Contacts of the strand formed by residues 520 - 538 (chain A) in PDB entry 2W77
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 GLN 520 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A TYR* 5.5 1.4 - - - -
488A LYS* 3.5 6.1 - - - +
489A SER* 3.1 42.7 + - - +
491A TRP* 3.6 27.6 - - + -
518A PRO* 3.4 3.9 + - - +
519A SER* 1.3 80.9 - - - +
521A TYR* 1.3 75.0 + - - +
522A ILE* 3.3 26.3 - - + +
559A LEU* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A GLY 3.6 11.0 - - - -
488A LYS* 3.9 27.2 + - + -
518A PRO* 3.5 36.6 - - + +
520A GLN* 1.3 84.6 - - - +
522A ILE* 1.3 63.4 + - - +
523A ASP* 5.2 0.2 - - - +
559A LEU* 3.0 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A TYR* 5.1 1.6 - - - +
485A TRP* 3.5 57.2 - - + -
486A GLU* 3.8 4.9 - - - +
487A GLY* 3.0 42.2 + - - +
488A LYS 4.4 0.4 - - - +
489A SER* 4.1 9.0 - - - +
520A GLN* 3.3 34.3 - - + +
521A TYR* 1.3 75.6 - - - +
523A ASP* 1.3 69.6 + - - +
524A ASP* 4.8 1.6 - - + -
559A LEU* 4.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A HIS* 2.9 30.6 + - - -
485A TRP 3.4 4.5 - - - -
486A GLU* 3.6 12.0 - - - +
521A TYR 4.0 1.2 + - - +
522A ILE* 1.3 78.0 - - - +
524A ASP* 1.3 60.7 + - - +
525A LYS* 4.6 12.1 - - - +
558A GLY* 3.3 8.5 - - - -
559A LEU* 3.2 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ARG* 4.5 3.1 + - - -
228A ASN* 5.1 1.6 + - - -
231A TYR* 2.6 33.7 + - - +
484A HIS* 3.3 3.5 - - - -
485A TRP* 2.8 59.0 + - + +
522A ILE* 4.8 1.8 - - + -
523A ASP* 1.3 77.7 - - - +
525A LYS* 1.3 63.7 + - - +
556A VAL* 3.9 20.5 - - - +
557A THR 3.6 7.4 - - - +
559A LEU 4.9 2.8 + - - -
560A ASN* 4.3 18.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
231A TYR* 4.0 0.2 - - - -
483A SER 3.4 6.7 - - - +
484A HIS* 3.6 40.1 + - + +
523A ASP* 4.6 10.5 - - - +
524A ASP* 1.3 74.5 - - - +
526A THR* 1.3 62.9 + - - +
555A ARG 3.8 0.7 - - - +
556A VAL* 3.4 3.2 - - - +
557A THR* 2.6 66.6 + - + +
558A GLY* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A THR* 4.5 12.3 - - + +
227A ARG* 3.7 10.6 - - - -
231A TYR* 2.8 25.5 + - - -
481A SER 3.8 0.7 - - - +
482A PHE* 3.5 3.8 - - - -
483A SER* 2.9 43.1 + - - +
525A LYS* 1.3 74.5 + - - +
527A ARG* 1.3 66.6 + - - +
528A GLN* 4.2 2.9 - - + +
554A TYR* 3.7 38.1 - - + +
555A ARG 3.5 6.1 - - - +
556A VAL* 4.2 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A SER 3.2 4.5 - - - +
482A PHE* 3.5 34.8 - - + -
526A THR* 1.3 79.1 - - - +
528A GLN* 1.3 60.3 + - - +
529A LEU* 3.8 32.3 - - - +
553A ASP* 3.3 29.8 + - - +
554A TYR* 3.5 1.4 - - - -
555A ARG* 2.8 60.0 + - + +
564A ARG* 3.1 33.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PRO* 6.1 0.2 - - - +
257A THR 3.9 9.4 - - - +
258A GLY* 4.6 3.2 - - - -
259A ALA* 3.2 28.9 + - - +
479A SER* 4.5 3.1 + - - +
480A ALA* 3.3 2.6 - - - -
481A SER* 2.8 56.7 + - - +
526A THR* 4.2 3.0 - - + +
527A ARG* 1.3 72.6 - - - +
529A LEU* 1.3 75.3 + - - +
530A GLY* 4.6 1.4 - - - +
550A ARG* 4.7 6.7 - - - +
552A VAL* 3.6 27.7 - - - +
553A ASP 3.5 2.2 + - - +
554A TYR* 3.4 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A SER 3.4 3.8 - - - +
480A ALA* 3.5 24.9 - - + -
482A PHE* 4.6 10.1 - - + -
527A ARG* 3.8 38.4 - - - +
528A GLN* 1.3 88.6 + - - +
530A GLY* 1.3 58.1 + - - +
551A VAL 4.1 0.4 - - - +
552A VAL* 3.5 2.8 - - - -
553A ASP* 2.9 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A THR* 3.1 7.4 + - - -
479A SER* 2.7 38.5 + - - +
528A GLN* 4.8 1.1 - - - -
529A LEU* 1.3 72.8 - - - +
531A SER* 1.3 58.8 + - - -
532A TYR* 5.1 0.4 - - - -
550A ARG* 3.8 26.2 - - - -
551A VAL 3.4 7.6 - - - -
552A VAL* 4.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLY 3.6 7.9 - - - -
478A THR* 3.1 21.3 + - - -
530A GLY* 1.3 70.0 + - - -
532A TYR* 1.3 60.1 + - - +
549A GLY 3.9 0.3 - - - +
550A ARG* 3.0 4.3 - - - +
551A VAL* 2.6 56.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR 5.7 0.9 - - - -
157A ARG* 3.6 16.0 + - + -
255A LEU* 4.1 11.9 - - + +
256A LEU* 4.1 20.9 - - + -
458A ASP* 3.2 24.7 + - - -
460A TYR* 3.6 19.8 - - + +
475A VAL* 4.7 14.4 - - + -
476A VAL* 3.5 6.8 - - - +
477A GLY* 2.9 58.4 + - - +
478A THR* 4.2 5.2 - - - -
479A SER* 4.8 1.1 - - - -
531A SER* 1.3 76.9 - - - +
533A MET* 1.3 66.7 - - - +
534A THR* 5.5 2.5 - - - -
549A GLY 3.1 11.9 - - - +
550A ARG* 3.3 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LEU* 4.2 23.6 - - + -
475A VAL 3.2 11.4 - - - +
476A VAL* 4.7 18.2 - - + -
532A TYR* 1.3 77.4 - - - +
534A THR* 1.3 63.8 + - - +
535A ALA* 5.2 1.8 - - + +
547A LEU 5.5 0.7 - - - +
548A GLY* 2.8 25.3 - - - -
549A GLY 2.9 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR* 3.9 29.6 + - + +
158A LEU* 4.5 4.3 - - + +
255A LEU* 3.3 29.5 - - - +
256A LEU* 5.7 0.3 - - - +
474A LEU* 3.5 4.1 - - - +
475A VAL* 3.0 44.8 + - - +
532A TYR* 5.5 3.0 - - - -
533A MET* 1.3 77.1 + - - +
535A ALA* 1.3 66.3 + - - +
546A PHE* 4.0 17.9 - - + -
547A LEU 3.7 9.0 - - - +
548A GLY* 4.0 1.5 - - - -
572A TYR* 4.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A PHE* 5.3 2.7 - - + -
473A GLU 3.6 7.2 - - - +
474A LEU* 3.9 17.5 - - + -
533A MET* 5.7 1.6 - - + -
534A THR* 1.3 77.6 - - - +
536A ARG* 1.3 62.0 + - - +
537A PHE* 4.0 26.0 - - + -
545A LEU 3.6 1.4 - - - +
546A PHE* 3.5 5.2 - - - -
547A LEU* 2.8 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLY* 2.8 35.1 + - - -
129A ALA 4.4 1.4 + - - -
130A THR* 3.9 26.9 + - - +
131A MET 5.1 0.4 - - - +
158A LEU* 3.8 19.5 - - + +
160A LEU* 3.9 22.4 - - - +
164A GLU* 4.1 16.5 + - - +
472A HIS* 3.2 21.6 - - - +
473A GLU* 2.9 32.2 + - + +
535A ALA* 1.3 73.0 - - - +
537A PHE* 1.3 60.8 + - - +
538A ASN* 3.9 1.1 + - - +
544A ASN* 3.2 28.2 + - + +
545A LEU 3.5 4.5 - - - +
546A PHE* 3.4 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A PHE* 3.9 24.5 - + - -
467A PHE* 5.1 13.0 - + + -
472A HIS* 3.4 24.5 - + + +
535A ALA* 4.1 24.5 - - + -
536A ARG* 1.3 73.7 - - - +
538A ASN* 1.3 60.2 + - - +
539A VAL* 3.3 16.6 + - + -
544A ASN* 3.2 8.6 - - - -
545A LEU* 2.8 50.0 + - + +
547A LEU* 4.5 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP* 2.7 34.0 + - - +
128A GLY 3.4 9.3 + - - -
129A ALA* 4.8 3.4 - - - -
130A THR* 4.4 4.9 + - - +
470A ARG* 2.2 57.9 + - - +
471A GLU 3.3 21.9 + - - +
472A HIS* 2.9 15.1 + - - +
536A ARG 3.9 1.6 + - - -
537A PHE* 1.3 70.3 - - - +
539A VAL* 1.3 56.3 + - - +
540A THR 3.5 6.2 + - - +
544A ASN* 2.6 29.7 + - - +
----------------------------------------------------------
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