Contacts of the helix formed by residues 1249 - 1266 (chain W) in PDB entry 5O9G
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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1195W TRP* 5.3 1.4 - - - -
1210W ILE* 5.8 1.0 - - - +
1211W PHE 4.6 4.8 - - - +
1212W LEU 4.4 11.0 - - - -
1246W LYS 5.9 0.2 - - - -
1247W VAL 2.9 9.0 + - - -
1248W PRO* 1.3 74.4 - - - +
1250W ALA* 1.3 65.8 + - - +
1251W ILE 3.7 0.7 - - - -
1252W HIS* 3.5 26.8 + - - +
1253W LEU* 3.3 24.7 - - - +
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Residues in contact with ALA1250 (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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73I T 3.7 24.7 - - - +
1195W TRP* 3.4 31.2 + - + -
1211W PHE 5.0 1.4 + - - -
1212W LEU* 5.2 3.0 - - - +
1249W GLY* 1.3 74.2 - - - +
1251W ILE* 1.3 64.2 + - + +
1252W HIS* 4.1 2.0 + - - -
1254W GLY* 3.3 15.1 + - - -
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Residues in contact with ILE1251 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I T 6.5 0.7 - - + -
74I A 5.2 13.0 - - + +
1192W TYR* 5.4 4.5 - - - +
1250W ALA* 1.3 77.4 - - + +
1252W HIS* 1.3 83.1 + - + +
1253W LEU 3.2 0.7 - - - -
1254W GLY* 4.3 2.5 - - - +
1255W ARG* 2.9 61.0 + - + +
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Residues in contact with HIS1252 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-79J A 4.4 6.6 + - - +
-78J T 3.0 38.9 - + + +
-77J C 5.1 8.9 + - - -
1171W TRP* 5.2 3.9 - - + -
1247W VAL 4.4 7.2 - - - +
1249W GLY* 3.5 30.3 - - - +
1250W ALA 3.4 1.5 - - - -
1251W ILE* 1.3 92.5 - - + +
1253W LEU* 1.3 63.0 + - + +
1255W ARG* 3.5 26.6 + - - +
1256W ARG* 3.6 16.6 + - - +
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Residues in contact with LEU1253 (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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1171W TRP* 3.7 36.3 - - + -
1175W TRP* 5.8 7.0 - - + -
1183W LEU* 5.4 1.9 - - + +
1195W TRP* 3.6 30.5 - - + -
1209W LYS 4.5 1.3 - - - +
1210W ILE* 4.3 18.6 - - + -
1248W PRO* 3.8 30.3 - - + -
1249W GLY 3.3 25.4 + - - +
1251W ILE 3.2 0.4 - - - -
1252W HIS* 1.3 79.5 - - + +
1254W GLY* 1.3 59.7 + - - +
1255W ARG 3.3 0.4 - - - -
1256W ARG* 3.1 6.1 + - + +
1257W VAL* 2.9 30.3 + - - +
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Residues in contact with GLY1254 (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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1192W TYR* 3.2 28.9 - - - -
1195W TRP* 3.4 16.1 - - - -
1250W ALA 3.3 11.0 + - - -
1251W ILE* 3.2 5.0 + - - -
1253W LEU* 1.3 79.4 - - - +
1255W ARG* 1.3 56.3 + - - +
1257W VAL* 3.1 2.1 + - - -
1258W ASP* 2.9 31.2 + - - +
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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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-80J C 5.5 0.7 - - - +
-79J A 3.2 67.0 + - - +
-78J T 3.5 23.6 - - - +
1192W TYR* 3.7 1.8 + - - +
1251W ILE* 2.9 46.9 + - + +
1252W HIS* 3.5 27.3 + - - +
1254W GLY* 1.3 75.1 - - - +
1256W ARG* 1.3 58.6 + - - +
1258W ASP* 3.4 13.4 + - - +
1259W TYR* 2.9 26.5 + - - +
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Residues in contact with ARG1256 (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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-79J A 3.7 8.0 + - - +
1165W PRO* 3.5 21.8 - - - +
1166W LYS* 2.8 64.1 + - - +
1167W PRO 4.6 5.1 + - - -
1168W VAL* 5.4 3.7 - - - +
1171W TRP* 4.1 28.0 - - + -
1175W TRP* 4.9 12.2 - - + +
1180W ASP* 4.8 6.9 + - - -
1183W LEU* 5.3 6.1 - - + -
1252W HIS 3.6 12.5 + - - +
1253W LEU* 3.1 15.0 + - + +
1255W ARG* 1.3 76.4 - - - +
1257W VAL* 1.3 60.4 + - - +
1259W TYR* 3.1 22.1 + - - +
1260W LEU* 2.9 43.3 + - + +
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Residues in contact with VAL1257 (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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1183W LEU* 3.7 27.4 - - + -
1184W LEU* 4.4 15.0 - - + -
1187W VAL* 3.9 26.5 - - + -
1192W TYR* 4.5 10.5 - - + -
1195W TRP* 3.8 19.3 - - + -
1253W LEU 2.9 19.5 + - - +
1254W GLY* 3.1 7.6 + - - +
1256W ARG* 1.3 75.0 - - - +
1258W ASP* 1.3 58.5 + - - +
1260W LEU* 3.1 8.4 + - - +
1261W LEU* 2.9 39.3 + - + +
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Residues in contact with ASP1258 (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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1136W ARG* 5.0 8.4 + - - -
1139W ASP* 5.1 8.6 - - - +
1192W TYR* 3.1 38.1 + - - -
1254W GLY 2.9 13.1 + - - +
1255W ARG* 3.6 15.8 - - - +
1256W ARG 3.3 0.2 - - - -
1257W VAL* 1.3 75.8 - - - +
1259W TYR* 1.3 58.3 + - - +
1261W LEU* 3.9 13.0 - - - +
1262W SER* 2.9 31.1 + - - -
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Residues in contact with TYR1259 (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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-80J C 4.7 20.9 - - - +
-79J A 5.1 4.3 - - - +
1165W PRO* 4.0 17.3 - - + -
1166W LYS* 3.6 49.7 + - + +
1255W ARG 2.9 14.2 + - - +
1256W ARG* 3.1 31.6 + - - +
1258W ASP* 1.3 77.0 - - - +
1260W LEU* 1.3 59.7 + - - +
1262W SER* 3.8 6.0 - - - -
1263W PHE* 2.9 45.3 + + + +
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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
----------------------------------------------------------
1165W PRO* 3.7 33.9 - - + -
1180W ASP* 3.9 33.9 - - + +
1183W LEU* 3.9 24.9 - - + -
1184W LEU* 4.6 15.5 - - + -
1256W ARG* 2.9 36.7 + - + +
1257W VAL* 3.1 9.1 + - - +
1259W TYR* 1.3 75.9 - - + +
1261W LEU* 1.3 60.4 + - - +
1263W PHE* 3.2 5.8 + - + +
1264W LEU* 2.9 36.4 + - + +
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Residues in contact with LEU1261 (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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1139W ASP* 3.7 41.3 - - + +
1140W LEU* 5.3 3.6 - - + +
1142W TYR* 5.0 6.9 - - + -
1143W LEU* 4.6 24.0 - - + -
1184W LEU* 4.0 25.4 - - + -
1187W VAL* 5.3 9.0 - - + -
1192W TYR* 6.0 1.6 - - + -
1257W VAL* 2.9 30.2 + - + +
1258W ASP* 3.9 12.3 - - - +
1260W LEU* 1.3 76.4 - - - +
1262W SER* 1.3 57.5 + - - +
1264W LEU* 3.2 8.8 + - + +
1265W ARG* 2.9 36.8 + - - +
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Residues in contact with SER1262 (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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1139W ASP* 4.9 2.6 + - - -
1258W ASP 2.9 19.1 + - - -
1259W TYR* 4.1 7.9 - - - -
1261W LEU* 1.3 76.9 - - - +
1263W PHE* 1.3 60.0 + - - +
1265W ARG* 3.7 9.6 + - - +
1266W GLY* 3.4 16.3 + - - -
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Residues in contact with PHE1263 (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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1163W ASN* 3.8 37.5 - - + -
1164W THR 3.7 22.2 - - - -
1165W PRO* 4.1 22.9 - - + -
1259W TYR* 2.9 37.9 + + + +
1260W LEU* 3.6 7.6 - - + +
1261W LEU 3.2 0.4 - - - -
1262W SER* 1.3 77.3 - - - +
1264W LEU* 1.3 69.0 + - + +
1266W GLY* 3.2 21.0 + - - +
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Residues in contact with LEU1264 (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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1142W TYR* 3.1 30.3 + - + +
1146W LEU* 4.3 15.5 - - + -
1160W LEU* 4.1 29.2 - - + -
1163W ASN* 4.6 19.1 - - + +
1184W LEU* 3.8 28.9 - - + -
1260W LEU* 2.9 22.0 + - + +
1261W LEU* 3.2 10.5 + - + +
1263W PHE* 1.3 87.1 - - + +
1265W ARG* 1.3 63.7 + - - +
1266W GLY 3.4 5.9 + - - +
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Residues in contact with ARG1265 (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 GLU* 2.9 54.2 + - - +
1139W ASP* 3.2 24.8 + - - +
1141W LYS* 5.8 0.4 - - - +
1142W TYR* 3.4 44.0 - - + +
1261W LEU* 2.9 21.2 + - + +
1262W SER* 4.1 7.4 - - - +
1263W PHE 3.4 0.2 - - - -
1264W LEU* 1.3 76.7 - - - +
1266W GLY* 1.3 58.9 + - - +
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Residues in contact with GLY1266 (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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1262W SER 3.4 12.2 + - - -
1263W PHE 3.2 16.5 + - - +
1264W LEU* 3.2 6.3 - - - +
1265W ARG* 1.3 82.0 - - - +
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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