Contacts of the helix formed by residues 1209 - 1214 (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 VAL1209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1207B ARG* 3.8 9.7 + - + +
1208B LEU* 1.3 71.0 - - - +
1210B GLU* 1.3 68.0 + - - +
1211B LEU 3.1 2.2 - - - -
1212B VAL* 3.0 22.3 + - + +
1213B THR* 3.3 9.0 + - - +
1246B LEU* 4.0 34.5 - - + -
1250B ARG* 3.5 34.7 - - - +
1486B LEU* 5.7 9.0 - - + -
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Residues in contact with GLU1210 (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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32A LEU* 3.7 35.2 - - + +
33A PRO* 6.2 1.6 - - - -
37A SER* 5.5 2.8 + - - -
1208B LEU* 3.1 29.0 - - + +
1209B VAL* 1.3 74.6 - - - +
1211B LEU* 1.3 68.5 + - + +
1213B THR* 2.7 25.2 + - - -
1214B MET* 2.7 12.3 + - - -
1250B ARG* 3.9 23.6 + - - +
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Residues in contact with LEU1211 (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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1208B LEU* 3.6 40.2 - - + +
1210B GLU* 1.3 85.0 - - + +
1212B VAL* 1.3 62.3 + - + +
1214B MET* 3.4 32.8 - - + +
1223B ILE* 3.1 22.5 - - + +
1514B PRO* 4.9 4.9 - - + +
1517B LYS* 4.6 13.0 - - + +
1518B MET* 3.8 50.0 - - + +
1521B LEU* 5.2 10.8 - - + -
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Residues in contact with VAL1212 (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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1208B LEU 5.9 0.2 - - - +
1209B VAL* 3.0 16.8 + - + +
1211B LEU* 1.3 81.5 - - + +
1213B THR* 1.3 57.7 + - - +
1214B MET 3.3 8.0 + - - +
1221B LEU* 4.3 3.5 - - - +
1223B ILE* 4.0 26.5 + - + +
1224B ALA* 4.4 9.6 + - + -
1227B LEU* 5.9 4.7 - - + -
1243B LEU* 4.0 22.7 - - + -
1246B LEU* 3.9 22.2 - - + -
1247B PHE* 3.9 13.4 - - + -
1486B LEU* 6.2 3.8 - - + -
1490B LEU* 4.6 22.7 - - + -
1518B MET* 5.8 0.4 - - + -
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Residues in contact with THR1213 (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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31A TRP 4.6 1.4 - - - +
32A LEU* 4.7 4.5 - - - +
33A PRO* 5.1 3.6 - - - +
1209B VAL 3.8 9.6 - - - +
1210B GLU* 2.7 22.7 + - - -
1212B VAL* 1.3 71.0 - - - +
1214B MET* 1.3 61.6 + - - -
1215B MET* 3.5 13.5 + - - +
1221B LEU* 4.1 2.7 - - - +
1246B LEU* 4.0 21.8 - - + -
1247B PHE* 3.8 26.0 - - + -
1250B ARG* 4.0 28.4 + - - +
1252B LEU* 4.1 23.6 - - + +
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Residues in contact with MET1214 (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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28A SER* 3.5 35.7 - - - +
29A GLY 4.2 1.1 - - - -
30A GLY* 3.6 33.4 - - - -
31A TRP 3.4 16.6 - - - +
32A LEU* 3.9 13.2 - - + -
1210B GLU 2.7 10.3 + - - +
1211B LEU* 3.4 38.6 - - + +
1212B VAL 3.1 4.3 - - - +
1213B THR* 1.3 76.3 - - - +
1215B MET* 1.3 62.9 + - - +
1221B LEU* 3.5 9.0 - - - +
1222B PRO* 3.2 28.5 - - + +
1514B PRO* 5.1 11.9 - - + -
1517B LYS* 6.5 0.4 - - + -
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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