Contacts of the helix formed by residues 717 - 726 (chain A) in PDB entry 2HHT
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 SER 717 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715A GLY 3.7 1.5 + - - -
716A ILE* 1.3 78.7 - - - +
718A ASP* 1.3 67.4 + - - +
719A TYR* 4.4 5.5 - - - +
720A GLY* 3.0 21.0 + - - -
721A LEU* 2.9 19.9 + - - +
736A ILE* 3.8 4.3 - - - -
789A ARG* 4.2 27.7 + - - -
914A SO4 3.7 8.1 - - - -
5C A 4.6 3.6 + - - -
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Residues in contact with ASP 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717A SER* 1.3 71.8 - - - +
719A TYR* 1.3 74.1 + - - +
722A ALA* 2.7 38.4 + - - +
729A ARG* 3.8 33.4 - - - +
732A ALA* 3.4 4.0 - - - +
733A ALA* 3.9 20.6 - - + +
736A ILE* 3.7 12.0 - - - +
914A SO4 3.9 18.9 + - - +
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Residues in contact with TYR 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717A SER* 3.2 4.9 - - - +
718A ASP* 1.3 86.3 + - - +
720A GLY* 1.3 63.2 + - - +
722A ALA* 3.7 0.8 - - + +
723A GLN* 2.9 68.1 + - + +
729A ARG* 4.4 22.9 - - + -
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Residues in contact with GLY 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717A SER* 3.0 20.0 + - - -
719A TYR* 1.3 85.1 - - - +
721A LEU* 1.3 60.0 + - - +
723A GLN* 3.6 7.8 + - - +
724A ASN* 3.2 22.2 + - - +
5C A 3.6 29.4 - - - +
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Residues in contact with LEU 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A ALA 3.7 20.0 - - - +
708A VAL* 4.1 12.6 - - + -
716A ILE* 4.7 5.2 - - + -
717A SER 2.9 16.1 + - - +
718A ASP* 3.9 3.1 - - - +
720A GLY* 1.3 73.5 - - - +
722A ALA* 1.3 62.2 + - - +
724A ASN* 3.0 2.9 + - - +
725A LEU* 2.8 51.8 + - + +
732A ALA* 3.8 28.9 - - + +
735A PHE* 4.0 17.3 - - + -
736A ILE* 4.0 14.1 - - + -
5C A 3.4 29.4 - - + +
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Residues in contact with ALA 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A ASP 2.7 23.7 + - - +
719A TYR* 3.7 6.3 - - + +
721A LEU* 1.3 72.1 - - - +
723A GLN* 1.3 59.1 + - - +
726A ASN* 2.8 27.7 + - - -
727A ILE* 3.0 37.4 + - - +
728A SER 3.7 17.9 - - - +
729A ARG* 3.9 7.6 - - + +
732A ALA* 3.6 2.8 - - + +
913A SO4 5.2 0.7 - - - +
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Residues in contact with GLN 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A TYR* 2.9 55.2 + - + +
720A GLY* 3.7 6.3 - - - +
722A ALA* 1.3 77.2 - - - +
724A ASN* 1.3 62.2 + - - +
725A LEU 3.7 0.2 + - - -
726A ASN* 3.7 16.0 + - - +
5C A 4.8 15.1 + - - +
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Residues in contact with ASN 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A ARG* 5.5 2.1 + - - -
707A ALA* 3.8 15.6 - - - +
720A GLY 3.2 14.4 + - - +
721A LEU 3.0 5.6 + - - +
723A GLN* 1.3 82.0 - - - +
725A LEU* 1.3 59.9 + - + +
726A ASN* 3.4 7.0 + - - -
5C A 3.3 43.1 + - + +
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Residues in contact with LEU 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A ARG* 3.8 31.6 + - - +
704A GLN* 3.9 31.0 - - + +
707A ALA* 3.7 24.2 - - + -
721A LEU* 2.8 37.2 + - + +
724A ASN* 1.3 76.2 - - - +
726A ASN* 1.3 74.8 + - - +
727A ILE* 3.4 36.5 - - + +
735A PHE* 3.9 17.3 - - + -
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Residues in contact with ASN 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A LYS* 3.5 31.8 + - - +
703A ARG* 6.1 0.8 - - - +
722A ALA 2.8 9.6 + - - -
723A GLN* 3.7 12.9 + - - +
724A ASN 3.4 7.4 + - - -
725A LEU* 1.3 83.8 + - - +
727A ILE* 1.3 58.8 + - - +
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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