Contacts of the helix formed by residues 1249 - 1266 (chain M) 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 GLY1249 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1195M TRP* 5.3 1.4 - - - -
1210M ILE* 5.8 0.9 - - - +
1211M PHE 4.6 4.7 - - - -
1212M LEU 4.4 11.9 - - - -
1246M LYS 5.9 0.2 - - - -
1247M VAL 2.9 9.4 + - - -
1248M PRO* 1.3 73.6 - - - +
1250M ALA* 1.3 63.9 - - - +
1251M ILE 3.7 1.1 - - - -
1252M HIS* 3.5 26.0 + - - +
1253M LEU* 3.3 24.2 - - - +
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Residues in contact with ALA1250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I T 3.7 24.5 - - - +
1195M TRP* 3.4 30.7 + - + -
1211M PHE 5.0 1.6 + - - -
1212M LEU* 5.2 3.2 - - - +
1249M GLY* 1.3 72.6 - - - +
1251M ILE* 1.3 64.6 + - + +
1252M HIS* 4.1 2.8 + - - -
1254M GLY* 3.3 15.4 + - - -
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Residues in contact with ILE1251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I T 6.5 0.4 - - + -
74I A 5.2 13.5 - - + +
1192M TYR* 5.4 4.9 - - - +
1250M ALA* 1.3 77.7 - - + +
1252M HIS* 1.3 81.8 + - + +
1253M LEU 3.2 0.2 - - - -
1254M GLY* 4.3 2.5 - - - +
1255M ARG* 2.9 60.8 + - + +
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Residues in contact with HIS1252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-79J A 4.4 7.3 + - - +
-78J T 3.0 38.7 - + + +
-77J C 5.1 9.5 + - - -
1171M TRP* 5.2 3.5 - - - -
1247M VAL 4.4 7.8 + - - +
1249M GLY* 3.5 29.9 - - - +
1250M ALA 3.4 1.9 + - - -
1251M ILE* 1.3 92.5 - - + +
1253M LEU* 1.3 63.2 + - + +
1255M ARG* 3.5 26.9 + - - +
1256M ARG* 3.6 15.9 + - - +
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Residues in contact with LEU1253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1171M TRP* 3.7 37.0 - - + -
1175M TRP* 5.8 6.5 - - + -
1183M LEU* 5.4 1.9 - - + +
1195M TRP* 3.6 31.4 - - + -
1209M LYS 4.5 1.3 - - - +
1210M ILE* 4.3 18.6 - - + -
1247M VAL 5.5 0.2 - - - +
1248M PRO* 3.8 29.4 - - + -
1249M GLY 3.3 25.7 + - - +
1251M ILE 3.2 0.2 - - - -
1252M HIS* 1.3 77.3 - - + +
1254M GLY* 1.3 60.5 + - - +
1255M ARG 3.3 0.2 - - - -
1256M ARG* 3.1 6.4 + - + +
1257M VAL* 2.9 30.3 + - - +
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Residues in contact with GLY1254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192M TYR* 3.2 28.7 - - - -
1195M TRP* 3.4 16.7 - - - -
1250M ALA 3.3 10.5 + - - -
1251M ILE* 3.2 5.9 + - - -
1253M LEU* 1.3 79.3 - - - +
1255M ARG* 1.3 55.9 + - - +
1257M VAL* 3.1 2.6 + - - -
1258M ASP* 2.9 30.5 + - - +
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Residues in contact with ARG1255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-80J C 5.7 0.9 - - - +
-79J A 3.2 67.2 + - - +
-78J T 3.5 23.0 + - - +
1192M TYR* 3.7 1.8 + - - +
1251M ILE* 2.9 47.3 + - + +
1252M HIS* 3.5 26.8 + - - +
1254M GLY* 1.3 74.9 - - - +
1256M ARG* 1.3 57.5 + - - +
1258M ASP* 3.4 14.3 + - - +
1259M TYR* 2.9 26.7 + - - +
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Residues in contact with ARG1256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-79J A 3.7 8.0 + - - +
1165M PRO* 3.5 21.4 - - - +
1166M LYS* 2.8 64.9 + - - +
1167M PRO 4.6 4.0 + - - -
1168M VAL* 5.4 3.5 - - - +
1171M TRP* 4.1 28.9 - - + -
1175M TRP* 4.9 12.2 - - + +
1180M ASP* 4.8 7.3 + - - -
1183M LEU* 5.3 6.1 - - + -
1252M HIS 3.6 12.9 + - - +
1253M LEU* 3.1 16.1 + - + +
1255M ARG* 1.3 77.0 - - - +
1257M VAL* 1.3 59.2 + - - +
1259M TYR* 3.1 20.9 + - - +
1260M LEU* 2.9 42.6 + - + +
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Residues in contact with VAL1257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183M LEU* 3.7 26.9 - - + -
1184M LEU* 4.4 15.7 - - + -
1187M VAL* 3.9 26.7 - - + -
1192M TYR* 4.5 9.9 - - + -
1195M TRP* 3.8 19.5 - - + -
1253M LEU 2.9 18.5 + - - +
1254M GLY* 3.1 8.3 + - - +
1256M ARG* 1.3 74.8 - - - +
1258M ASP* 1.3 58.4 + - - +
1260M LEU* 3.1 9.3 + - - +
1261M LEU* 2.9 39.4 + - + +
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Residues in contact with ASP1258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136M ARG* 5.0 8.6 + - - -
1139M ASP* 5.1 9.1 - - - +
1192M TYR* 3.1 39.1 + - - -
1254M GLY 2.9 13.0 + - - +
1255M ARG* 3.6 16.0 - - - +
1257M VAL* 1.3 76.8 - - - +
1259M TYR* 1.3 57.3 + - - +
1261M LEU* 3.5 13.1 + - - +
1262M SER* 2.9 31.0 + - - -
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Residues in contact with TYR1259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-80J C 4.7 20.9 - - - +
-79J A 5.1 3.6 - - - +
1165M PRO* 4.0 16.6 - - + -
1166M LYS* 3.6 49.8 + - + +
1255M ARG 2.9 14.2 + - - +
1256M ARG* 3.1 31.8 + - - +
1258M ASP* 1.3 76.4 - - - +
1260M LEU* 1.3 59.2 + - - +
1262M SER* 3.8 5.7 - - - -
1263M PHE* 2.9 44.9 + + + +
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Residues in contact with LEU1260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160M LEU* 6.5 0.4 - - + -
1165M PRO* 3.7 33.0 - - + -
1180M ASP* 3.9 33.2 - - + +
1183M LEU* 3.9 24.7 - - + -
1184M LEU* 4.6 16.4 - - + -
1256M ARG* 2.9 36.2 + - + +
1257M VAL* 3.1 9.6 + - - +
1259M TYR* 1.3 75.1 - - + +
1261M LEU* 1.3 60.5 + - - +
1263M PHE* 3.2 6.2 + - + +
1264M LEU* 2.9 36.3 + - + +
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Residues in contact with LEU1261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139M ASP* 3.7 41.7 - - + +
1140M LEU* 5.3 3.6 - - + +
1142M TYR* 5.0 7.7 - - + -
1143M LEU* 4.6 23.6 - - + -
1184M LEU* 4.0 25.8 - - + -
1187M VAL* 5.3 8.7 - - + -
1192M TYR* 6.0 1.6 - - + -
1257M VAL* 2.9 30.4 + - + +
1258M ASP* 3.9 12.8 - - - +
1260M LEU* 1.3 76.0 - - - +
1262M SER* 1.3 57.5 + - - +
1264M LEU* 3.2 9.0 + - + +
1265M ARG* 2.9 37.0 + - + +
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Residues in contact with SER1262 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139M ASP* 4.9 2.4 + - - -
1258M ASP 2.9 18.1 + - - -
1259M TYR* 4.1 8.3 - - - -
1261M LEU* 1.3 77.0 - - - +
1263M PHE* 1.3 61.2 + - - +
1265M ARG* 3.7 9.4 + - - +
1266M GLY* 3.4 17.5 + - - -
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Residues in contact with PHE1263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1163M ASN* 3.8 36.8 - - + -
1164M THR 3.7 21.8 - - - -
1165M PRO* 4.1 20.9 - - + -
1259M TYR* 2.9 36.6 + + + +
1260M LEU* 3.6 7.9 - - + +
1261M LEU 3.2 0.2 - - - -
1262M SER* 1.3 78.5 - - - +
1264M LEU* 1.3 68.0 + - + +
1266M GLY* 3.2 20.7 + - - +
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Residues in contact with LEU1264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142M TYR* 3.1 29.2 + - + +
1146M LEU* 4.3 16.4 - - + -
1160M LEU* 4.1 28.9 - - + -
1163M ASN* 4.6 19.3 - - + +
1184M LEU* 3.8 28.9 - - + -
1260M LEU* 2.9 23.9 + - + +
1261M LEU* 3.8 10.3 - - + +
1263M PHE* 1.3 86.2 - - + +
1265M ARG* 1.3 64.9 + - - +
1266M GLY 3.4 5.8 + - - +
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Residues in contact with ARG1265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138M GLU* 2.9 54.8 + - - +
1139M ASP* 3.2 24.6 + - - +
1141M LYS* 5.8 0.8 - - - +
1142M TYR* 3.4 42.9 - - + +
1261M LEU* 2.9 20.1 + - - +
1262M SER* 4.1 8.1 - - - +
1263M PHE 3.4 0.4 - - - -
1264M LEU* 1.3 75.3 - - - +
1266M GLY* 1.3 58.6 + - - +
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Residues in contact with GLY1266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262M SER 3.4 12.6 + - - -
1263M PHE* 3.2 16.6 + - - +
1264M LEU 3.2 5.4 - - - +
1265M ARG* 1.3 81.9 - - - +
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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