Contacts of the helix formed by residues 656 - 667 (chain D) in PDB entry 2HVH
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 GLN 656 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655D SER* 1.3 92.4 + - - +
657D ILE* 1.3 64.0 + - - +
658D GLU 3.3 3.1 + - - -
659D LEU* 3.4 6.1 + - + -
660D ARG* 3.2 32.0 + - - +
675D PHE* 3.3 20.0 - - + -
678D ASP* 5.4 1.4 + - - -
679D LEU 3.5 7.2 + - - +
680D ASP* 3.3 16.5 + - - +
681D ILE* 3.1 29.5 + - - +
682D HIS* 3.5 23.3 + - + +
702D ARG* 4.8 0.6 - - - +
710D TYR* 3.8 2.2 - - - +
881D DCT 3.0 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 657 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654D TYR* 3.8 38.1 - - + -
655D SER 3.1 4.9 + - - -
656D GLN* 1.3 75.4 - - - +
658D GLU* 1.3 75.2 + - + +
660D ARG* 3.3 5.9 + - - +
661D VAL* 3.0 29.3 + - + +
800D ALA* 3.9 22.9 - - + +
803D ILE* 4.7 11.2 - - + -
830D ASP* 3.5 31.2 - - + +
862D LEU* 4.0 22.9 - - + -
881D DCT 3.3 20.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 658 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D ARG* 3.5 10.7 + - - -
657D ILE* 1.3 82.9 - - + +
659D LEU* 1.3 57.1 + - - +
661D VAL* 3.6 1.5 + - - -
662D LEU* 3.0 24.1 + - - +
710D TYR* 3.2 23.1 + - + +
714D TYR* 3.0 24.4 + - - +
793D ASN* 4.6 0.5 + - - -
796D ILE* 3.2 16.7 - - + +
797D GLN* 3.5 35.4 - - - +
800D ALA* 3.7 25.7 - - + +
881D DCT 3.2 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 659 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656D GLN* 3.4 6.3 + - + +
657D ILE 3.3 0.6 - - - -
658D GLU* 1.3 73.7 - - - +
660D ARG* 1.3 60.7 + - - +
662D LEU* 3.4 11.8 + - + +
663D ALA* 2.9 28.1 + - - +
671D LEU* 3.7 9.4 - - + +
675D PHE* 3.6 20.6 - - + -
681D ILE* 4.0 29.8 - - + -
682D HIS* 3.4 32.1 - - + +
709D ASN* 4.2 18.2 - - + +
710D TYR* 3.3 27.1 + - + +
713D VAL* 4.6 11.2 - - + -
739D TYR* 4.6 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 660 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655D SER* 2.9 37.1 + - - -
656D GLN* 3.2 17.1 + - - +
657D ILE* 3.3 8.0 + - - +
659D LEU* 1.3 72.5 - - - +
661D VAL* 1.3 66.9 + - - +
663D ALA* 3.2 4.7 + - - +
664D HIS* 3.0 19.4 + - - +
675D PHE* 3.6 58.7 + - + +
678D ASP* 3.4 24.7 + - - +
679D LEU 5.2 0.2 + - - -
858D LEU* 5.1 1.3 - - - -
860D VAL* 3.7 17.2 - - + +
861D PRO* 2.8 29.6 + - - +
862D LEU* 4.4 19.5 - - + +
863D LYS* 3.6 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 661 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657D ILE* 3.0 31.4 + - + +
658D GLU* 3.7 4.5 - - - +
660D ARG* 1.3 72.8 - - - +
662D LEU* 1.3 67.4 + - - +
664D HIS* 2.9 11.2 + - + +
665D ILE* 2.8 40.5 + - + +
796D ILE* 3.9 26.2 - - + +
799D SER* 3.9 8.3 - - - -
800D ALA* 4.5 8.3 - - + -
803D ILE* 3.8 28.5 - - + -
858D LEU* 4.5 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 662 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658D GLU 3.0 19.3 + - - +
659D LEU* 3.5 11.7 - - + +
661D VAL* 1.3 75.0 - - - +
663D ALA* 1.3 57.1 + - - +
665D ILE 3.0 0.7 + - - -
666D ALA* 2.7 52.1 + - + +
671D LEU* 4.4 7.6 - - + -
713D VAL* 3.9 29.2 - - + -
714D TYR* 6.1 0.7 - - + -
746D VAL* 3.9 34.3 - - + -
749D TYR* 4.0 14.6 - - + -
796D ILE* 3.8 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 663 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659D LEU 2.9 14.6 + - - +
660D ARG 3.2 10.5 + - - +
662D LEU* 1.3 74.4 - - - +
664D HIS* 1.3 58.4 + - - +
666D ALA* 5.1 0.9 - - - -
667D GLU* 3.0 28.3 + - - +
668D ASP* 3.7 2.7 + - - +
671D LEU* 3.7 28.0 - - + +
672D MET* 3.6 26.4 - - + +
675D PHE* 4.2 9.2 - - + -
860D VAL* 4.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 664 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A THR* 5.2 11.0 - - + -
660D ARG 3.0 11.5 + - - +
661D VAL* 2.9 11.1 + - + +
663D ALA* 1.3 78.8 - - - +
665D ILE* 1.3 75.9 + - + +
667D GLU* 3.6 4.3 - - - +
766D LEU* 4.3 16.3 - - + +
857D THR 4.5 4.0 - - - -
858D LEU* 3.6 41.8 - - + +
859D ARG* 2.9 87.4 + - + +
860D VAL* 5.1 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 665 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661D VAL* 2.8 31.3 + - + +
662D LEU 3.9 2.0 - - - +
664D HIS* 1.3 90.5 - - + +
666D ALA* 1.3 62.4 + - - +
667D GLU* 3.2 9.2 + - - +
749D TYR* 3.5 35.2 - - + +
765D THR* 6.2 0.2 - - - -
766D LEU* 5.5 6.1 - - + +
795D PRO* 3.9 13.7 - - + +
796D ILE* 4.1 10.3 - - + -
799D SER* 3.8 23.3 - - - +
859D ARG* 5.0 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 666 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662D LEU* 2.7 31.8 + - + +
665D ILE* 1.3 72.5 - - - +
667D GLU* 1.3 69.5 + - - +
668D ASP* 3.2 6.8 + - + +
745D GLY* 3.9 16.6 - - - +
746D VAL* 4.2 9.9 - - + -
749D TYR* 3.7 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 667 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A LYS* 6.0 0.5 - - - +
663D ALA 3.0 14.5 + - - -
664D HIS 3.6 3.6 - - - +
665D ILE 3.2 6.1 - - - +
666D ALA* 1.3 80.4 - - - +
668D ASP* 1.3 62.5 + - - +
669D ASP* 3.6 2.4 + - - +
672D MET* 3.9 16.7 - - + +
859D ARG* 3.3 51.9 + - - +
880D SO4 3.5 15.4 + - - -
----------------------------------------------------------
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