Contacts of the helix formed by residues 476 - 489 (chain A) in PDB entry 1H41
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 476 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A GLU* 3.4 22.9 - - - -
413A LYS* 4.0 4.0 - - - +
469A MET* 3.8 1.6 - - - -
474A GLN 3.3 2.6 + - - -
475A ILE* 1.3 81.7 - - - +
477A ALA* 1.3 65.2 + - - +
478A ALA* 3.6 9.9 + - - +
479A THR* 2.9 33.3 + - - -
480A ALA* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A TYR* 2.7 25.6 + - + -
405A GLY* 3.5 30.5 - - - -
406A PRO* 3.5 9.6 - - + -
409A GLU* 2.9 20.4 + - - +
469A MET* 3.6 8.2 - - - +
476A SER* 1.3 71.7 - - - +
478A ALA* 1.3 57.3 + - - +
481A ALA* 2.9 16.5 + - - +
504A LEU* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A GLU* 4.6 0.6 + - - -
476A SER* 3.2 8.8 + - - +
477A ALA* 1.3 76.9 - - - +
479A THR* 1.3 58.8 + - - +
481A ALA* 3.3 2.1 + - - -
482A ASP* 2.9 29.5 + - - +
500A LYS* 3.5 13.4 - - + +
501A GLN* 6.0 0.4 - - - +
504A LEU* 3.9 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ARG* 5.5 0.9 - - - +
475A ILE* 4.2 17.5 - - + -
476A SER* 2.9 24.0 + - - -
478A ALA* 1.3 74.9 - - - +
480A ALA* 1.3 63.6 + - - +
482A ASP* 3.3 7.6 + - - +
483A GLU* 3.1 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A TYR* 3.5 15.9 - - - +
464A TYR* 3.4 17.0 - - + -
465A ALA* 4.1 22.7 - - + -
468A ARG* 4.7 4.3 - - + -
469A MET* 4.9 2.0 - - + -
475A ILE* 4.3 10.5 - - + +
476A SER 3.0 13.9 + - - +
477A ALA* 4.7 0.4 - - - -
479A THR* 1.3 80.1 - - - +
481A ALA* 1.3 55.6 + - - +
483A GLU* 3.4 5.0 + - - -
484A TRP* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A TYR* 3.4 11.3 + - + -
477A ALA 2.9 19.8 + - - +
478A ALA* 3.7 5.2 - - - +
479A THR 3.3 0.2 - - - -
480A ALA* 1.3 74.3 - - - +
482A ASP* 1.3 59.6 + - - +
484A TRP* 3.3 2.8 + - - +
485A LEU* 2.9 37.8 + - - +
500A LYS* 4.2 15.3 - - + -
503A MET* 3.8 31.6 - - + -
504A LEU* 5.0 0.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
139A HIS* 5.6 3.1 - - - -
478A ALA 2.9 16.1 + - - +
479A THR* 3.3 8.7 + - - +
481A ALA* 1.3 76.6 - - - +
483A GLU* 1.3 64.7 + - + +
485A LEU* 3.9 1.8 - - - +
486A ARG* 2.9 60.9 + - - +
496A ILE* 3.5 16.9 - - - +
500A LYS* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 3.9 1.1 - - - -
137A THR* 4.0 12.8 - - + -
139A HIS* 6.0 1.8 - - + -
464A TYR* 2.7 34.5 + - - +
468A ARG* 2.8 27.8 + - - +
479A THR* 3.1 28.2 + - + +
480A ALA* 3.7 5.6 - - - +
482A ASP* 1.3 81.7 + - + +
484A TRP* 1.3 62.8 + - - +
486A ARG* 3.2 2.3 + - - +
487A MET* 3.0 32.7 + - - +
1726A EDO 2.7 38.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 3.9 11.2 - + + -
403A TYR* 6.3 0.4 - - + -
457A PRO* 3.7 17.0 - - + -
458A PHE* 3.6 34.5 - + - -
460A GLN* 3.7 12.6 + - + +
461A SER* 3.4 39.8 - - - +
464A TYR* 3.6 36.5 - + + -
480A ALA 2.9 19.0 + - - +
481A ALA* 3.8 3.4 - - - +
483A GLU* 1.3 76.4 - - - +
485A LEU* 1.3 75.3 + - + +
487A MET* 3.8 5.5 - - - -
488A THR* 2.8 62.9 + - + -
489A PHE* 3.8 20.0 - + - -
503A MET* 3.6 9.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
458A PHE* 4.7 0.2 - - + -
481A ALA 2.9 21.0 + - - +
482A ASP* 3.9 2.9 - - - +
483A GLU 3.2 0.2 - - - -
484A TRP* 1.3 99.3 - - + +
486A ARG* 1.3 57.8 + - - +
488A THR* 4.8 0.2 - - - -
489A PHE* 2.9 34.9 + - + +
490A SER 3.1 10.1 + - - +
495A PHE* 4.0 15.7 - - + -
496A ILE* 3.8 22.7 - - + +
499A VAL* 3.6 24.9 - - + -
500A LYS* 3.5 38.6 - - + +
503A MET* 3.7 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 4.6 3.5 + - - -
136A GLN 4.0 2.1 - - - +
137A THR* 3.6 36.8 + - + -
138A GLN* 4.3 6.5 + - - +
139A HIS* 5.3 4.4 - - - -
482A ASP* 2.9 39.2 + - - +
483A GLU 3.6 3.8 - - - +
485A LEU* 1.3 78.5 - - - +
487A MET* 1.3 60.2 + - - +
489A PHE 4.2 0.2 + - - -
490A SER* 3.3 15.6 + - - -
491A ASN* 2.7 69.9 + - - +
493A PRO* 5.5 5.7 - - - +
496A ILE* 3.4 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 3.4 53.3 - - + +
12A LEU* 4.8 2.7 - - + -
13A ARG* 2.9 32.1 + - - +
133A ARG* 3.9 24.9 - - + +
136A GLN* 3.7 33.2 + - + +
137A THR* 3.9 12.3 - - + -
199A SER* 6.3 0.2 - - - -
464A TYR* 3.4 28.5 - - + +
483A GLU* 3.0 24.3 + - - +
484A TRP* 3.9 3.4 - - - +
486A ARG* 1.3 76.1 - - - +
488A THR* 1.3 59.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MET 4.4 6.3 - - - +
11A TRP* 3.7 11.8 + - - +
13A ARG* 3.2 16.9 - - - +
460A GLN* 4.1 12.1 - - - +
484A TRP* 2.8 53.8 + - + -
487A MET* 1.3 77.8 - - - +
489A PHE* 1.3 72.3 + - + +
641A ARG* 2.9 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 4.2 14.8 + - - -
457A PRO* 5.0 8.7 - - + -
458A PHE* 4.1 17.9 - + - -
484A TRP* 3.8 24.0 - + - -
485A LEU* 2.9 27.0 + - + +
487A MET 3.8 0.6 - - - -
488A THR* 1.3 90.4 - - + +
490A SER* 1.3 61.7 + - - +
495A PHE* 3.5 22.4 - + + -
630A TRP* 4.2 13.5 - + - -
636A TYR 4.0 8.8 - - - +
637A VAL* 3.9 28.6 - - + -
641A ARG* 3.5 44.7 + - + +
645A VAL* 5.2 1.1 - - + -
----------------------------------------------------------
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