Contacts of the helix formed by residues 1221 - 1232 (chain B) in PDB entry 1U8C
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 GLY1221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1156B PHE* 4.0 8.5 - - - +
1157B VAL 2.5 18.1 + - - -
1158B ASP* 3.5 17.9 + - - -
1159B LYS 5.2 0.2 - - - -
1189B GLY 5.0 0.9 - - - +
1220B GLU* 1.3 72.8 - - - +
1222B GLY* 1.3 65.1 + - - +
1223B PHE 3.4 2.0 - - - -
1224B ASP* 3.0 26.2 + - - +
1225B ALA* 3.6 2.3 + - - +
1254B THR* 5.0 0.2 - - - -
1255B HIS 5.8 0.4 - - - -
1289B TYR* 3.9 13.2 - - - -
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Residues in contact with GLY1222 (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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1156B PHE* 3.4 27.6 - - - -
1220B GLU* 3.4 4.6 + - - +
1221B GLY* 1.3 76.2 - - - +
1223B PHE* 1.3 56.9 + - - +
1225B ALA* 2.8 23.0 + - - +
1226B ILE* 2.9 12.5 + - - +
1248B PHE* 3.6 22.2 - - - -
1254B THR* 4.2 4.5 + - - -
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Residues in contact with PHE1223 (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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1221B GLY 3.4 0.8 - - - -
1222B GLY* 1.3 76.3 - - - +
1224B ASP* 1.3 63.0 + - - +
1226B ILE* 3.7 9.9 - - + +
1227B MET 3.0 18.9 + - - -
1248B PHE* 4.5 3.4 - + - -
1254B THR* 3.9 34.2 + - + -
1255B HIS 4.2 16.6 - - - +
1256B ILE* 5.1 10.8 - - + -
1289B TYR* 5.2 2.5 - - + -
1290B PRO* 3.6 29.4 - - + +
1292B LEU* 3.7 26.5 - - + -
1295B MET* 3.3 31.7 - - + +
1308B PHE* 4.2 26.0 - + - -
1318B TYR* 4.5 8.1 - + - -
1321B TYR* 4.9 11.9 - + + -
1325B ILE* 5.4 0.2 - - + -
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Residues in contact with ASP1224 (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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1159B LYS* 2.9 29.6 + - - +
1189B GLY* 5.8 2.2 - - - +
1190B TYR* 5.4 2.9 - - + -
1221B GLY* 3.0 16.6 + - - +
1223B PHE* 1.3 78.6 - - - +
1225B ALA* 1.3 62.1 + - - +
1227B MET* 3.4 4.7 + - - +
1228B GLN* 3.3 25.2 + - - +
1269B ASN* 4.7 1.3 + - - +
1281B TYR* 2.8 38.3 + - + -
1284B SER* 3.2 9.4 + - - -
1287B MET 4.5 0.5 - - - +
1288B ASP 4.5 0.9 - - - +
1289B TYR* 3.3 26.5 - - + -
1290B PRO* 3.9 6.8 - - - +
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Residues in contact with ALA1225 (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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1117B LEU* 3.7 15.7 - - + -
1156B PHE* 3.7 20.4 - - + -
1190B TYR* 3.5 35.9 - - + +
1221B GLY 3.6 0.6 + - - -
1222B GLY 2.8 10.2 + - - +
1224B ASP* 1.3 78.2 - - - +
1226B ILE* 1.3 66.9 + - - +
1228B GLN* 2.7 14.4 + - - +
1229B ALA* 2.8 14.6 + - - +
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Residues in contact with ILE1226 (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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1117B LEU* 3.7 10.7 - - + +
1222B GLY 2.9 7.3 + - - +
1223B PHE* 3.7 6.3 - - + +
1225B ALA* 1.3 76.1 - - - +
1227B MET* 1.3 60.2 + - - +
1229B ALA 3.7 2.6 + - - -
1230B THR* 2.8 28.5 + - - +
1246B LEU* 3.8 14.5 - - + +
1248B PHE* 3.2 52.9 - - + -
1295B MET* 3.4 30.5 - - + -
1299B LEU* 5.0 8.1 - - + -
1306B LEU* 4.0 13.7 - - + -
1308B PHE* 3.8 19.1 - - + -
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Residues in contact with MET1227 (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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1223B PHE 3.0 13.0 + - - +
1224B ASP 3.6 9.0 - - - +
1226B ILE* 1.3 79.0 - - - +
1228B GLN* 1.3 74.0 + - - +
1230B THR* 3.4 5.2 - - - -
1231B VAL* 3.4 36.0 + - + +
1269B ASN* 4.1 15.9 - - - +
1271B GLY* 3.8 18.4 - - - +
1281B TYR* 6.0 0.2 - - - +
1290B PRO* 3.5 29.4 - - + -
1294B LEU* 3.8 21.5 - - + +
1295B MET* 4.0 25.8 - - + +
1298B LYS* 4.1 6.5 - - + -
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Residues in contact with GLN1228 (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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1190B TYR* 3.8 22.0 - - + -
1224B ASP 3.3 11.9 + - - +
1225B ALA 2.7 13.4 + - - +
1227B MET* 1.3 80.9 - - - +
1229B ALA* 1.3 55.2 + - - +
1230B THR 3.0 10.5 + - - -
1231B VAL* 4.5 1.0 - - - +
1232B CYS* 3.2 32.7 + - - +
1236B ILE* 3.9 2.1 - - - +
1269B ASN* 5.6 0.6 + - - -
1272B GLN 3.3 23.8 + - - -
1273B CYS* 4.2 1.4 - - - +
1274B HIS* 2.8 23.1 + - - -
1275B VAL* 3.3 17.2 + - + +
1281B TYR* 3.6 40.7 + - + -
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Residues in contact with ALA1229 (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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1115B TYR* 3.5 36.3 - - + -
1117B LEU* 4.2 5.4 - - + -
1190B TYR* 3.8 8.7 + - - +
1225B ALA 2.8 17.3 + - - +
1226B ILE 3.8 0.4 - - - -
1228B GLN* 1.3 69.3 - - - +
1230B THR* 1.3 67.0 + - - +
1236B ILE* 3.3 16.2 - - + -
1238B TRP* 3.6 10.8 - - - -
1246B LEU* 3.3 19.6 - - + +
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Residues in contact with THR1230 (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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1226B ILE 2.8 20.4 + - - -
1227B MET* 3.4 6.5 - - - +
1228B GLN 3.0 1.6 + - - -
1229B ALA* 1.3 83.6 + - - +
1231B VAL* 1.3 72.2 + - + +
1232B CYS 3.5 2.5 - - - +
1233B ASP* 3.6 6.7 - - - +
1236B ILE* 4.7 0.4 - - - +
1238B TRP* 4.2 10.3 + - - +
1246B LEU* 3.2 12.5 - - - +
1298B LYS* 4.0 20.4 - - + +
1299B LEU* 4.1 21.5 - - + +
1302B LYS* 3.0 21.3 - - - +
1304B ILE* 4.2 13.3 - - + +
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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
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1227B MET* 3.4 21.5 + - - +
1228B GLN* 4.5 4.5 - - - +
1230B THR* 1.3 85.1 - - + +
1232B CYS* 1.3 61.4 + - - +
1233B ASP* 3.5 13.4 - - - +
1271B GLY 3.4 21.3 - - - +
1272B GLN* 3.8 3.8 - - - +
1273B CYS* 3.4 28.5 + - - +
1298B LYS* 3.7 40.8 - - + +
1302B LYS* 4.1 12.6 + - + +
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Residues in contact with CYS1232 (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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1228B GLN* 3.2 37.6 + - - +
1230B THR 4.1 0.2 - - - +
1231B VAL* 1.3 78.5 - - - +
1233B ASP* 1.3 56.7 + - - +
1234B GLU* 2.5 24.7 + - - +
1235B LYS* 2.9 25.1 + - + +
1236B ILE* 4.4 4.3 - - + -
1273B CYS* 2.0 50.0 - - - -
1275B VAL* 3.4 15.9 - - + -
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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
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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