Contacts of the helix formed by residues 774 - 778 (chain A) in PDB entry 2HVI
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 PRO 774 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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761A GLY* 4.5 4.6 - - - +
772A TYR* 3.4 15.9 - - + +
773A LEU* 1.3 87.2 - - - +
775A ASP* 1.3 69.2 + - - +
776A ILE* 3.2 2.8 + - + +
777A THR* 4.0 14.0 + - - -
778A SER* 4.9 0.9 + - - -
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Residues in contact with ASP 775 (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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773A LEU* 3.2 1.4 + - - -
774A PRO* 1.3 83.4 - - - +
776A ILE* 1.3 64.0 + - - +
777A THR 3.2 3.6 - - - -
778A SER* 3.0 23.8 + - - -
783A VAL* 3.4 29.3 - - + +
784A ARG* 3.7 7.4 - - - -
787A ALA* 3.7 13.0 - - + -
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Residues in contact with ILE 776 (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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754A VAL* 3.6 4.5 - - + +
757A ALA* 3.2 38.4 - - + +
758A LYS* 3.5 51.3 - - + +
761A GLY* 5.3 2.5 - - - -
773A LEU* 3.1 22.9 + - + +
774A PRO* 3.2 1.5 - - + +
775A ASP* 1.3 77.7 - - - +
777A THR* 1.3 64.7 + - + +
778A SER 3.3 0.7 - - - -
784A ARG* 3.4 19.0 - - - +
787A ALA* 3.5 20.6 - - + +
788A GLU* 4.2 12.6 - - + -
791A ALA* 4.4 11.7 - - + -
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Residues in contact with THR 777 (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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758A LYS* 3.9 23.1 - - + +
774A PRO 4.0 9.5 + - - -
775A ASP 3.2 1.0 - - - -
776A ILE* 1.3 91.9 - - + +
778A SER* 1.3 66.4 + - - +
779A ARG 3.7 0.5 + - - -
784A ARG* 4.7 1.1 - - - +
664D HIS* 4.7 11.1 - - + +
857D THR 4.7 10.4 + - - -
858D LEU 5.6 1.0 - - - -
859D ARG* 3.7 47.1 + - - +
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Residues in contact with SER 778 (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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774A PRO 4.9 0.8 + - - -
775A ASP* 3.0 22.1 + - - -
776A ILE 3.3 1.0 + - - -
777A THR* 1.3 83.5 + - - +
779A ARG* 1.3 64.8 + - - +
780A ASN* 3.2 12.7 + - - +
783A VAL* 3.6 28.0 - - - +
784A ARG* 3.4 24.9 + - - +
857D THR* 6.5 0.9 - - - -
859D ARG* 5.0 2.3 + - - -
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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