Contacts of the helix formed by residues 1248 - 1265 (chain W) in PDB entry 6G0L
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 GLY1248 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210W PHE 3.6 19.9 + - - -
1211W LEU* 3.9 6.1 - - - -
1245W LYS 4.5 1.7 + - - -
1246W VAL* 4.2 2.2 - - - +
1247W PRO* 1.3 76.1 - - - +
1249W ALA* 1.3 65.4 + - - -
1250W ILE* 3.4 2.7 - - - -
1251W HIS* 3.0 27.6 + - - +
1252W LEU* 3.4 9.6 + - - +
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Residues in contact with ALA1249 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72J A 5.9 3.1 - - - +
1194W TRP* 3.8 32.0 - - + -
1211W LEU* 3.5 29.3 + - + +
1248W GLY* 1.3 71.4 - - - +
1250W ILE* 1.3 61.6 + - - +
1252W LEU* 3.8 2.6 + - - +
1253W GLY 3.4 13.2 + - - -
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Residues in contact with ILE1250 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J T 6.0 3.1 - - + +
1191W TYR* 5.2 3.8 - - - +
1194W TRP* 6.5 0.2 - - + -
1248W GLY 5.2 0.2 - - - -
1249W ALA* 1.3 77.6 - - - +
1251W HIS* 1.3 77.2 + - + +
1253W GLY* 2.9 9.8 + - - +
1254W ARG* 2.7 73.2 + - + +
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Residues in contact with HIS1251 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-77I C 2.8 49.5 + - - -
-76I G 4.9 11.6 + - - -
1170W TRP* 4.4 6.8 - + + -
1245W LYS 5.7 0.2 - - - -
1246W VAL* 3.4 28.8 - - + +
1247W PRO* 3.0 24.2 - - + -
1248W GLY* 3.0 25.1 + - - +
1250W ILE* 1.3 85.2 - - + +
1252W LEU* 1.3 56.7 + - - +
1254W ARG* 3.5 12.3 + - - +
1255W ARG* 3.0 31.4 + - - +
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Residues in contact with LEU1252 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1170W TRP* 5.1 2.7 - - + -
1174W TRP* 5.0 4.5 - - + -
1182W LEU* 3.9 34.5 - - + -
1194W TRP* 3.4 42.4 - - + +
1197W ILE* 5.8 0.9 - - + -
1209W ILE* 4.7 18.8 - - + -
1211W LEU* 5.5 1.6 - - + -
1247W PRO* 3.4 37.2 - - + +
1248W GLY 3.4 8.4 + - - +
1249W ALA 4.1 5.4 - - - +
1250W ILE 3.2 0.6 - - - -
1251W HIS* 1.3 75.8 - - - +
1253W GLY* 1.3 58.6 + - - +
1254W ARG 3.1 1.8 - - - -
1255W ARG* 2.7 25.6 + - + +
1256W VAL* 3.0 15.8 + - - +
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Residues in contact with GLY1253 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191W TYR* 3.0 35.7 + - - -
1194W TRP* 4.1 5.3 - - - -
1249W ALA 3.4 8.0 + - - -
1250W ILE* 2.9 13.4 + - - -
1252W LEU* 1.3 77.9 - - - +
1254W ARG* 1.3 60.8 + - - +
1256W VAL* 3.4 15.1 - - - +
1257W ASP* 3.7 14.1 + - - +
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Residues in contact with ARG1254 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-78I C 3.2 51.3 + - - +
-77I C 1.8 71.4 + - - +
-76I G 5.5 0.2 + - - -
1250W ILE* 2.7 47.6 + - + +
1251W HIS* 3.5 13.5 + - - +
1253W GLY* 1.3 77.4 - - - +
1255W ARG* 1.3 61.7 + - + +
1257W ASP* 4.0 4.3 + - - +
1258W TYR* 3.5 23.6 + - - +
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Residues in contact with ARG1255 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-78I C 5.4 5.6 + - - -
1164W PRO* 5.0 1.0 - - - +
1165W LYS* 3.1 65.2 + - - +
1167W VAL* 3.2 20.5 - - - +
1170W TRP* 3.3 28.8 - - + -
1179W ASP* 3.8 26.8 + - - -
1182W LEU* 5.2 11.4 - - + -
1251W HIS 3.0 21.2 + - - +
1252W LEU* 2.7 25.7 + - + +
1254W ARG* 1.3 74.6 - - - +
1256W VAL* 1.4 56.4 + - - +
1258W TYR* 3.8 15.8 - - - +
1259W LEU* 3.5 32.4 + - + +
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Residues in contact with VAL1256 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1183W LEU* 6.1 4.3 - - - -
1186W VAL* 5.2 16.8 - - + -
1191W TYR* 3.3 39.7 - - + -
1194W TRP* 6.3 0.4 - - - +
1252W LEU 3.0 10.5 + - - +
1253W GLY 3.4 6.5 - - - +
1255W ARG* 1.4 70.6 - - - +
1257W ASP* 1.3 83.0 + - - +
1258W TYR 3.1 2.0 - - - -
1259W LEU* 3.0 8.3 + - - +
1260W LEU* 3.0 52.6 + - + +
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Residues in contact with ASP1257 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135W ARG* 3.7 36.8 + - - +
1138W ASP* 4.7 7.8 - - - +
1191W TYR* 4.7 2.5 + - - -
1253W GLY 3.7 16.5 + - - +
1254W ARG* 4.5 3.7 - - - +
1255W ARG 3.7 0.2 - - - -
1256W VAL* 1.3 92.0 - - - +
1258W TYR* 1.3 61.4 + - - +
1260W LEU* 4.2 5.2 - - - +
1261W SER* 3.5 26.3 + - - -
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Residues in contact with TYR1258 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-79I G 5.9 9.4 - - - -
-78I C 5.1 9.6 - - - +
1163W THR 5.2 1.4 + - - -
1164W PRO* 4.6 4.0 - - + +
1165W LYS* 3.8 44.5 + - + +
1254W ARG 3.5 17.0 + - - +
1255W ARG* 3.8 18.8 - - - +
1256W VAL 3.1 0.4 - - - -
1257W ASP* 1.3 79.1 - - - +
1259W LEU* 1.3 75.0 + - + +
1261W SER* 4.4 2.2 - - - -
1262W PHE* 3.0 43.4 + + + +
1267W LEU* 6.1 4.5 - - + -
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Residues in contact with LEU1259 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1159W LEU* 6.0 4.9 - - + -
1164W PRO* 3.2 35.2 - - + -
1179W ASP* 3.5 37.0 - - + +
1182W LEU* 6.0 2.9 - - + -
1183W LEU* 5.7 8.7 - - + -
1255W ARG* 3.5 21.9 + - + +
1256W VAL* 3.0 10.2 + - - +
1258W TYR* 1.3 83.6 - - + +
1260W LEU* 1.4 69.4 - - + +
1262W PHE* 3.3 8.9 + - + +
1263W LEU* 3.2 34.3 + - + +
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Residues in contact with LEU1260 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138W ASP* 3.2 51.6 - - + +
1139W LEU* 4.0 6.3 - - + +
1141W TYR* 4.9 10.0 - - + -
1142W LEU* 4.1 27.8 - - + -
1183W LEU* 5.6 4.3 - - + -
1256W VAL* 3.0 43.4 + - + +
1257W ASP* 4.2 5.2 - - - +
1259W LEU* 1.4 78.8 - - + +
1261W SER* 1.3 68.1 + - - +
1263W LEU* 3.8 2.2 + - - +
1264W ARG* 3.7 18.4 + - - +
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Residues in contact with SER1261 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138W ASP* 3.7 18.5 + - - -
1257W ASP 3.5 15.7 + - - -
1258W TYR* 4.4 2.7 - - - -
1260W LEU* 1.3 80.3 - - - +
1262W PHE* 1.3 61.7 - - - +
1264W ARG* 3.4 4.9 + - - +
1265W GLY 3.2 4.7 + - - -
1266W GLY* 2.9 40.4 + - - +
1267W LEU* 4.8 8.1 - - - -
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Residues in contact with PHE1262 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1162W ASN* 4.5 9.6 - - + -
1163W THR 3.4 41.1 - - - -
1164W PRO* 4.3 4.3 - - + -
1258W TYR* 3.0 37.4 + + + +
1259W LEU* 3.4 15.3 - - + +
1260W LEU 3.3 0.4 - - - -
1261W SER* 1.3 79.3 - - - +
1263W LEU* 1.3 90.6 + - + +
1265W GLY* 3.5 10.4 + - - -
1266W GLY 5.2 0.4 - - - +
1267W LEU* 5.8 8.5 - - + +
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Residues in contact with LEU1263 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141W TYR* 4.1 18.0 + - + +
1157W PHE* 5.9 6.5 - - + -
1159W LEU* 5.2 22.4 - - + +
1162W ASN* 3.7 33.7 + - + +
1164W PRO* 6.0 1.1 - - + -
1259W LEU* 3.2 22.3 + - + +
1260W LEU 3.8 2.2 + - - +
1261W SER 3.4 0.2 - - - -
1262W PHE* 1.3 104.6 - - + +
1264W ARG* 1.3 60.3 + - - +
1265W GLY 3.3 0.2 - - - -
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Residues in contact with ARG1264 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138W ASP* 5.9 2.9 - - - -
1141W TYR* 3.5 53.9 - - + +
1260W LEU 3.7 14.2 + - - +
1261W SER* 3.4 5.6 + - - +
1263W LEU* 1.3 77.0 - - - +
1265W GLY* 1.3 58.5 + - - +
1266W GLY* 4.8 2.9 - - - +
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Residues in contact with GLY1265 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261W SER 3.2 3.5 + - - -
1262W PHE* 3.5 8.3 + - - -
1263W LEU 3.3 3.2 - - - -
1264W ARG* 1.3 79.0 - - - +
1266W GLY* 1.4 61.4 + - - +
1267W LEU 3.6 3.6 - - - -
1268W ASN* 3.5 24.9 + - - +
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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
------------------------------------------------------------
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