.5 16.6 - - - +
1258N ARG* 3.5 37.2 + - + +
1261N GLU* 5.0 3.9 - - - +
1355N VAL* 5.7 1.3 - - + -
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Residues in contact with GLY1255 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1236N LEU* 4.3 0.7 - - - -
1237N THR 5.1 0.4 - - - -
1238N MET* 3.5 27.4 - - - +
1253N THR* 3.5 2.2 - - - -
1254N GLN* 1.3 78.8 - - - +
1256N LEU* 1.3 65.7 + - - +
1257N PRO* 4.4 0.2 - - - -
1258N ARG* 3.1 18.9 + - - +
1259N VAL 3.5 2.9 + - - -
1355N VAL* 3.7 25.5 - - - +
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Residues in contact with LEU1256 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087N ARG* 3.3 47.1 - - + +
1090N ASP* 3.9 15.0 - - + +
1091N SER* 4.3 10.5 - - - +
1094N LEU* 4.3 12.6 - - + -
1233N GLY* 5.0 10.8 - - - +
1236N LEU* 3.4 43.3 + - + +
1255N GLY* 1.3 70.1 - - - -
1257N PRO* 1.3 72.7 - - + +
1259N VAL* 3.1 15.5 + - + +
1260N ILE* 3.2 28.4 + - + +
1356N TYR* 6.0 0.4 - - - +
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Residues in contact with PRO1257 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087N ARG* 4.6 25.1 - - - +
1090N ASP* 6.1 0.9 - - - +
1254N GLN* 3.5 11.2 - - - +
1255N GLY 3.5 4.7 - - - -
1256N LEU* 1.3 95.7 - - + +
1258N ARG* 1.3 49.0 + - - +
1260N ILE* 3.1 12.7 + - + +
1261N GLU* 2.7 35.0 + - - +
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Residues in contact with ARG1258 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254N GLN* 3.5 36.8 + - + +
1255N GLY 3.1 13.2 + - - +
1257N PRO* 1.3 75.1 - - - +
1259N VAL* 1.3 68.3 + - - +
1261N GLU* 2.6 51.0 + - - +
1262N LEU* 2.8 51.8 + - + +
1268N PRO* 4.2 4.8 - - - +
1329N ALA* 3.5 21.0 - - - +
1330N ILE 5.0 1.0 + - - +
1347N TYR* 3.2 18.8 + - - -
1351N GLU* 3.1 33.5 + - - +
1355N VAL* 4.1 16.4 - - + -
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Residues in contact with VAL1259 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094N LEU* 3.9 11.9 - - + -
1236N LEU* 3.6 28.5 - - + -
1256N LEU* 3.1 10.9 + - + +
1258N ARG* 1.3 77.9 - - - +
1260N ILE* 1.3 58.3 + - - +
1262N LEU* 3.1 11.4 + - - +
1263N PHE* 2.9 54.8 + - + -
1352N ILE* 4.7 5.5 - - + +
1355N VAL* 3.8 16.6 - - + -
1356N TYR* 3.6 30.5 - - + +
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Residues in contact with ILE1260 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090N ASP* 4.3 23.1 - - + +
1094N LEU* 3.7 29.8 - - + -
1097N LYS* 4.9 6.7 - - - +
1256N LEU* 3.3 30.1 - - + +
1257N PRO* 3.1 11.6 + - + +
1259N VAL* 1.3 72.8 - - - +
1261N GLU* 1.3 65.9 + - - +
1263N PHE* 4.3 5.4 - - - +
1264N GLU* 3.1 41.3 + - + +
1266N ARG* 4.5 13.2 - - - +
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Residues in contact with GLU1261 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254N GLN* 5.0 4.8 - - - +
1257N PRO 2.7 17.8 + - - +
1258N ARG* 2.6 50.3 + - - +
1260N ILE* 1.3 72.9 - - - +
1262N LEU* 1.3 57.2 + - - +
1265N ALA* 3.5 0.7 + - - -
1266N ARG* 3.1 57.6 + - + +
1268N PRO* 3.2 29.8 - - + +
1269N LYS* 3.8 5.9 + - - +
1329N ALA* 4.6 1.6 - - - +
1332N PRO* 5.6 0.5 - - - +
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Residues in contact with LEU1262 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258N ARG* 2.8 56.8 + - + +
1259N VAL* 3.4 8.5 - - - +
1260N ILE 3.1 0.2 - - - -
1261N GLU* 1.3 74.9 - - - +
1263N PHE* 1.3 59.9 + - - +
1264N GLU 3.1 1.8 - - - -
1265N ALA* 2.8 23.0 + - - +
1330N ILE 6.0 0.2 - - - +
1332N PRO* 5.2 5.8 - - + -
1347N TYR* 4.3 6.1 - - + -
1348N LEU* 3.9 33.1 - - + +
1351N GLU* 3.6 15.9 - - + +
1352N ILE* 3.6 47.1 - - + +
1355N VAL* 5.5 0.2 - - + -
1375N MET* 4.5 5.0 - - - +
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Residues in contact with PHE1263 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094N LEU* 3.9 22.7 - - + -
1098N LEU* 4.2 11.7 - - + -
1229N ILE* 3.9 35.7 - - + -
1259N VAL* 2.9 47.5 + - + +
1260N ILE* 3.3 4.0 + - - +
1262N LEU* 1.3 72.8 - - - +
1264N GLU* 1.3 60.0 + - + +
1265N ALA 3.3 0.4 - - - -
1352N ILE* 3.6 27.6 - - + -
1356N TYR* 4.5 0.2 - - - -
1368N ILE* 4.9 3.8 - - + -
1371N VAL* 3.7 27.4 - - + -
1375N MET* 3.4 27.0 - - + +
1423N GLY* 3.4 3.6 - - - -
1424N VAL* 3.0 34.9 + - + +
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Residues in contact with GLU1264 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094N LEU* 6.3 0.2 - - - -
1097N LYS* 2.4 33.6 + - - -
1260N ILE* 3.1 23.5 + - + +
1263N PHE* 1.3 78.1 - - + +
1265N ALA* 1.3 70.5 + - - +
1266N ARG* 3.3 42.4 + - + +
1333N HIS* 5.4 0.2 - - - -
1423N GLY* 3.3 14.6 + - - -
1424N VAL* 3.3 18.0 + - + +
1425N THR* 2.7 28.3 + - - -
19R G 4.2 8.7 + - - +
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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