Contacts of the strand formed by residues 1221 - 1230 (chain B) in PDB entry 1G24
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 SER1221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1167B ARG 3.8 0.9 - - - +
1168B LEU* 3.6 0.4 - - - -
1169B GLU* 2.9 31.0 + - - +
1173B ILE* 4.4 12.1 - - - -
1217B LEU* 5.1 1.4 - - - +
1218B PRO* 2.8 29.0 + - - +
1219B ARG 3.2 0.2 - - - -
1220B HIS* 1.3 77.3 - - - +
1222B THR* 1.3 61.9 + - - +
1223B TYR* 4.6 2.5 - - - -
1243B MET* 4.1 18.5 - - - -
1245B GLY 3.1 10.9 + - - -
1246B THR* 3.5 16.2 - - - +
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Residues in contact with THR1222 (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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1166B ASP* 3.9 27.1 - - + +
1167B ARG 3.2 12.8 - - - +
1168B LEU* 3.6 21.2 - - + +
1220B HIS 4.2 0.9 + - - -
1221B SER* 1.3 72.3 - - - +
1223B TYR* 1.3 65.8 + - - +
1243B MET* 3.7 2.5 - - - +
1244B MET* 2.9 45.4 + - + +
1245B GLY 2.9 12.2 + - - -
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Residues in contact with TYR1223 (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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1134B TYR* 2.6 33.3 + - - -
1165B LYS 4.0 0.5 - - - +
1166B ASP* 3.4 1.6 - - - -
1167B ARG* 2.8 67.2 + - + +
1169B GLU* 4.4 14.8 + - + -
1173B ILE* 4.2 15.0 - - + -
1190B THR* 5.6 1.1 - - + -
1192B PHE* 3.7 36.2 - + + -
1221B SER 4.6 2.2 - - - -
1222B THR* 1.3 76.9 - - - +
1224B HIS* 1.3 60.2 + - - +
1225B ILE* 4.3 12.1 - - + -
1239B ILE* 6.1 0.4 - - + -
1241B ALA* 3.8 13.2 - - + -
1242B THR 3.3 15.7 - - - +
1243B MET* 3.9 22.2 - - + -
1244B MET* 4.0 5.8 - - - +
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Residues in contact with HIS1224 (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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1164B ASN* 3.3 42.4 + - - +
1165B LYS* 3.5 7.4 - - - -
1166B ASP* 2.8 25.0 + - - +
1223B TYR* 1.3 72.8 - - - +
1225B ILE* 1.3 66.5 + - - +
1226B ASP* 3.2 27.8 + - - +
1241B ALA* 3.1 5.0 - - - -
1242B THR* 2.9 41.9 + - - +
1244B MET* 3.9 9.3 - - + -
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Residues in contact with ILE1225 (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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1134B TYR* 4.6 13.7 - - + +
1135B LEU* 6.5 0.2 - - + -
1162B PHE* 3.4 48.0 - - + +
1163B LEU* 4.2 3.1 - - - -
1164B ASN* 2.9 33.1 + - - -
1165B LYS 3.2 10.3 + - - +
1167B ARG* 5.1 4.7 - - + -
1223B TYR* 4.3 17.3 - - + -
1224B HIS* 1.3 73.4 - - - +
1226B ASP* 1.3 58.9 + - - +
1227B ASP 4.1 3.1 - - - +
1228B MET* 3.6 31.4 - - + -
1239B ILE* 3.8 28.0 - - + -
1240B THR 3.8 4.7 - - - +
1241B ALA* 4.0 1.3 - - + -
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Residues in contact with ASP1226 (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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1163B LEU* 3.6 11.2 - - - +
1164B ASN* 4.1 8.7 - - - +
1193B LYS* 4.9 7.7 + - - +
1224B HIS* 3.2 28.8 + - - +
1225B ILE* 1.3 74.4 - - - +
1227B ASP* 1.3 64.2 + - + +
1240B THR* 2.9 13.6 + - + +
1241B ALA* 3.7 3.3 + - - -
1242B THR* 2.7 36.8 + - - -
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Residues in contact with ASP1227 (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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1163B LEU* 3.9 4.7 - - - +
1225B ILE* 3.7 1.4 - - - +
1226B ASP* 1.3 81.9 - - + +
1228B MET* 1.3 74.8 + - - +
1229B ARG* 2.8 51.1 + - - +
1238B ILE* 4.4 1.6 - - - +
1239B ILE* 3.4 0.9 - - - +
1240B THR* 2.8 51.3 + - + +
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Residues in contact with MET1228 (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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1135B LEU* 4.7 5.4 - - + -
1155B PHE* 3.6 18.2 - - + -
1158B ALA* 4.0 28.5 - - + +
1159B LYS* 3.8 29.9 - - + +
1162B PHE* 4.1 9.0 - - + -
1163B LEU* 3.9 30.2 - - + +
1225B ILE* 3.6 18.2 - - + -
1227B ASP* 1.3 83.3 + - - +
1229B ARG* 1.3 62.6 + - - +
1237B ILE* 4.5 11.0 - - + -
1238B ILE 3.4 4.9 - - - +
1239B ILE* 4.2 26.5 - - + -
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Residues in contact with ARG1229 (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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1155B PHE* 3.6 13.1 - - - -
1227B ASP* 2.8 34.3 + - - +
1228B MET* 1.3 73.5 - - - +
1230B LEU* 1.3 65.6 + - - +
1237B ILE* 3.5 3.8 - - - +
1238B ILE* 2.6 55.9 + - + +
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Residues in contact with LEU1230 (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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1150B ILE* 3.3 45.1 - - + +
1152B LYS* 5.0 14.1 - - + -
1155B PHE* 3.7 38.3 - - + -
1229B ARG* 1.3 86.4 - - - +
1231B SER* 1.3 71.0 + - - +
1234B GLY* 4.4 13.2 - - - -
1236B GLN 3.3 10.1 - - - +
1237B ILE* 3.8 4.3 - - + -
1238B ILE* 4.7 1.3 - - - +
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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