Contacts of the strand formed by residues 437 - 445 (chain A) in PDB entry 3HS0
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 ASN 437 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A SER* 4.8 0.5 + - - -
435A GLY 4.7 4.6 + - - -
436A ASP* 1.3 75.6 - - - +
438A LEU* 1.3 64.4 + - - +
439A PRO* 3.2 13.0 - - - +
485A ASN* 3.0 30.8 + - - +
486A LEU 3.6 1.3 - - - -
487A HIS* 3.2 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 4.1 22.9 - - + -
429A SER* 3.4 33.4 - - - +
432A ILE* 3.6 35.4 - - + -
436A ASP* 4.1 7.8 - - + +
437A ASN* 1.3 74.8 - - - +
439A PRO* 1.3 64.1 - - - +
440A VAL* 3.1 9.0 + - + +
484A MET 3.3 1.4 - - - +
485A ASN* 3.5 3.7 + - - -
486A LEU* 2.8 46.9 + - + +
488A ILE* 3.7 23.1 - - + -
496A PHE* 4.4 11.7 - - + -
516A VAL* 4.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ALA 4.1 6.9 - - - +
427A ILE* 4.4 12.0 - - - +
428A THR* 4.7 10.1 + - + +
429A SER* 3.5 20.1 + - - +
437A ASN 3.2 12.1 - - - +
438A LEU* 1.3 80.3 - - + +
440A VAL* 1.3 61.8 - - - +
441A ASN* 4.3 9.5 + - - +
483A THR* 4.6 11.7 - - + -
484A MET 3.7 5.6 - - - +
485A ASN* 5.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A VAL* 3.8 25.6 - - + -
426A ALA 3.9 4.3 - - - +
427A ILE* 3.9 20.9 - - + -
438A LEU* 3.5 16.6 - - + +
439A PRO* 1.3 74.0 - - - +
441A ASN* 1.3 66.8 + - - +
442A PHE* 4.6 2.7 - - + -
482A VAL 3.7 0.7 - - - +
483A THR* 3.1 5.9 - - - -
484A MET* 2.8 51.7 + - + +
486A LEU* 4.2 20.9 - - + -
498A PHE* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A HIS 3.7 1.2 - - - +
425A VAL* 3.3 11.3 - - - +
426A ALA* 3.2 47.8 + - + +
428A THR* 4.4 15.8 - - - +
439A PRO* 4.3 10.9 + - - +
440A VAL* 1.3 80.8 + - - +
442A PHE* 1.3 63.0 + - - +
443A ASN* 3.8 15.5 - - - +
481A LEU* 4.7 12.1 - - + +
482A VAL 3.5 3.1 - - - +
483A THR* 2.7 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 4.7 4.0 - - + -
424A HIS 4.1 2.5 - - - -
425A VAL* 4.2 11.7 - - + +
440A VAL* 4.6 4.3 - - + -
441A ASN* 1.3 72.3 - - - +
443A ASN* 1.3 63.3 + - - +
444A VAL* 4.7 0.2 - - - +
457A PHE* 3.5 49.2 - + + -
459A TYR* 4.5 5.2 - + + -
473A GLN* 3.8 30.5 - - + -
480A ASN 3.5 2.9 - - - +
481A LEU* 3.5 4.7 - - - -
482A VAL* 2.8 42.7 + - + +
484A MET* 3.4 37.7 - - + -
498A PHE* 3.7 14.6 - + - -
500A ALA* 3.6 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A MET* 4.4 16.7 - - + +
337A PRO* 5.8 6.1 - - - +
423A LEU* 3.8 4.2 - - - +
424A HIS* 3.0 55.9 + - + +
426A ALA* 4.4 10.5 - - - +
441A ASN* 4.0 8.7 - - - +
442A PHE* 1.3 77.3 - - - +
444A VAL* 1.3 63.7 + - - +
480A ASN 3.6 4.0 - - - +
481A LEU* 3.2 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A MET* 4.6 3.1 - - - +
422A TYR 4.1 5.2 - - - +
423A LEU* 4.6 0.4 - - + -
442A PHE 4.7 0.2 - - - +
443A ASN* 1.3 80.1 - - - +
445A LYS* 1.3 64.4 + - - +
451A LEU* 4.1 17.7 - - + -
454A ILE* 4.7 6.1 - - + -
457A PHE* 3.6 35.4 - - + -
475A ARG* 5.1 7.0 - - - +
479A GLN 4.7 2.2 - - - +
480A ASN* 3.1 54.1 + - - +
502A TYR* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PRO* 3.6 27.0 + - - +
335A GLY* 3.9 23.8 - - - +
336A MET* 4.0 20.8 - - + -
382A LEU* 4.3 16.7 - - - +
420A GLY 3.6 5.2 + - - +
421A ASN* 4.0 0.2 - - - -
422A TYR* 3.1 49.3 + - - +
444A VAL* 1.3 79.9 - - - +
446A GLY* 1.3 62.1 + - - +
451A LEU* 4.2 8.3 - - - +
480A ASN* 5.1 1.3 - - - +
502A TYR* 4.9 0.2 + - - -
----------------------------------------------------------
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