Contacts of the helix formed by residues 1221 - 1229 (chain B) in PDB entry 6V65
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 LEU1221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1212B VAL 4.3 3.8 - - - +
1213B THR 4.1 3.1 - - - +
1214B MET 3.5 15.3 + - - +
1215B MET* 3.9 20.1 - - + +
1216B GLY 4.1 1.8 - - - +
1219B GLY 3.5 0.8 - - - -
1220B GLU* 1.3 79.2 - - - +
1222B PRO* 1.3 73.8 - - - +
1223B ILE 3.4 2.2 - - - -
1224B ALA* 3.6 8.9 + - + -
1225B MET* 3.2 19.9 + - + +
1247B PHE* 3.5 34.1 - - + -
1255B GLN* 3.8 4.3 - - + +
1256B LEU* 3.8 35.9 - - + +
1259B ASN* 3.3 26.7 - - + +
1260B MET* 6.4 0.4 - - - -
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Residues in contact with PRO1222 (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 MET* 3.2 27.6 - - + +
1216B GLY* 4.0 12.1 - - - +
1220B GLU* 3.5 17.7 - - + +
1221B LEU* 1.3 88.3 - - - +
1223B ILE* 1.3 74.5 + - + +
1225B MET* 4.1 2.5 - - + +
1226B ALA* 3.1 26.3 + - - +
1514B PRO* 5.0 13.2 - - + -
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Residues in contact with ILE1223 (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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1211B LEU* 3.1 28.3 - - + +
1212B VAL* 4.0 26.2 + - + +
1214B MET* 5.5 0.7 - - + -
1221B LEU 3.4 0.4 - - - -
1222B PRO* 1.3 84.4 - - + +
1224B ALA* 1.3 59.5 + - - +
1226B ALA* 3.8 4.5 - - + +
1227B LEU* 2.8 33.9 + - + +
1490B LEU* 4.9 8.1 - - + -
1497B ILE* 6.2 1.1 - - + -
1514B PRO* 3.8 32.3 - - + -
1515B PHE* 5.1 1.6 - - + +
1518B MET* 3.6 35.2 - - + -
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Residues in contact with ALA1224 (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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1212B VAL* 4.4 13.4 + - + +
1221B LEU* 3.6 15.0 + - + +
1223B ILE* 1.3 80.6 - - - +
1225B MET* 1.3 51.6 + - - +
1227B LEU* 3.1 9.0 + - - +
1228B ALA* 2.7 36.3 + - - +
1243B LEU* 4.1 30.1 - - + +
1247B PHE* 4.7 10.5 - - + -
1256B LEU* 4.9 6.3 - - + -
1260B MET* 5.6 4.3 - - - -
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Residues in contact with MET1225 (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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1220B GLU 4.5 7.0 - - - +
1221B LEU* 3.2 17.8 + - + +
1222B PRO* 4.2 3.1 - - + +
1224B ALA* 1.3 78.4 - - - +
1226B ALA* 1.3 62.1 + - - +
1228B ALA* 3.3 12.8 + - - +
1229B ASN* 3.4 15.4 + - - +
1259B ASN* 4.8 15.0 - - - +
1260B MET* 3.5 34.8 - - - +
1263B LYS* 4.8 10.8 - - - -
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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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1222B PRO 3.1 18.7 + - - +
1223B ILE* 3.9 5.2 - - + +
1225B MET* 1.3 77.8 - - - +
1227B LEU* 1.3 61.2 + - - +
1228B ALA 3.4 0.3 + - - -
1229B ASN* 3.6 5.9 + - - -
1230B VAL* 3.2 29.1 - - + +
1497B ILE* 4.7 22.2 - - + +
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Residues in contact with LEU1227 (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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1212B VAL* 5.9 4.7 - - + -
1223B ILE* 2.8 23.2 + - + +
1224B ALA* 3.1 7.8 + - - +
1226B ALA* 1.3 76.9 - - - +
1228B ALA* 1.3 62.1 + - - +
1230B VAL* 4.1 7.0 - - + -
1231B VAL* 3.1 53.1 + - + +
1239B LEU* 3.9 26.0 - - + +
1243B LEU* 5.1 10.3 - - + -
1489B LEU* 4.4 12.8 - - + +
1490B LEU* 4.2 31.4 - - + +
1493B ASN* 4.6 11.2 - - + +
1497B ILE* 5.6 6.5 - - + +
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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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1224B ALA 2.7 19.1 + - - +
1225B MET* 3.7 11.7 - - - +
1226B ALA 3.2 0.6 - - - -
1227B LEU* 1.3 75.9 - - - +
1229B ASN* 1.3 58.5 + - - +
1230B VAL 3.4 0.6 + - - -
1231B VAL 4.5 0.9 + - - +
1236B TRP* 3.9 25.3 + - - -
1239B LEU* 4.3 4.3 - - + -
1243B LEU* 6.0 2.0 - - + -
1260B MET* 4.3 17.0 - - + -
1280B LEU* 3.6 29.9 - - + +
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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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1225B MET 3.4 12.7 + - - +
1226B ALA* 3.6 4.4 + - - +
1227B LEU 3.4 0.4 - - - -
1228B ALA* 1.3 77.7 - - + +
1230B VAL* 1.3 64.8 + - + +
1231B VAL 5.1 0.9 - - - -
1236B TRP* 6.2 0.4 - - - -
1499B GLN* 6.3 1.1 - - - +
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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