Contacts of the helix formed by residues 480 - 500 (chain A) in PDB entry 5HG1
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 480 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLN 4.0 1.4 + - - -
479A LEU* 1.3 76.1 - - - +
481A HIS* 1.3 66.9 + - - +
482A ASP* 3.8 9.5 + - - +
483A GLN* 2.7 39.8 + - - +
484A LEU* 2.9 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU 4.0 0.2 + - - -
480A SER* 1.3 70.7 - - - +
482A ASP* 1.3 76.5 + - - +
484A LEU* 3.0 19.6 + - - +
485A LEU* 3.0 29.2 + - + +
881A ASP* 2.6 49.4 + - - -
882A LEU* 4.2 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A SER* 3.2 7.9 + - - +
481A HIS* 1.3 91.6 - - - +
483A GLN* 1.3 64.5 + - + +
485A LEU* 3.1 13.6 + - - +
486A GLU* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLN 3.8 3.8 - - - +
479A LEU* 3.1 24.3 - - + +
480A SER* 2.7 50.2 + - - +
482A ASP* 1.3 76.6 - - + +
484A LEU* 1.3 59.5 + - - +
486A GLU* 3.2 7.1 + - - +
487A VAL* 3.0 31.6 + - - +
720A ASP 5.6 1.0 + - - -
721A PHE* 3.6 32.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU* 4.0 31.2 - - + +
480A SER 2.9 19.8 + - - +
481A HIS* 3.0 9.6 + - - +
483A GLN* 1.3 73.9 - - - +
485A LEU* 1.3 60.5 + - - +
487A VAL* 3.5 2.8 + - + -
488A LYS* 3.0 24.1 + - - +
832A GLN* 3.8 61.9 - - + +
833A LEU* 4.4 8.1 - - + +
836A ALA* 3.5 12.7 - - + +
878A THR* 4.6 9.4 - - + -
882A LEU* 3.9 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A HIS* 3.0 34.6 + - + +
482A ASP* 3.1 13.7 + - - +
484A LEU* 1.3 73.7 - - - +
486A GLU* 1.3 55.5 + - - +
488A LYS* 3.0 13.0 + - + +
489A ARG* 2.7 35.8 + - - +
881A ASP 5.5 0.4 - - - +
882A LEU* 3.3 41.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ASP 3.1 11.2 + - - +
483A GLN* 3.2 9.6 + - - +
485A LEU* 1.3 75.5 - - - +
487A VAL* 1.3 57.9 + - - +
489A ARG* 2.9 45.3 + - - +
490A ARG* 2.8 75.1 + - - +
721A PHE* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU* 5.1 1.3 - - + -
483A GLN 3.0 17.2 + - - +
484A LEU* 3.6 11.2 - - + +
486A GLU* 1.3 75.6 - - - +
488A LYS* 1.3 61.3 + - - +
490A ARG* 3.3 7.3 + - - +
491A MET* 3.0 22.9 + - - +
712A PHE* 3.9 19.9 - - + -
718A LEU* 4.5 4.9 - - + -
721A PHE* 3.7 29.6 - - + -
741A PHE* 4.9 3.4 - - + -
833A LEU* 4.0 27.6 - - + +
836A ALA* 3.7 20.9 - - + -
837A GLY 5.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A LEU 3.0 14.2 + - - +
485A LEU* 3.0 16.6 + - + +
487A VAL* 1.3 76.5 - - - +
489A ARG* 1.3 63.0 + - - +
491A MET* 3.2 1.6 + - - -
492A LYS* 3.2 18.2 + - - +
836A ALA* 3.6 17.7 - - + +
839A ALA* 3.7 24.9 - - + -
840A ALA* 3.4 24.5 - - + +
843A ASP* 3.2 33.7 + - - +
882A LEU* 2.9 35.6 + - + +
883A ALA* 3.9 4.0 - - - +
884A PRO* 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A LEU 2.7 16.7 + - - +
486A GLU* 2.9 45.8 + - - +
488A LYS* 1.3 74.4 - - - +
490A ARG* 1.3 74.2 + - - +
492A LYS* 3.1 28.3 + - + +
493A VAL* 3.3 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A GLU* 2.8 55.6 + - - +
487A VAL* 3.3 5.6 + - - +
489A ARG* 1.3 82.2 - - - +
491A MET* 1.3 62.0 + - - +
493A VAL* 3.6 9.6 + - + +
494A GLU* 3.2 27.9 + - - +
712A PHE* 3.9 12.8 - - + -
717A CYS* 2.5 48.4 + - + +
718A LEU* 5.4 2.0 - - - -
720A ASP* 3.1 39.3 + - - -
721A PHE* 3.8 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A VAL 3.0 16.3 + - - +
488A LYS* 3.6 7.0 - - - +
489A ARG 3.2 0.2 - - - -
490A ARG* 1.3 74.1 - - - +
492A LYS* 1.3 59.6 + - - +
494A GLU* 3.4 0.9 + - - -
495A MET* 2.9 41.5 + - - +
509A VAL* 4.7 7.2 - - - -
707A MET* 4.0 16.2 - - + -
709A TRP* 3.5 39.9 - - + -
712A PHE* 3.7 43.2 - - + -
741A PHE* 4.2 4.5 - - + -
837A GLY* 3.9 18.6 - - - +
840A ALA* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A LYS 3.2 10.9 + - - +
489A ARG* 3.1 19.8 + - + +
491A MET* 1.3 76.3 - - - +
493A VAL* 1.3 67.9 + - + +
495A MET* 3.0 22.2 + - - +
496A GLU* 2.9 48.0 + - + +
840A ALA* 4.2 6.7 - - + +
844A ARG* 5.8 10.3 - - + +
847A GLU* 4.3 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ARG* 3.3 38.0 + - + +
490A ARG* 3.6 9.4 + - - +
492A LYS* 1.3 82.4 - - + +
494A GLU* 1.3 74.7 + - - +
496A GLU* 3.4 15.1 + - - +
497A ARG* 2.9 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ARG 3.2 18.4 + - - +
491A MET 3.8 4.3 - - - +
492A LYS 3.2 1.0 - - - -
493A VAL* 1.3 87.4 - - + +
495A MET* 1.3 60.5 + - - +
497A ARG* 3.1 36.5 + - - +
498A GLY 3.3 16.1 + - - -
507A ALA* 4.9 0.2 - - - +
508A PRO* 3.2 20.1 - - + +
509A VAL* 3.8 30.6 - - + +
712A PHE* 3.9 20.0 - - + -
715A ASN* 2.7 27.6 + - - +
717A CYS* 4.1 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A MET* 2.9 38.3 + - + +
492A LYS* 3.0 12.5 + - - +
494A GLU* 1.3 75.2 - - - +
496A GLU* 1.3 64.4 + - - +
498A GLY 3.4 1.4 + - - -
499A LEU* 3.1 28.6 + - - +
509A VAL* 4.9 0.7 - - + -
511A MET* 3.4 19.4 - - + +
686A TYR* 3.2 39.7 - - + +
707A MET* 3.7 31.0 - - + -
840A ALA 4.4 14.8 - - - +
841A VAL* 4.0 14.4 - - + -
844A ARG* 3.7 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LYS* 2.9 47.8 + - - +
493A VAL* 3.7 14.9 - - - +
495A MET* 1.3 73.1 - - - +
497A ARG* 1.3 66.3 + - - +
499A LEU* 2.9 19.2 + - - +
500A SER* 2.9 15.8 + - - -
844A ARG* 3.8 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A VAL* 2.9 29.2 + - - +
494A GLU* 3.1 36.6 + - - +
495A MET 3.4 0.4 - - - -
496A GLU* 1.3 75.6 - - - +
498A GLY* 1.3 60.5 + - - +
500A SER* 3.5 3.0 - - - +
503A THR* 2.7 54.0 + - + +
504A HIS 3.5 0.9 + - - -
506A SER* 4.3 9.5 + - - -
507A ALA* 3.2 31.6 - - + +
508A PRO* 4.1 1.8 - - - -
715A ASN* 4.1 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLU 3.3 7.9 + - - -
496A GLU 3.1 0.8 - - - -
497A ARG* 1.3 77.8 - - - +
499A LEU* 1.3 64.4 + - - +
500A SER 3.2 0.8 + - - -
504A HIS* 2.8 32.9 + - - +
507A ALA* 3.7 8.0 - - - +
509A VAL 3.4 22.0 - - - -
510A LYS 3.7 1.8 - - - +
511A MET* 3.9 9.6 - - - +
695A LEU* 4.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A MET 3.1 20.8 + - - +
496A GLU* 2.9 6.5 + - - +
498A GLY* 1.3 77.0 - - - +
500A SER* 1.3 60.1 + - - +
501A LYS 3.4 3.1 + - - -
511A MET* 3.7 37.5 - - + +
688A GLU* 3.8 16.8 - - + +
692A ASN 3.5 19.2 - - - +
693A VAL* 4.5 11.4 - - + -
694A GLU* 3.5 23.1 + - - +
695A LEU* 4.2 4.3 - - - +
705A VAL* 4.6 13.0 - - + -
844A ARG* 3.2 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A GLU 2.9 13.0 + - - -
497A ARG* 4.6 0.4 - - - -
498A GLY 3.2 0.4 - - - -
499A LEU* 1.3 75.6 - - - +
501A LYS* 1.3 59.0 + - - +
502A GLU* 3.4 20.6 + - - +
503A THR* 3.1 21.4 + - - +
504A HIS* 2.7 31.5 + - - +
694A GLU* 3.7 13.0 + - - -
----------------------------------------------------------
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