Contacts of the helix formed by residues 726 - 731 (chain G) in PDB entry 1H1V
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 726 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681G PHE* 4.3 8.7 - - + -
718G THR* 6.3 1.3 - - + -
720G VAL* 4.2 14.8 - - + -
724G PHE 3.6 5.4 - - - +
725G GLU* 1.3 88.9 - - + +
727G PRO* 1.3 71.4 - - + +
728G SER* 4.2 13.2 - - - +
729G PHE* 2.8 34.3 + - + +
730G VAL* 3.0 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 727 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623G ALA 5.9 1.3 - - - +
624G TYR 3.5 26.5 - - - +
625G ARG* 3.7 23.7 - - + +
626G THR 4.4 2.4 + - - +
630G LEU* 4.6 0.2 - - - +
725G GLU 4.6 0.9 - - - +
726G PRO* 1.3 88.4 - - + +
728G SER* 1.3 62.9 + - - +
729G PHE 2.9 1.4 + - - -
730G VAL* 3.8 9.1 - - + -
731G GLY* 3.1 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 728 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626G THR 4.0 12.5 + - - -
627G SER* 3.8 25.1 + - - -
630G LEU* 4.6 3.2 - - - +
679G GLN* 4.4 4.0 + - - -
681G PHE* 3.0 29.6 - - - -
726G PRO* 3.1 6.9 + - - +
727G PRO* 1.3 78.6 - - - +
729G PHE* 1.3 56.9 + - - +
732G TRP* 3.1 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 729 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642G LEU* 5.4 0.4 - - + -
666G LEU* 4.2 11.4 - - + -
674G LEU* 3.4 31.6 - - + -
681G PHE* 3.4 33.9 - + + -
683G TRP* 3.6 39.5 - + + -
720G VAL* 4.7 2.7 - - + -
725G GLU* 3.5 21.8 - - + -
726G PRO* 2.8 27.0 + - + +
728G SER* 1.3 79.5 + - - +
730G VAL* 1.3 64.7 + - - +
731G GLY 3.2 2.7 + - - -
732G TRP* 3.3 18.5 + - - -
733G PHE* 3.5 37.6 - + - -
736G TRP* 4.4 3.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 730 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625G ARG* 3.7 21.6 + - - +
725G GLU* 4.1 16.8 - - + +
726G PRO 3.0 25.4 - - - +
727G PRO* 3.8 5.8 - - + -
729G PHE* 1.3 72.9 - - - +
731G GLY* 1.3 58.5 + - - +
732G TRP 2.9 12.3 + - - -
733G PHE* 3.1 21.9 + - - +
736G TRP* 2.7 62.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 731 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540G GLN* 5.2 0.2 + - - -
542G ARG* 3.3 4.0 + - - -
562G ASN* 2.5 32.1 + - - -
625G ARG* 3.5 28.6 - - - +
630G LEU* 3.6 12.9 - - - +
727G PRO 3.1 11.9 + - - -
729G PHE 3.2 1.0 - - - -
730G VAL* 1.3 75.1 - - - +
732G TRP* 1.3 59.5 + - - +
733G PHE 3.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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