Contacts of the helix formed by residues 1209 - 1217 (chain H) in PDB entry 6C3P
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 GLY1209 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777H TRP* 3.4 31.3 - - - -
1205H GLU 2.9 10.9 + - - -
1206H THR 3.7 3.4 - - - -
1208H GLU* 1.3 77.2 - - - +
1210H LEU* 1.3 60.0 + - - -
1211H THR* 3.4 3.6 - - - -
1212H THR* 2.6 25.4 + - - -
1213H ILE* 3.1 14.3 - - - +
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Residues in contact with LEU1210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399H ILE* 3.6 33.2 - - + +
400H MET* 4.5 17.0 - - + -
402H LEU* 4.3 17.0 - - + +
404H THR* 5.3 3.8 - - - +
407H LEU* 6.0 3.4 - - + -
1206H THR* 3.1 33.8 + - + +
1207H VAL* 3.4 17.0 + - + +
1208H GLU 3.5 0.6 - - - -
1209H GLY* 1.3 74.6 - - - +
1211H THR* 1.3 62.2 + - + +
1213H ILE* 3.3 6.7 + - + +
1214H ARG* 3.0 55.9 + - + +
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Residues in contact with THR1211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404H THR* 4.0 15.9 - - + +
724H LEU* 5.4 11.7 - - + -
727H LEU* 5.2 3.3 - - - +
729H GLU* 4.5 11.1 - - + +
771H TYR* 3.9 21.9 + - - -
773H SER* 5.1 3.1 - - - -
1209H GLY* 4.9 1.2 - - - -
1210H LEU* 1.3 78.1 + - + +
1212H THR* 1.3 68.1 + - - +
1214H ARG* 3.3 28.3 + - - +
1215H ALA* 2.9 29.6 + - - +
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Residues in contact with THR1212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771H TYR* 3.4 35.2 - - + +
773H SER* 4.7 10.8 - - - +
777H TRP* 3.4 31.0 - - + -
789H PHE* 6.1 0.7 - - - -
1209H GLY* 2.6 23.5 + - - +
1211H THR* 1.3 85.7 + - - +
1213H ILE* 1.3 65.0 + - - +
1215H ALA* 3.0 3.0 + - - +
1216H PHE* 2.8 46.3 + - + -
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Residues in contact with ILE1213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400H MET* 4.2 22.2 - - + -
777H TRP* 4.7 6.5 - - + -
789H PHE* 5.2 4.0 - - + -
1205H GLU 4.5 2.9 - - - +
1206H THR* 4.1 27.6 - - + +
1209H GLY 3.1 21.7 + - - +
1210H LEU* 3.3 8.2 + - + +
1212H THR* 1.3 84.4 + - - +
1214H ARG* 1.3 64.6 + - - +
1215H ALA 3.2 0.3 + - - -
1216H PHE* 3.2 7.4 + - - +
1217H ARG* 2.9 18.5 + - - -
1218H TYR* 3.8 8.1 + - + +
1219H GLU* 4.4 14.6 + - - +
1222H PHE* 3.4 44.2 - - + -
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Residues in contact with ARG1214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400H MET* 4.6 25.6 + - - +
402H LEU 3.3 17.4 + - - -
404H THR* 2.6 19.5 + - - -
619H ILE* 4.7 18.4 - - - -
729H GLU* 2.4 49.2 + - - +
1210H LEU* 3.0 50.2 + - + +
1211H THR* 3.3 23.0 - - - +
1213H ILE* 1.3 75.3 - - - +
1215H ALA* 1.3 64.1 + - - +
1217H ARG* 3.1 34.5 + - - +
1219H GLU* 5.9 3.4 - - - +
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Residues in contact with ALA1215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727H LEU* 3.8 23.3 - - + -
729H GLU* 5.2 0.6 + - - -
767H GLY 3.9 1.2 - - - +
769H VAL* 3.5 23.4 + - + +
771H TYR* 3.7 27.4 - - + -
1211H THR 2.9 15.1 + - - +
1212H THR 3.0 8.9 + - - +
1214H ARG* 1.3 77.3 - - - +
1216H PHE* 1.3 62.7 + - - +
1217H ARG* 3.0 12.3 + - - +
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Residues in contact with PHE1216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768H PRO* 3.3 11.2 - - - +
769H VAL 4.0 8.3 - - - -
770H ALA* 3.7 11.4 - - + -
771H TYR* 3.5 27.6 - - + -
789H PHE* 3.2 44.4 - + + -
841H ARG* 4.7 17.0 - - + -
845H GLN* 3.3 41.1 - - + -
1212H THR* 2.8 50.9 + - - +
1213H ILE 3.9 3.1 - - - +
1215H ALA* 1.3 71.0 - - + +
1217H ARG* 1.3 61.7 + - - +
1218H TYR* 3.0 30.4 - - + +
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Residues in contact with ARG1217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766H ARG* 5.3 12.4 - - + +
767H GLY 3.9 17.9 - - - +
768H PRO* 4.1 9.9 - - + -
1213H ILE 2.9 7.9 + - - -
1214H ARG* 3.1 24.5 + - - +
1215H ALA 3.0 15.4 - - - +
1216H PHE* 1.3 77.4 - - - +
1218H TYR* 1.3 60.2 + - - +
1219H GLU* 3.3 36.1 + - - +
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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