Contacts of the helix formed by residues 650 - 662 (chain R) in PDB entry 1HI0
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 650 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168R GLU* 3.8 5.3 + - - -
649R VAL* 1.3 72.4 - - - +
651R VAL* 1.3 65.4 + - - +
652R GLU* 2.8 25.7 + - - -
653R LYS* 2.7 54.9 + - - +
654R THR* 3.1 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 651 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140R PRO* 4.6 7.4 - - + +
141R VAL* 4.2 8.3 - - - +
142R PRO* 3.9 38.1 - - + -
649R VAL 3.1 3.4 + - - -
650R SER* 1.3 72.0 - - - +
652R GLU* 1.3 63.5 + - - +
654R THR* 3.2 5.7 + - - -
655R GLU* 2.8 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 652 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650R SER* 2.8 29.6 + - - -
651R VAL* 1.3 91.0 + - - +
653R LYS* 1.3 62.8 + - + +
655R GLU* 3.2 15.1 + - - +
656R ARG* 2.8 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 653 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168R GLU* 3.2 42.3 + - + +
171R LEU* 4.0 9.0 - - + +
172R GLU* 3.6 22.6 + - - +
649R VAL* 4.5 7.0 - - + -
650R SER* 2.7 32.3 + - - +
652R GLU* 1.3 79.2 - - + +
654R THR* 1.3 59.3 + - + +
656R ARG* 3.7 7.5 + - - +
657R PHE* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 654 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140R PRO* 5.0 0.7 - - - -
141R VAL 2.8 26.4 + - - -
143R LEU* 3.6 37.5 - - + +
171R LEU* 3.8 20.4 - - + -
285R ALA* 5.2 9.0 - - - -
649R VAL* 4.2 8.5 - - + +
650R SER 3.1 10.9 + - - +
651R VAL 3.2 8.7 + - - -
653R LYS* 1.3 74.4 - - - +
655R GLU* 1.3 66.7 + - - +
657R PHE* 2.9 3.5 + - - +
658R LEU* 2.6 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 655 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140R PRO* 3.6 34.6 - - + +
651R VAL* 2.8 21.6 + - + +
652R GLU* 3.5 14.7 - - - +
654R THR* 1.3 81.1 + - - +
656R ARG* 1.3 60.3 + - - +
658R LEU* 3.6 2.0 + - - +
659R ARG* 3.1 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 656 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172R GLU* 5.1 15.9 + - - +
652R GLU 2.8 20.3 + - - +
653R LYS* 3.9 7.4 - - - +
655R GLU* 1.3 75.1 - - - +
657R PHE* 1.3 62.5 + - - +
659R ARG* 3.3 30.6 + - - +
660R SER* 3.3 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 657 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171R LEU* 3.2 45.3 - - + +
174R ALA* 3.8 24.0 - - + -
282R PRO* 3.5 37.0 - - + -
285R ALA* 3.5 18.4 - - + -
286R VAL* 4.4 5.2 - - + -
352R TRP* 3.9 9.0 - + - -
353R TRP* 3.8 5.8 - + - -
653R LYS 3.2 13.1 + - - +
654R THR 2.9 8.2 + - - +
656R ARG* 1.3 79.8 - - - +
658R LEU* 1.3 67.5 + - - +
660R SER* 3.0 25.5 + - - -
661R VAL* 3.3 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 658 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138R LEU* 4.5 1.1 - - + +
139R GLU 4.2 3.1 - - - -
140R PRO* 3.5 36.1 - - + -
285R ALA* 3.4 25.6 - - + +
286R VAL* 3.9 24.9 - - + -
289R PRO* 4.3 10.8 - - + -
654R THR* 2.6 21.5 + - - +
655R GLU* 3.8 5.6 - - - +
657R PHE* 1.3 79.0 - - + +
659R ARG* 1.3 56.8 + - - +
661R VAL* 3.2 3.3 + - + +
662R MET* 3.0 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 659 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140R PRO* 5.6 1.8 - - - +
655R GLU* 3.1 50.2 + - - +
656R ARG* 3.4 28.9 - - - +
657R PHE 3.1 0.4 - - - -
658R LEU* 1.3 74.3 - - - +
660R SER* 1.3 57.7 + - - +
661R VAL 3.0 8.9 + - - -
662R MET* 3.6 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 660 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175R GLU* 4.0 12.4 + - - +
350R ALA* 3.8 7.8 - - - +
352R TRP* 3.4 28.4 + - - -
656R ARG 3.3 7.2 + - - -
657R PHE* 3.0 19.4 + - - -
659R ARG* 1.3 78.1 - - - +
661R VAL* 1.3 58.1 + - - +
662R MET 4.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 661 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286R VAL* 4.2 9.9 - - + -
349R TYR* 3.8 21.5 - - + -
350R ALA* 3.1 29.1 + - - +
352R TRP* 3.3 28.0 - - + -
353R TRP* 3.6 25.4 - - + -
657R PHE* 3.4 32.5 - - + +
658R LEU* 3.2 9.8 + - + +
659R ARG 3.0 0.6 - - - -
660R SER* 1.3 79.0 - - - +
662R MET* 1.3 73.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 662 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136R SER 4.3 4.3 - - - +
138R LEU* 3.5 48.7 - - + +
140R PRO* 5.2 2.9 - - + -
286R VAL* 5.8 0.4 - - + -
348R GLY 4.2 0.8 - - - +
349R TYR* 3.8 20.9 - - + +
658R LEU* 3.0 50.6 + - + +
659R ARG* 3.6 14.7 + - - +
660R SER 4.7 0.7 - - - -
661R VAL* 1.3 88.2 - - + +
663R PRO* 1.3 71.2 - - + +
664R ARG* 4.0 19.9 + - - +
----------------------------------------------------------
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