Contacts of the strand formed by residues 521 - 529 (chain A) in PDB entry 4QDR
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 VAL 521 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ILE* 3.9 19.2 - - + +
520A PHE* 1.3 76.3 - - - +
522A ARG* 1.3 59.7 + - - +
523A LYS 3.3 30.5 - - - +
524A PHE* 4.1 2.2 - - + -
551A GLY* 3.2 3.6 - - - -
552A ASN* 2.9 30.1 + - - +
575A PRO* 3.8 23.8 - - + -
577A ARG 3.6 6.1 - - - +
578A TRP* 4.3 2.7 - - + -
583A ILE* 3.8 17.7 - - + -
584A GLY 3.7 8.5 + - - +
585A MET* 3.4 27.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
520A PHE* 3.6 42.9 + - + -
521A VAL* 1.3 70.4 - - - +
523A LYS* 1.3 66.2 + - + +
550A GLU* 3.6 8.0 - - - +
551A GLY* 2.7 27.2 + - - -
552A ASN 3.9 7.9 - - - +
553A MET* 6.1 1.8 - - - +
577A ARG* 3.0 19.0 + - + +
578A TRP* 2.8 28.0 + - - +
579A SER* 3.5 13.5 - - - +
580A PRO* 3.9 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A VAL* 3.3 9.7 - - - +
522A ARG* 1.3 82.5 - - + +
524A PHE* 1.3 59.0 + - - +
548A LEU* 4.5 29.3 + - + +
549A PHE 3.3 11.9 - - - +
550A GLU* 2.7 35.2 + - - -
551A GLY 4.3 0.4 - - - +
576A GLU* 2.7 33.1 + - + -
577A ARG* 3.3 39.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
501A VAL* 4.0 18.4 - - + -
503A ILE* 3.6 32.8 - - + -
521A VAL* 4.1 7.0 - - + -
523A LYS* 1.3 78.2 - - - +
525A LYS* 1.3 74.0 + - - +
526A VAL* 3.7 20.4 - - + -
547A LYS 3.6 1.0 - - - +
548A LEU* 3.7 2.5 - - - -
549A PHE* 2.8 55.3 + + + +
550A GLU 3.3 22.4 - - - -
551A GLY* 4.3 2.0 - - - -
561A ARG* 3.9 15.3 - - + -
573A VAL* 3.9 16.4 - - + -
574A TYR 3.1 19.7 - - - +
576A GLU* 4.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A GLY* 5.9 4.4 - - - -
524A PHE* 1.3 78.9 - - - +
526A VAL* 1.3 67.1 + - - +
527A SER 4.3 0.2 - - - -
537A TYR* 4.1 27.0 + - + -
546A PRO* 4.2 23.7 - - + +
547A LYS 3.7 10.3 - - - +
548A LEU* 3.9 22.9 - - + -
549A PHE* 4.7 0.2 - - - -
573A VAL* 3.6 0.5 - - - -
574A TYR* 2.9 41.8 + - + -
576A GLU* 3.7 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A VAL* 4.8 4.0 - - + -
524A PHE* 3.7 24.7 - - + -
525A LYS* 1.3 79.9 - - - +
527A SER* 1.3 67.7 - - - +
528A TYR* 5.1 2.0 - - + -
537A TYR* 3.4 7.5 - - - +
538A ILE* 3.0 57.6 + - + +
547A LYS 4.6 1.0 + - - -
549A PHE* 3.8 16.3 - - + -
563A PHE* 4.7 11.2 - - + -
566A ILE* 5.4 1.1 - - + -
571A VAL* 4.1 14.8 - - + -
572A ARG 3.4 7.2 - - - +
573A VAL* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A LYS 4.3 0.4 - - - -
526A VAL* 1.3 74.8 - - - +
528A TYR* 1.3 58.3 + - - +
535A TRP* 3.7 16.5 - - - +
536A GLU 3.0 17.0 - - - -
537A TYR* 3.6 26.4 - - - -
571A VAL* 3.5 5.0 - - - +
572A ARG* 2.7 46.6 + - - +
574A TYR* 3.2 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A VAL* 5.3 0.2 - - + -
527A SER* 1.3 78.0 - - - +
529A SER* 1.3 64.8 + - - +
534A ASP 4.2 0.2 - - - +
535A TRP* 3.6 4.2 - - - -
536A GLU* 2.7 74.5 + - + +
537A TYR 3.9 6.0 + - - -
538A ILE* 3.8 27.8 - - + -
566A ILE* 3.4 49.9 - - + +
567A PRO* 3.7 25.1 - - + -
568A ALA* 3.8 9.2 - - + -
570A TYR 3.2 13.2 - - - +
571A VAL* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A TYR* 1.3 78.9 - - - +
530A LEU* 1.3 62.9 + - - +
531A ASN* 3.2 2.9 + - - -
532A GLY* 2.9 26.7 + - - -
533A LYS 3.7 0.5 + - - -
534A ASP 2.9 23.4 + - - -
535A TRP* 3.6 25.8 - - - -
567A PRO 5.0 0.7 - - - -
568A ALA* 4.2 2.9 - - - +
569A GLN 2.9 23.2 + - - -
570A TYR* 3.0 16.0 + - - -
----------------------------------------------------------
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