Contacts of the helix formed by residues 1210 - 1218 (chain H) in PDB entry 5YWB
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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778H TRP* 3.6 36.5 - - - -
1206H GLU 3.0 12.6 + - - -
1207H THR 3.9 4.7 - - - -
1209H GLU* 1.3 74.1 - - - +
1211H LEU* 1.3 63.7 + - - +
1212H THR* 3.5 3.6 - - - -
1213H THR* 3.6 4.1 + - - -
1214H ILE* 3.5 24.8 + - - +
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Residues in contact with LEU1211 (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* 4.0 31.9 - - + +
400H MET* 4.6 17.0 - - + -
402H LEU* 4.4 13.2 - - + -
404H THR* 5.3 1.6 - - - +
407H LEU* 4.8 14.1 - - + -
417H ILE* 6.5 0.2 - - + -
1207H THR* 3.7 14.9 + - + +
1208H VAL* 3.3 23.6 - - + +
1209H GLU 2.9 6.3 + - - +
1210H GLY* 1.3 76.4 - - - +
1212H THR* 1.3 67.6 + - + +
1214H ILE* 3.1 6.7 + - + -
1215H ARG* 3.0 56.5 + - - +
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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
----------------------------------------------------------
404H THR* 4.2 25.1 - - + +
724H LEU* 4.3 26.9 - - + -
727H LEU* 4.5 3.6 - - - +
729H GLU* 4.6 16.6 - - + +
772H TYR* 4.1 19.6 - - - -
774H SER* 4.2 12.0 + - - +
1209H GLU 4.9 1.2 + - - -
1210H GLY 4.9 1.2 - - - -
1211H LEU* 1.3 79.5 + - + +
1213H THR* 1.3 58.1 + - - +
1215H ARG* 3.4 1.8 + - - +
1216H ALA* 2.9 31.1 + - - +
1480H GLU* 5.9 0.2 - - - +
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Residues in contact with THR1213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772H TYR* 3.9 23.7 + - - +
774H SER* 4.6 8.1 + - - -
778H TRP* 3.6 33.2 + - + +
790H PHE* 4.7 11.2 - - + -
842H ARG* 5.0 8.3 - - - +
1210H GLY 3.6 1.9 + - - -
1211H LEU 3.2 0.8 - - - -
1212H THR* 1.3 80.3 + - - +
1214H ILE* 1.3 63.2 + - - +
1216H ALA* 3.1 5.4 + - - +
1217H PHE* 3.0 56.1 + - + -
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Residues in contact with ILE1214 (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* 4.1 22.7 - - + -
778H TRP* 3.7 24.2 - - + -
790H PHE* 4.7 4.0 - - + -
1207H THR* 4.2 23.8 - - + +
1210H GLY 3.5 11.2 - - - +
1211H LEU* 3.1 8.3 + - + +
1213H THR* 1.3 76.7 - - - +
1215H ARG* 1.3 61.1 + - - +
1217H PHE* 3.8 3.6 + - - +
1218H ARG* 3.4 16.1 + - - -
1219H TYR* 3.5 9.8 + - + -
1220H GLU* 4.4 6.9 - - - +
1223H PHE* 3.5 59.2 - - + -
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Residues in contact with ARG1215 (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* 2.8 33.0 + - + -
401H HIS* 4.0 5.0 + - - +
402H LEU* 2.4 33.2 + - - +
403H SER* 4.2 1.4 - - - +
404H THR* 3.8 14.6 + - - +
619H ILE* 4.4 11.3 - - - +
727H LEU 5.3 2.6 - - - +
729H GLU* 2.9 45.3 + - - +
1211H LEU* 3.0 42.4 + - - +
1212H THR 3.7 1.3 - - - +
1214H ILE* 1.3 75.4 - - - +
1216H ALA* 1.3 63.4 + - - +
1218H ARG* 3.9 17.3 + - - +
1220H GLU* 3.4 25.8 - - - +
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Residues in contact with ALA1216 (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* 3.6 36.1 - - + -
770H VAL* 3.4 33.9 + - - +
772H TYR* 4.2 11.0 - - + -
1212H THR 2.9 18.0 + - - +
1213H THR* 3.1 5.6 + - - +
1215H ARG* 1.3 75.3 - - - +
1217H PHE* 1.3 66.6 + - + +
1218H ARG* 3.0 13.2 + - - +
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Residues in contact with PHE1217 (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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769H PRO* 3.3 22.4 - - + +
770H VAL 3.8 10.3 - - - +
771H ALA* 3.8 24.2 - - + -
772H TYR 4.0 17.7 - - - -
790H PHE* 4.5 13.7 - + + -
842H ARG* 4.8 14.6 - - - -
843H ALA* 4.8 5.4 - - - -
846H GLN* 3.6 34.8 - - + -
1213H THR* 3.0 50.6 + - + +
1214H ILE* 4.3 2.0 - - - +
1216H ALA* 1.3 76.7 - - + +
1218H ARG* 1.3 67.9 + - - +
1219H TYR* 3.6 38.4 - + + +
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Residues in contact with ARG1218 (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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622H GLU* 4.7 5.9 + - - -
727H LEU 4.1 12.5 + - - -
728H GLY* 5.2 1.6 - - - -
739H TRP* 3.6 27.7 - - - +
768H GLY* 2.4 45.9 + - - +
769H PRO* 4.8 2.9 - - + +
770H VAL* 3.8 7.5 - - - +
1214H ILE 3.4 7.4 + - - -
1215H ARG 3.9 13.2 + - - +
1216H ALA* 3.0 18.1 + - - +
1217H PHE* 1.3 79.0 - - - +
1219H TYR* 1.3 58.9 + - - +
1220H GLU* 3.3 22.0 + - - +
1221H ALA* 5.1 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