Contacts of the helix formed by residues 1210 - 1218 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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778E TRP* 4.5 11.4 - - - +
1206E GLU 3.0 12.2 + - - -
1207E THR 4.0 3.1 - - - -
1209E GLU* 1.3 80.1 - - - +
1211E LEU* 1.3 61.2 + - - -
1212E THR 3.5 2.0 - - - -
1213E THR* 3.3 18.2 + - - -
1214E ILE* 3.1 30.3 + - - +
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Residues in contact with LEU1211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399E ILE* 3.5 35.7 - - + +
400E MET* 4.1 14.6 - - + -
402E MET* 3.7 32.3 - - + +
1207E THR* 3.6 8.7 - - + +
1208E VAL* 3.4 19.7 + - + +
1209E GLU 3.5 1.2 + - - -
1210E GLY* 1.3 76.6 - - - +
1212E THR* 1.3 63.1 + - - +
1214E ILE* 3.2 6.5 + - + +
1215E ARG* 2.9 50.2 + - + +
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Residues in contact with THR1212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724E LEU* 6.1 1.8 - - + -
727E LEU* 4.8 14.1 - - + -
729E GLU* 4.6 20.4 - - + -
772E TYR* 4.8 15.0 - - + +
1210E GLY 3.5 0.4 - - - -
1211E LEU* 1.3 80.9 - - - +
1213E THR* 1.3 57.9 + - - +
1215E ARG* 3.7 14.1 - - + +
1216E ALA* 3.0 30.7 + - + +
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Residues in contact with THR1213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772E TYR* 3.8 33.5 - - + +
774E SER* 4.6 8.0 - - - +
778E TRP* 4.8 11.3 - - + +
1210E GLY* 3.3 20.0 + - - -
1211E LEU 3.1 0.4 - - - -
1212E THR* 1.3 79.5 - - - +
1214E ILE* 1.3 57.8 + - + +
1216E ALA* 3.9 1.0 - - - +
1217E PHE* 2.9 60.5 + - + -
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Residues in contact with ILE1214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400E MET* 5.5 4.0 - - + -
1206E GLU 5.0 0.9 - - - +
1207E THR* 4.2 26.2 - - + +
1210E GLY* 3.1 22.5 + - - +
1211E LEU* 3.2 7.2 + - + +
1213E THR* 1.3 75.3 - - + +
1215E ARG* 1.3 55.5 + - + +
1217E PHE* 3.5 10.5 - - + -
1218E ARG* 2.7 29.6 + - - -
1219E TYR* 3.1 15.6 + - + -
1220E GLU* 3.8 27.4 - - + +
1223E PHE* 3.6 44.4 - - + -
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Residues in contact with ARG1215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399E ILE 3.8 2.0 + - - -
400E MET* 2.6 36.6 + - - +
401E HIS* 4.4 1.2 - - - +
402E MET* 2.9 29.2 + - - +
403E SER* 3.0 34.1 - - - +
1211E LEU* 2.9 44.1 + - + +
1212E THR* 3.7 13.2 - - + +
1213E THR 3.3 0.2 - - - -
1214E ILE* 1.3 77.0 - - + +
1216E ALA* 1.3 58.2 + - - +
1218E ARG* 3.0 21.0 + - - +
1220E GLU* 4.5 10.3 - - + +
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Residues in contact with ALA1216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727E LEU* 4.5 22.9 - - + +
770E VAL* 3.3 36.2 - - + +
772E TYR* 4.6 19.5 - - + -
1212E THR* 3.0 16.8 + - + +
1213E THR 4.3 0.9 - - - +
1215E ARG* 1.3 73.6 - - - +
1217E PHE* 1.3 66.7 + - - +
1218E ARG* 3.1 3.9 + - - +
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Residues in contact with PHE1217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770E VAL* 3.7 20.5 + - - +
771E ALA* 3.9 6.7 - - + -
772E TYR* 3.3 43.3 - - + -
790E PHE* 5.7 8.5 - - + -
842E ARG* 6.0 6.1 - - + -
843E ALA* 5.7 7.4 - - - -
1213E THR* 2.9 42.0 + - + +
1214E ILE* 3.5 11.9 - - + +
1216E ALA* 1.3 75.9 - - - +
1218E ARG* 1.3 66.5 + - - +
1219E TYR* 3.3 50.1 - + + -
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Residues in contact with ARG1218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740E ASN 5.3 0.6 + - - -
741E SER* 3.4 37.4 + - - +
743E LEU 4.6 8.5 + - - -
770E VAL* 6.3 3.1 - - + -
1214E ILE 2.7 10.4 + - - -
1215E ARG 3.0 12.6 + - - +
1216E ALA 4.4 2.9 - - - +
1217E PHE* 1.3 75.9 - - - +
1219E TYR* 1.3 61.6 + - - +
1220E GLU* 3.3 28.8 + - - +
1221E ALA* 5.3 0.7 + - - +
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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