Contacts of the helix formed by residues 1210 - 1218 (chain G) in PDB entry 6BAA
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 GLY1210 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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778G TRP* 4.5 11.7 - - - -
1206G GLU 3.0 12.2 + - - -
1207G THR 4.0 3.1 - - - -
1209G GLU* 1.3 78.8 - - - +
1211G LEU* 1.3 61.9 + - - -
1212G THR 3.5 2.0 - - - -
1213G THR* 3.3 18.3 + - - -
1214G ILE* 3.1 30.7 + - - +
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Residues in contact with LEU1211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399G ILE* 3.5 35.2 - - + +
400G MET* 4.1 14.4 - - + -
402G MET* 3.7 32.8 - - + +
1207G THR* 3.6 9.1 + - + +
1208G VAL* 3.4 19.7 + - + +
1209G GLU 3.5 1.0 + - - -
1210G GLY* 1.3 75.9 - - - +
1212G THR* 1.3 63.5 + - - +
1214G ILE* 3.2 7.1 + - + +
1215G ARG* 2.9 47.8 + - + +
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Residues in contact with THR1212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724G LEU* 6.1 1.8 - - + -
727G LEU* 4.8 12.8 - - + -
729G GLU* 4.6 21.3 - - + -
772G TYR* 4.8 15.4 - - + +
1211G LEU* 1.3 82.2 - - - +
1213G THR* 1.3 57.3 + - - +
1215G ARG* 3.7 13.6 - - + +
1216G ALA* 3.0 30.8 + - + +
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Residues in contact with THR1213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772G TYR* 3.8 32.8 - - + +
774G SER* 4.6 8.4 - - - +
778G TRP* 4.8 11.2 - - + +
1210G GLY* 3.3 20.0 + - - -
1212G THR* 1.3 78.5 - - - +
1214G ILE* 1.3 58.1 + - + +
1216G ALA* 4.1 0.9 - - - +
1217G PHE* 2.9 60.7 + - + -
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Residues in contact with ILE1214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400G MET* 5.5 4.0 - - + -
1206G GLU 5.0 0.9 - - - +
1207G THR* 4.2 26.5 - - + +
1210G GLY* 3.1 22.9 + - - +
1211G LEU* 3.8 7.0 - - + +
1213G THR* 1.3 76.2 - - + +
1215G ARG* 1.3 55.8 + - + +
1217G PHE* 3.5 10.3 - - + -
1218G ARG* 2.7 29.6 + - - -
1219G TYR* 3.1 15.8 + - + -
1220G GLU* 3.8 27.3 - - + +
1223G PHE* 3.6 44.0 - - + -
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Residues in contact with ARG1215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399G ILE 3.8 2.0 + - - -
400G MET* 2.6 38.5 + - - +
401G HIS* 4.4 1.4 - - - +
402G MET* 2.9 28.6 + - - +
403G SER* 3.0 33.5 - - - +
1211G LEU* 2.9 42.6 + - + +
1212G THR* 3.7 13.9 - - + +
1214G ILE* 1.3 77.6 - - + +
1216G ALA* 1.3 58.4 + - - +
1218G ARG* 3.0 21.1 + - - +
1220G GLU* 4.5 10.2 - - + +
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Residues in contact with ALA1216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727G LEU* 4.5 22.4 - - + +
770G VAL* 3.3 35.6 - - + +
772G TYR* 4.6 19.1 - - + -
1212G THR* 3.0 17.1 + - + +
1213G THR 4.3 1.8 - - - +
1215G ARG* 1.3 72.7 - - - +
1217G PHE* 1.3 66.7 + - - +
1218G ARG* 3.1 3.5 + - - +
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Residues in contact with PHE1217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770G VAL* 3.7 21.0 + - - +
771G ALA* 3.9 5.8 - - + -
772G TYR* 3.3 42.8 - - + -
790G PHE* 5.7 9.2 - - + -
842G ARG* 6.0 5.8 - - + -
843G ALA* 5.7 8.3 - - + -
1213G THR* 2.9 42.7 + - + +
1214G ILE* 3.5 10.8 - - + +
1216G ALA* 1.3 75.1 - - - +
1218G ARG* 1.3 66.9 + - - +
1219G TYR* 3.3 48.1 - + + -
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Residues in contact with ARG1218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740G ASN 5.3 0.6 + - - -
741G SER* 3.4 37.9 + - - +
743G LEU 4.6 8.5 + - - -
770G VAL* 6.3 2.7 - - + -
1214G ILE 2.7 11.6 + - - -
1215G ARG 3.0 12.7 + - - +
1216G ALA 4.4 3.1 - - - +
1217G PHE* 1.3 76.0 - - - +
1219G TYR* 1.3 61.9 + - - +
1220G GLU* 3.3 28.1 + - - +
1221G ALA* 5.3 0.5 + - - +
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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