Contacts of the helix formed by residues 1220 - 1238 (chain B) in PDB entry 2O8C
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 ALA1220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668A THR* 5.9 5.8 - - + -
669A GLY 5.7 4.9 - - - +
783A HIS* 3.3 19.1 - - - +
785A HIS* 5.3 4.5 - - + +
1216B GLY 4.5 0.2 - - - +
1219B THR* 1.3 88.5 + - - +
1221B THR* 1.3 62.7 + - - +
1222B PHE* 3.5 9.4 - - + +
1223B ASP* 4.2 17.9 - - - +
1224B GLY* 3.1 19.9 + - - -
1249B TYR* 4.1 3.6 + - - -
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Residues in contact with THR1221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A THR* 3.9 32.1 - - + +
783A HIS* 3.2 21.3 + - - -
784A PHE* 3.3 27.9 - - + -
785A HIS* 3.4 26.0 + - + -
1220B ALA* 1.3 73.2 - - - +
1222B PHE* 1.3 65.3 + - - +
1224B GLY* 3.3 8.0 + - - -
1225B THR* 3.3 21.2 + - + +
1249B TYR* 4.0 6.4 - - + -
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Residues in contact with PHE1222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A HIS* 3.4 37.1 + + + -
825A SER* 3.8 22.4 - - - -
828A ILE* 4.7 1.3 - - + -
848A ALA* 3.4 40.8 - - + -
851A LEU* 3.7 29.0 - - + +
852A GLU* 3.7 27.4 - - + -
1220B ALA* 3.5 3.5 - - + +
1221B THR* 1.3 80.2 - - - +
1223B ASP* 1.3 75.2 + - - +
1225B THR* 3.1 19.2 + - - -
1226B ALA* 3.8 10.0 + - + +
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Residues in contact with ASP1223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A SER* 2.9 50.0 + - - +
827A GLY* 3.3 23.1 + - - -
828A ILE* 3.5 11.8 - - + +
1219B THR* 3.8 17.7 + - - +
1220B ALA* 4.0 14.4 + - + +
1221B THR 3.3 0.2 - - - -
1222B PHE* 1.3 82.6 - - - +
1224B GLY* 1.3 63.3 + - - +
1225B THR 3.4 0.7 - - - -
1226B ALA* 4.2 4.0 - - - -
1227B ILE* 3.3 32.3 + - + +
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Residues in contact with GLY1224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B LEU* 4.2 2.9 - - - +
1216B GLY* 4.6 3.5 - - - -
1219B THR* 4.2 8.9 - - - +
1220B ALA 3.1 15.0 + - - -
1221B THR 3.3 1.7 + - - -
1223B ASP* 1.3 78.0 - - - +
1225B THR* 1.3 60.6 + - - +
1227B ILE* 4.6 1.8 - - - +
1228B ALA* 3.4 25.6 + - - +
1249B TYR* 3.3 29.6 - - - -
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Residues in contact with THR1225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A THR* 5.4 0.7 - - + -
851A LEU* 3.3 20.7 - - + +
1221B THR* 3.3 14.8 + - + +
1222B PHE* 3.1 13.5 + - - -
1224B GLY* 1.3 74.8 - - - +
1226B ALA* 1.3 63.3 + - - -
1227B ILE 3.2 0.3 + - - -
1228B ALA* 3.3 3.9 + - - +
1229B ASN* 2.8 38.1 + - - +
1249B TYR* 3.4 27.4 - - + -
1251B SER* 3.5 22.0 - - - +
1252B LEU* 5.4 3.7 - - + +
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Residues in contact with ALA1226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A ILE* 5.2 5.6 - - + -
844A ALA* 3.8 29.2 - - + +
847A LYS* 4.6 12.7 - - + +
848A ALA* 4.5 17.3 - - + +
851A LEU* 5.3 2.2 - - + -
1222B PHE* 3.8 13.2 + - + +
1223B ASP* 4.3 6.3 - - - +
1224B GLY 3.6 0.4 - - - -
1225B THR* 1.3 82.7 + - - +
1227B ILE* 1.3 63.5 + - + +
1229B ASN* 3.7 2.7 + - - +
1230B ALA* 3.3 22.2 + - - +
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Residues in contact with ILE1227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827A GLY 3.8 18.4 - - - +
828A ILE* 4.7 6.3 - - + -
831A ALA* 4.7 10.1 - - + -
836A PHE* 4.1 30.7 - - + -
844A ALA* 4.6 12.8 - - + -
1190B PHE* 3.7 28.9 - - + -
1194B LEU* 4.2 11.2 - - + -
1215B LEU* 5.0 7.9 - - + -
1223B ASP* 3.3 20.8 + - - +
1224B GLY* 4.6 1.8 - - - +
1225B THR 3.3 0.4 - - - -
1226B ALA* 1.3 75.8 - - + +
1228B ALA* 1.3 61.8 + - - +
1230B ALA* 3.0 5.0 + - - +
1231B VAL* 2.9 37.0 + - + +
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Residues in contact with ALA1228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B LEU* 4.3 24.6 - - + +
1224B GLY 3.4 18.2 + - - +
1225B THR* 3.3 4.1 + - - +
1227B ILE* 1.3 78.4 - - - +
1229B ASN* 1.3 59.5 + - - +
1231B VAL* 4.0 0.8 - - - +
1232B VAL* 3.3 30.3 + - - +
1245B PHE* 4.0 20.2 - - + -
1249B TYR* 5.1 4.0 - - + -
1252B LEU* 4.0 15.0 - - + +
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Residues in contact with ASN1229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A CYS* 5.1 1.9 - - - -
847A LYS* 3.3 38.6 - - + +
1225B THR* 2.8 19.8 + - - +
1226B ALA* 4.0 6.1 - - - +
1227B ILE 3.2 0.2 - - - -
1228B ALA* 1.3 77.6 - - - +
1230B ALA* 1.3 61.5 + - - +
1233B LYS* 3.6 7.8 + - - +
1252B LEU* 3.4 15.5 - - + +
1255B ASP* 3.5 19.1 + - - +
1256B TYR* 3.2 49.3 + - - -
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Residues in contact with ALA1230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840A VAL* 3.6 36.5 - - + +
843A CYS* 3.8 24.9 - - + -
844A ALA* 4.0 7.2 - - + +
1226B ALA 3.3 12.6 + - - +
1227B ILE* 3.0 8.8 + - - +
1229B ASN* 1.3 79.3 - - - +
1231B VAL* 1.3 64.2 + - - +
1233B LYS* 3.4 13.2 + - - +
1234B GLU* 3.5 6.9 + - - +
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Residues in contact with VAL1231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A PHE* 4.1 25.6 - - + -
840A VAL* 4.8 2.5 - - + -
1197B THR* 4.2 12.1 - - + -
1201B LEU* 4.0 25.0 - - + +
1212B VAL* 5.8 2.9 - - + -
1215B LEU* 4.1 26.0 - - + -
1227B ILE* 2.9 21.5 + - + +
1228B ALA 4.0 4.5 - - - +
1230B ALA* 1.3 76.0 - - - +
1232B VAL* 1.3 67.4 + - - +
1233B LYS 3.2 0.5 + - - -
1234B GLU* 3.4 0.7 + - - -
1235B LEU* 3.1 34.5 + - + +
1245B PHE* 4.6 9.0 - - + -
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Residues in contact with VAL1232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129B CYS* 3.8 25.4 - - - -
1131B LEU* 4.8 7.4 - - + -
1228B ALA 3.3 18.7 + - - +
1231B VAL* 1.3 76.0 - - - +
1233B LYS* 1.3 63.8 + - - +
1235B LEU* 4.3 7.4 - - + +
1236B ALA* 3.0 23.4 + - - +
1245B PHE* 3.9 37.0 - - + -
1252B LEU* 4.7 7.6 - - + -
1256B TYR* 3.8 34.0 - - + +
1262B VAL* 4.6 2.2 - - + -
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Residues in contact with LYS1233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A CYS* 3.7 24.9 - - - -
1229B ASN 3.6 6.6 + - - +
1230B ALA 3.4 11.6 + - - +
1231B VAL 3.1 0.8 - - - -
1232B VAL* 1.3 78.1 - - - +
1234B GLU* 1.3 58.2 + - - +
1236B ALA* 4.5 0.4 - - - +
1237B GLU* 2.9 61.5 + - - +
1256B TYR* 3.3 20.5 + - + +
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Residues in contact with GLU1234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837A PRO* 4.3 7.3 - - - +
839A HIS* 2.7 35.0 + - + +
840A VAL* 3.1 30.4 - - + +
1201B LEU* 3.5 26.6 - - + +
1230B ALA 3.5 3.6 + - - +
1231B VAL 3.4 5.8 + - - +
1233B LYS* 1.3 78.0 - - - +
1235B LEU* 1.3 56.1 + - - +
1238B THR* 2.8 42.4 + - - +
1239B ILE* 2.8 32.8 + - + +
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Residues in contact with LEU1235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129B CYS* 4.4 15.3 - - + -
1200B ILE* 4.9 7.0 - - + -
1201B LEU* 4.6 5.8 - - + +
1210B VAL* 3.9 20.6 - - + -
1212B VAL* 5.3 3.4 - - + -
1231B VAL* 3.1 31.8 + - + +
1232B VAL* 4.3 11.4 - - + +
1234B GLU* 1.3 78.1 - - - +
1236B ALA* 1.3 58.7 + - - +
1239B ILE* 3.9 16.8 - - + -
1240B LYS 3.6 14.4 + - - -
1241B CYS* 3.7 19.6 + - - +
1243B THR* 3.5 47.3 - - + +
1245B PHE* 5.7 3.1 - - + -
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Residues in contact with ALA1236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128B TYR* 4.5 8.4 - - + -
1129B CYS* 3.8 29.2 - - + +
1232B VAL 3.0 17.4 + - - +
1233B LYS* 4.5 0.7 - - - +
1235B LEU* 1.3 77.1 - - - +
1237B GLU* 1.3 62.4 + - + +
1238B THR 3.7 0.4 - - - -
1240B LYS* 3.5 27.2 + - - +
1241B CYS 5.4 1.1 - - - +
1256B TYR* 5.8 0.9 - - + -
1261B ALA* 4.6 11.0 - - + +
1262B VAL* 3.8 18.2 - - + -
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Residues in contact with GLU1237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233B LYS* 2.9 49.9 + - - +
1236B ALA* 1.3 80.0 - - + +
1238B THR* 1.3 62.9 + - - +
1240B LYS* 3.5 22.3 - - - +
1261B ALA* 6.0 1.3 - - - -
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Residues in contact with THR1238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839A HIS* 4.9 13.8 + - + +
1234B GLU* 2.8 38.0 + - + +
1237B GLU* 1.3 80.8 - - - +
1239B ILE* 1.3 64.9 + - + +
1240B LYS* 3.5 7.8 - - - +
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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
------------------------------------------------------------
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