Contacts of the helix formed by residues 480 - 499 (chain A) in PDB entry 3SRH
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 ALA 480 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLN* 4.2 3.6 - - - +
479A GLU* 1.3 77.6 - - - +
481A TRP* 1.3 65.2 + - - +
482A ALA* 4.6 2.9 - - + +
483A GLU* 3.4 25.6 + - + +
484A ASP* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 6.4 0.9 - - + -
432A LYS* 4.1 13.5 - - - -
478A GLN 5.7 0.4 - - - -
479A GLU 3.6 4.4 + - - +
480A ALA* 1.3 73.1 - - - +
482A ALA* 1.3 65.4 + - - +
484A ASP* 3.3 13.4 + - + +
485A VAL* 3.1 38.0 + - + +
488A ARG* 3.4 28.7 - - - -
513A GLY* 3.3 34.2 + - - -
514A TRP* 3.4 19.2 + - - +
515A ARG* 3.9 14.8 - - - -
516A PRO* 3.5 42.0 - - + -
517A GLY 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A ALA* 3.4 3.0 - - + +
481A TRP* 1.3 82.7 - - + +
483A GLU* 1.3 70.7 + - + +
485A VAL* 3.6 5.9 + - - +
486A ASP* 2.9 35.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
478A GLN* 3.0 25.6 - - + +
480A ALA* 3.4 24.6 + - + +
481A TRP 3.2 0.6 - - - -
482A ALA* 1.3 87.1 - - - +
484A ASP* 1.3 59.8 + - - +
485A VAL 3.2 0.4 - - - -
486A ASP* 3.5 14.7 + - - +
487A LEU* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ARG* 2.6 37.1 + - - -
476A PRO 4.1 0.7 - - - +
477A VAL* 3.7 10.3 - - - +
478A GLN* 3.0 38.6 + - + +
480A ALA 3.2 11.9 + - - +
481A TRP* 3.3 17.9 + - + +
483A GLU* 1.3 74.5 - - - +
485A VAL* 1.3 65.6 + - - +
487A LEU* 3.6 3.0 - - - +
488A ARG* 3.1 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 4.6 4.0 - - + -
481A TRP* 3.1 47.1 + - + +
482A ALA* 3.6 9.9 - - - +
483A GLU 3.2 0.2 - - - -
484A ASP* 1.3 74.0 - - - +
486A ASP* 1.3 69.0 + - - +
488A ARG* 2.9 18.9 + - - +
489A VAL* 2.8 38.5 + - + +
512A THR* 3.8 32.3 - - + +
513A GLY 5.0 0.4 - - - +
525A ARG* 4.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ALA* 2.9 20.0 + - - +
483A GLU* 3.5 17.3 + - - +
485A VAL* 1.3 82.6 - - - +
487A LEU* 1.3 56.2 + - - +
489A VAL* 4.3 7.2 - - - -
490A ASN* 2.8 48.2 + - - +
525A ARG* 5.2 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ARG* 4.4 9.9 - - - +
473A CYS* 5.5 1.6 - - - -
475A ASP* 3.6 40.6 - - + +
476A PRO* 4.1 10.5 - - + +
478A GLN* 3.4 29.6 - - + +
483A GLU 3.0 16.4 + - - +
484A ASP 3.6 5.8 - - - +
485A VAL 3.2 0.2 - - - -
486A ASP* 1.3 75.6 - - - +
488A ARG* 1.3 58.5 + - + +
490A ASN* 4.1 4.5 - - - +
491A PHE* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 3.6 37.6 - - + +
431A THR 5.1 4.2 + - - +
432A LYS* 4.0 19.0 - - - +
452A VAL* 3.8 29.9 + - + +
453A THR* 6.0 1.6 - - - +
454A ARG* 3.6 37.6 - - - +
473A CYS* 4.2 12.1 - - - -
481A TRP* 3.4 35.6 - - - -
484A ASP* 3.1 32.9 + - - +
485A VAL* 2.9 16.3 + - - +
487A LEU* 1.3 79.5 - - + +
489A VAL* 1.3 64.3 + - - +
491A PHE* 3.4 8.5 + - - +
492A ALA 3.2 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE* 4.9 7.4 - - + -
430A LEU* 3.7 25.6 - - + -
485A VAL* 2.8 31.3 + - + +
486A ASP* 3.9 7.0 - - - +
488A ARG* 1.3 75.4 - - - +
490A ASN* 1.3 67.1 + - - +
492A ALA* 3.0 18.5 + - - +
493A MET* 3.0 26.6 + - + +
510A VAL* 4.0 32.3 - - + -
525A ARG* 4.5 9.4 - - - +
527A VAL* 5.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ASP* 2.8 34.2 + - - +
487A LEU* 4.1 3.9 - - - +
489A VAL* 1.3 74.8 - - - +
491A PHE* 1.3 63.3 + - - +
493A MET* 3.2 10.8 + - - +
494A ASN* 3.0 31.6 + - - +
530A PRO* 4.2 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PRO* 3.5 32.8 - - + -
102A ILE* 3.7 23.3 - - + -
452A VAL* 4.1 18.2 - - + -
471A VAL* 3.8 31.9 - - + -
472A LEU 3.6 25.8 - - - -
473A CYS* 4.2 11.0 - - + -
475A ASP* 4.9 13.5 - - - +
487A LEU* 3.2 19.5 + - + +
488A ARG* 3.5 4.7 - - - +
489A VAL 3.2 0.2 - - - -
490A ASN* 1.3 76.4 - - - +
492A ALA* 1.3 57.0 + - - +
494A ASN* 3.1 11.0 + - - +
495A VAL* 3.1 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE* 3.8 22.7 - - + -
450A ILE* 4.0 14.8 - - + +
452A VAL* 3.6 27.8 - - + -
488A ARG 3.2 2.9 + - - +
489A VAL 3.0 10.4 + - - +
491A PHE* 1.3 76.8 - - - +
493A MET* 1.3 65.8 + - - +
495A VAL* 3.1 11.6 + - - +
496A GLY 3.1 18.9 + - - -
502A PHE* 3.9 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE* 3.5 22.0 - - + -
489A VAL* 3.0 23.0 + - + +
490A ASN* 3.2 17.0 + - - +
492A ALA* 1.3 75.7 - - - +
494A ASN* 1.3 59.8 + - - +
497A LYS* 3.2 41.8 + - - +
502A PHE* 3.4 36.7 - - + -
508A VAL* 3.6 18.8 - - + -
527A VAL* 5.0 4.3 - - - -
528A PRO 4.7 1.6 - - - +
529A VAL* 3.7 8.1 - - + -
530A PRO* 3.4 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 3.8 25.1 - - + +
490A ASN* 3.0 21.5 + - - +
491A PHE* 3.1 12.1 + - - +
493A MET* 1.3 77.1 - - - +
495A VAL* 1.3 62.6 + - - +
497A LYS* 3.8 23.0 + - - +
498A ALA* 3.3 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 4.1 20.0 - - + +
450A ILE* 4.9 5.8 - - + -
469A PHE* 4.2 12.6 - - + -
471A VAL* 3.8 33.4 - - + -
491A PHE* 3.1 32.1 + - + +
492A ALA* 3.1 10.9 + - - +
494A ASN* 1.3 76.1 - - - +
496A GLY* 1.3 67.1 + - - +
498A ALA* 3.2 4.2 + - - -
499A ARG* 2.9 44.2 + - + +
501A PHE* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ILE* 4.4 1.9 - - - +
492A ALA 3.1 10.5 + - - -
493A MET 3.6 0.2 + - - -
495A VAL* 1.3 77.3 - - - +
497A LYS* 1.3 56.1 + - - +
499A ARG 3.6 0.2 - - - -
500A GLY* 2.9 8.5 + - - -
501A PHE* 2.8 43.6 + - - -
502A PHE* 3.4 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A MET* 3.2 25.3 + - - +
494A ASN* 3.8 22.1 + - - +
496A GLY* 1.3 74.2 - - - +
498A ALA* 1.3 63.6 + - - +
500A GLY* 3.2 11.8 + - - -
502A PHE* 3.4 24.0 - - + +
503A LYS* 4.5 5.2 - - - -
504A LYS* 4.7 8.1 - - + +
529A VAL* 4.1 9.9 - - + -
530A PRO* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 3.7 20.4 - - + -
103A LEU* 4.2 17.1 - - + +
494A ASN 3.3 18.8 + - - +
495A VAL 3.2 4.5 + - - +
497A LYS* 1.3 79.5 - - - +
499A ARG* 1.3 60.8 + - + +
500A GLY 3.3 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 3.7 11.3 + - - -
102A ILE 3.6 8.5 + - - +
103A LEU* 3.1 58.7 + - + +
104A TYR 4.5 2.8 + - - -
105A ARG* 3.4 45.4 - - - +
469A PHE* 3.5 31.7 - - - -
495A VAL* 2.9 26.9 + - + +
496A GLY 4.3 0.4 - - - +
498A ALA* 1.3 81.2 - - + +
500A GLY* 1.3 62.1 + - - +
501A PHE* 3.3 27.6 + - + -
----------------------------------------------------------
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