Contacts of the helix formed by residues 1263 - 1270 (chain B) in PDB entry 3QBV
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 PHE1263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1258B LEU 5.9 0.4 - - - -
1259B VAL* 2.9 28.1 + - + +
1261B GLU 3.6 0.2 - - - -
1262B ILE* 1.3 88.6 - - + +
1264B GLN* 1.3 64.6 + - - +
1266B PRO* 3.4 3.1 - - - +
1267B LEU* 3.1 30.0 + - + +
1282B PHE* 4.2 7.2 - - + -
1357B VAL* 4.1 7.2 - - + -
1360B LEU* 3.9 15.6 - - + +
1361B ALA* 3.8 43.5 - - + -
1366B CYS* 4.0 13.5 - - - -
1369B MET 4.5 1.3 - - - -
1371B LEU* 3.6 52.5 - - + -
1374B PHE* 3.9 25.6 - + - -
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Residues in contact with GLN1264 (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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1259B VAL 3.0 7.4 + - - +
1260B THR* 3.6 33.5 + - + +
1263B PHE* 1.3 72.7 - - - +
1265B LYS* 1.3 69.5 + - - +
1267B LEU* 3.1 4.2 + - - +
1268B MET* 3.0 24.5 + - + +
1278B VAL* 4.5 13.5 - - + +
1279B ALA* 6.3 0.2 - - - +
1282B PHE* 3.6 51.9 - - + +
1283B VAL 5.3 3.8 + - - -
1285B TRP* 4.3 10.0 - - - +
1286B LYS* 5.4 2.6 + - - +
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Residues in contact with LYS1265 (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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1260B THR* 3.1 16.2 + - + +
1261B GLU* 4.4 4.3 - - - +
1264B GLN* 1.3 79.5 - - - +
1266B PRO* 1.3 70.7 - - + +
1268B MET* 3.3 5.0 + - - +
1269B GLU* 3.0 30.9 + - + +
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Residues in contact with PRO1266 (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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1261B GLU 3.4 17.5 - - - +
1262B ILE* 3.5 14.6 - - - +
1263B PHE 3.4 12.3 - - - +
1264B GLN 3.5 0.2 - - - -
1265B LYS* 1.3 95.2 - - + +
1267B LEU* 1.3 61.0 + - - +
1269B GLU* 3.3 6.8 + - + +
1270B SER* 3.0 24.4 + - - -
1356B PHE* 4.0 10.1 - - + -
1360B LEU* 3.9 26.7 - - + -
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Residues in contact with LEU1267 (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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1263B PHE* 3.1 22.8 + - + +
1264B GLN* 3.7 3.4 - - - +
1266B PRO* 1.3 76.6 - - - +
1268B MET* 1.3 61.1 + - - +
1270B SER* 2.6 26.6 + - - +
1271B GLU 4.3 0.3 + - - -
1272B LEU* 5.2 1.1 - - + -
1273B LEU* 4.6 19.4 + - + +
1278B VAL* 4.4 7.1 - - + +
1281B ILE* 4.9 1.8 - - + -
1282B PHE* 4.1 24.2 - - + -
1353B PHE* 3.9 34.1 - - + -
1356B PHE* 4.0 23.1 - - + -
1357B VAL* 4.3 9.4 - - + -
1360B LEU* 4.5 8.1 - - + -
1371B LEU* 4.1 18.4 - - + -
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Residues in contact with MET1268 (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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1264B GLN* 3.0 18.6 + - + +
1265B LYS* 3.7 6.5 - - - +
1267B LEU* 1.3 79.5 - - - +
1269B GLU* 1.3 66.4 + - + +
1270B SER 3.3 0.9 + - - -
1271B GLU* 3.7 7.8 + - - -
1273B LEU 4.3 7.6 - - - +
1274B THR 4.2 2.9 - - - +
1275B GLU* 4.1 29.6 - - + +
1278B VAL* 3.6 39.2 - - + +
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Residues in contact with GLU1269 (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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1265B LYS* 3.0 24.3 + - + +
1266B PRO* 3.8 6.7 - - + +
1268B MET* 1.3 79.7 - - + +
1270B SER* 1.3 64.5 + - - +
1271B GLU* 3.1 5.3 + - - +
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Residues in contact with SER1270 (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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1266B PRO 3.0 16.3 + - - -
1267B LEU* 2.6 22.1 + - - +
1268B MET 3.1 0.2 - - - -
1269B GLU* 1.3 79.1 - - - +
1271B GLU* 1.3 60.9 + - - +
1272B LEU* 3.0 33.1 + - - +
1356B PHE* 3.9 22.7 - - - -
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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