Contacts of the helix formed by residues 511 - 525 (chain A) in PDB entry 2HWK
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 511 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A FMT 3.6 12.3 - - - -
478A TRP* 4.5 1.1 - - - -
510A HIS* 1.3 81.0 + - - +
512A ALA* 1.3 62.3 + - - +
513A GLU* 3.3 18.2 + - - +
514A ILE* 3.4 33.0 + - - +
515A VAL* 3.1 25.1 + - - +
547A TRP* 3.8 7.9 - - - +
698A ILE* 3.7 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A TRP* 3.8 28.0 - - + +
481A ALA* 4.9 0.2 - - + -
482A LEU* 3.5 20.9 - - + +
510A HIS 3.7 1.0 + - - -
511A SER* 1.3 72.8 + - - +
513A GLU* 1.3 57.8 + - - +
515A VAL* 4.5 0.2 - - - -
516A LEU* 2.9 29.0 + - - +
540A LEU* 4.4 10.5 - - + -
547A TRP* 3.5 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A SER* 3.1 7.0 + - - +
512A ALA* 1.3 76.5 - - - +
514A ILE* 1.3 65.1 + - + +
516A LEU* 3.5 6.9 + - - +
517A ASN* 3.0 22.2 + - - +
528A LEU* 4.1 7.3 - - + +
540A LEU* 4.7 3.6 - - + -
547A TRP* 3.7 24.8 - - + -
554A ASN* 2.8 27.3 + - - +
556A TYR* 2.8 33.2 + - + +
727A ARG* 4.6 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A HIS* 3.8 15.9 - - + +
511A SER* 3.4 26.0 + - - +
513A GLU* 1.3 77.7 - - + +
515A VAL* 1.3 63.1 + - - +
517A ASN* 3.0 8.8 + - - +
518A GLN* 2.9 23.8 + - - +
694A GLU* 3.9 29.1 - - + +
697A ALA* 4.3 4.3 - - + +
698A ILE* 4.2 28.3 - - + +
701A SER* 5.5 2.5 - - - -
727A ARG* 6.0 0.2 - - - +
728A ALA* 4.1 28.5 - - + -
732A ILE* 5.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A TRP* 3.6 26.2 - - + -
482A LEU* 3.5 25.4 - - + -
498A TRP* 4.4 2.2 - - + -
501A VAL* 4.4 12.8 - - + -
510A HIS* 3.5 32.3 - - + +
511A SER 3.1 18.3 + - - +
514A ILE* 1.3 77.3 - - + +
516A LEU* 1.3 56.6 + - - +
518A GLN* 3.1 10.9 + - + +
519A LEU* 2.8 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 3.9 12.2 - - + +
485A VAL* 4.0 27.4 - - + -
486A LEU* 4.1 20.9 - - + -
512A ALA 2.9 23.0 + - - +
513A GLU* 3.6 5.6 - - - +
514A ILE 3.4 0.2 - - - -
515A VAL* 1.3 72.6 - - - +
517A ASN* 1.3 61.6 + - - +
519A LEU* 3.3 2.8 + - + +
520A CYS* 2.9 23.7 + - - +
528A LEU* 3.9 17.9 - - + -
533A PHE* 4.5 16.8 - - + -
540A LEU* 4.3 8.1 - - + -
556A TYR* 3.5 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU 3.0 13.9 + - - +
514A ILE* 3.0 12.3 + - - +
516A LEU* 1.3 76.0 - - - +
518A GLN* 1.3 61.8 + - - +
520A CYS* 3.2 4.3 + - - +
521A VAL* 3.1 27.8 + - - +
527A ASP* 3.0 16.1 - - - +
528A LEU* 3.0 40.5 + - + +
690A TYR* 4.0 8.7 + - - -
694A GLU* 2.7 24.4 + - - +
726A ASP* 5.0 1.2 - - - +
727A ARG* 3.4 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A VAL* 4.4 20.8 - - - +
502A ASP 5.7 0.4 - - - +
510A HIS* 5.2 4.5 + - - -
514A ILE* 2.9 17.1 + - - +
515A VAL* 3.4 13.3 - - - +
517A ASN* 1.3 78.8 - - - +
519A LEU* 1.3 59.2 + - + +
521A VAL* 3.4 5.2 + - - +
522A ARG* 3.1 68.3 + - + +
694A GLU* 3.8 37.3 - - - +
695A ASP* 3.4 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 4.5 3.6 - - + -
486A LEU* 4.0 38.1 - - + -
493A MET* 4.1 21.5 - - + -
498A TRP* 4.0 12.8 - - + -
501A VAL* 4.3 15.9 - - + -
515A VAL* 2.8 36.6 + - + +
516A LEU* 3.9 3.8 - - - +
518A GLN* 1.3 73.9 - - + +
520A CYS* 1.3 57.5 + - - +
522A ARG* 4.4 9.0 - - - +
523A PHE* 2.7 52.1 + - + +
593A TYR* 4.4 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A LEU 2.9 17.7 + - - +
517A ASN* 3.5 6.7 - - - +
519A LEU* 1.3 76.5 - - - +
521A VAL* 1.3 57.1 + - - +
524A PHE* 2.8 32.7 + - - +
526A LEU 3.2 28.3 - - - +
527A ASP* 4.3 6.5 - - - -
528A LEU* 4.3 13.0 - - + -
532A LEU* 3.9 21.8 - - - -
533A PHE* 3.8 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ASN* 3.1 18.3 + - - +
518A GLN* 3.6 8.5 - - - +
520A CYS* 1.3 73.2 - - - +
522A ARG* 1.3 65.8 + - + +
525A GLY* 2.7 24.5 + - - -
526A LEU 3.4 15.9 - - - +
527A ASP* 4.0 17.0 - - + -
598A ASN* 3.2 24.1 - - + +
599A LEU 4.5 3.4 - - - +
600A VAL* 4.1 6.3 - - - +
601A PRO* 3.9 31.4 - - + -
690A TYR* 4.3 15.5 - - + +
694A GLU* 4.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A THR* 3.2 29.7 + - - -
501A VAL* 4.1 7.3 - - - +
518A GLN* 3.1 49.3 + - + +
519A LEU* 3.8 10.8 - - - +
521A VAL* 1.3 77.9 - - + +
523A PHE* 1.3 64.5 + - - +
582A VAL* 3.8 10.9 - - - +
593A TYR* 3.4 37.1 + - + -
594A ASP 5.0 4.1 - - - +
595A PRO* 3.6 24.2 - - + +
597A ILE* 5.3 0.2 - - - +
598A ASN* 3.0 29.1 + - - +
686A LYS* 5.0 4.8 - - - +
687A TYR* 2.9 27.4 + - - -
691A GLN* 5.1 1.6 - - - +
695A ASP* 4.9 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LEU* 5.8 0.2 - - + -
491A ILE* 3.6 39.5 - - + -
493A MET* 4.0 20.6 - - - -
497A GLN* 5.4 3.1 - - - -
519A LEU* 2.7 42.5 + - + +
522A ARG* 1.3 75.4 - - - +
524A PHE* 1.3 73.6 + - + +
525A GLY 3.8 0.2 - - - -
580A GLY 3.5 21.1 - - - -
581A ARG* 3.8 22.4 - - - -
582A VAL* 3.2 12.6 - - + +
583A TYR 2.7 32.1 + - - -
593A TYR* 3.6 41.5 - + + -
598A ASN* 3.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ALA* 4.0 28.5 - - + -
491A ILE* 4.0 9.6 - - + -
520A CYS* 2.8 16.1 + - - +
523A PHE* 1.3 95.9 - - + +
525A GLY* 1.3 64.3 + - - +
526A LEU* 3.1 7.3 + - - +
532A LEU* 3.7 31.4 - - + -
533A PHE* 4.1 16.8 - + - -
558A LEU* 5.6 0.2 - - + -
573A LEU* 4.0 21.6 - - + +
576A ALA* 4.0 10.8 - - + -
577A VAL* 3.8 23.1 - - + -
581A ARG 3.4 22.9 - - - -
583A TYR* 4.2 10.7 - - - -
585A MET* 3.2 18.2 - - - +
598A ASN* 4.0 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A VAL* 2.7 24.6 + - - -
524A PHE* 1.3 71.8 - - - +
526A LEU* 1.3 53.2 + - - +
585A MET* 3.8 9.4 - - - -
598A ASN* 3.4 21.8 - - - +
600A VAL 4.8 2.7 - - - -
601A PRO* 3.4 5.5 - - - +
602A VAL* 2.8 41.0 + - - +
----------------------------------------------------------
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