Contacts of the helix formed by residues 1229 - 1236 (chain B) in PDB entry 5XA0
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 LYS1229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1134B TYR* 3.1 26.8 - - + +
1221B PRO* 5.6 1.6 - - + +
1222B TYR 5.8 1.6 - - - +
1223B GLU* 4.3 6.0 - - - +
1227B ASP 3.8 4.1 + - - +
1228B THR* 1.3 73.4 - - - +
1230B MET* 1.3 64.9 + - - +
1231B GLN 3.5 0.4 - - - -
1232B GLU* 3.8 11.9 + - - +
1233B ILE 3.9 1.9 + - - -
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Residues in contact with MET1230 (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* 4.1 1.8 - - - -
1217B LEU 3.7 9.2 - - - +
1218B LEU* 2.3 50.2 - - - +
1219B GLN* 3.4 10.1 - - - +
1221B PRO* 2.9 30.1 + - + +
1222B TYR* 5.2 0.9 - - - -
1223B GLU 5.5 1.7 - - - +
1228B THR* 4.8 0.2 - - - +
1229B LYS* 1.3 78.9 - - - +
1231B GLN* 1.3 61.2 + - - +
1232B GLU 3.2 0.7 + - - -
1233B ILE* 3.2 4.3 + - - +
1234B MET 3.1 4.2 + - - -
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Residues in contact with GLN1231 (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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1218B LEU 3.0 6.3 + - - -
1228B THR* 4.8 14.4 + - - +
1229B LYS 3.5 0.6 - - - +
1230B MET* 1.3 76.7 - - - +
1232B GLU* 1.3 64.4 + - - +
1234B MET* 2.9 8.6 - - - +
1235B ARG* 2.9 24.7 + - - +
1236B LEU* 4.9 0.2 - - - -
1275B HIS* 6.2 4.0 - - + -
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Residues in contact with GLU1232 (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 5.1 4.0 - - - +
1184B SER* 5.6 9.2 - - - +
1187B CYS* 4.9 8.7 - - + +
1188B VAL* 6.4 1.8 - - + -
1228B THR 4.7 7.0 + - - +
1229B LYS* 3.8 11.5 + - - +
1230B MET 3.2 0.6 - - - -
1231B GLN* 1.3 78.1 - - - +
1233B ILE* 1.3 63.6 + - - +
1236B LEU* 3.0 42.9 + - + +
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Residues in contact with ILE1233 (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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1126B VAL* 5.7 8.0 - - + +
1130B GLU* 5.2 4.3 - - + -
1134B TYR* 2.9 49.0 - - + -
1184B SER* 6.4 0.7 - - - +
1187B CYS* 6.0 2.2 - - - -
1214B VAL* 3.5 20.7 - - - +
1217B LEU 4.4 1.1 - - - +
1218B LEU* 4.2 7.2 - - - +
1229B LYS 3.9 1.6 + - - -
1230B MET 3.2 3.6 + - - +
1232B GLU* 1.3 76.1 - - - +
1234B MET* 1.3 69.9 + - - +
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Residues in contact with MET1234 (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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1214B VAL* 3.7 13.7 - - - +
1215B LEU* 4.6 2.1 + - + +
1218B LEU* 2.8 35.2 - - + +
1219B GLN* 5.8 0.7 - - + -
1230B MET 3.1 6.0 + - - +
1231B GLN* 2.9 16.0 + - - +
1232B GLU 3.8 0.2 - - - -
1233B ILE* 1.3 81.1 - - - +
1235B ARG* 1.3 66.4 + - + +
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Residues in contact with ARG1235 (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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1231B GLN 2.9 9.3 + - - +
1234B MET* 1.3 85.0 - - + +
1236B LEU* 1.3 60.0 + - - +
1237B ALA 3.7 1.8 - - - +
1238B HIS 5.4 1.6 - - - -
1279B ASN* 6.3 3.6 - - + -
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Residues in contact with LEU1236 (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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1187B CYS* 4.1 6.0 - - + +
1188B VAL* 4.7 6.1 - - + -
1191B SER* 2.7 31.9 - - - -
1231B GLN 4.4 0.4 - - - +
1232B GLU* 3.0 40.9 + - + +
1234B MET 4.1 0.2 - - - -
1235B ARG* 1.3 75.9 - - - +
1237B ALA* 1.4 52.3 + - + +
1238B HIS 4.0 0.9 - - - -
1239B GLU* 6.1 2.7 - - - -
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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