Contacts of the strand formed by residues 579 - 587 (chain A) in PDB entry 3GVJ
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 579 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A HIS* 4.4 0.9 + - - -
549A ARG* 2.8 23.2 + - - +
550A GLU 4.9 0.2 - - - +
551A VAL* 3.6 20.2 - - + +
575A TYR 3.7 17.7 - - - +
576A GLU 3.4 13.8 + - - +
577A PRO 3.2 2.2 - - - +
578A ASP* 1.3 78.7 - - - +
580A SER* 1.3 63.2 + - - +
595A THR* 4.1 14.8 - - - +
596A ARG 3.1 10.1 - - - +
597A GLY* 5.3 0.2 - - - -
598A THR* 4.1 1.1 - - - +
604A GLY 5.9 1.8 - - - +
621A ARG* 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A HIS* 3.6 33.4 - - - -
549A ARG* 3.9 5.4 - - - -
551A VAL* 4.2 1.8 - - - +
579A ALA* 1.3 76.4 - - - +
581A GLU* 1.3 73.2 + - - +
582A PRO* 3.3 5.5 - - - +
595A THR* 4.0 2.3 - - - -
596A ARG* 2.9 49.7 + - - +
598A THR* 4.0 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLN* 3.0 25.4 + - - +
390A MET* 4.2 0.9 - - - +
525A GLU* 2.7 35.1 - - - +
527A HIS* 3.5 28.0 + - + +
542A HIS* 3.3 12.3 + - + +
580A SER* 1.3 83.9 - - - +
582A PRO* 1.3 75.1 - - - +
583A CYS* 3.6 1.4 + - - -
594A ILE 4.1 1.0 - - - +
596A ARG* 2.8 40.9 + - + -
630A THR* 3.5 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A HIS* 2.7 27.7 - - + +
528A SER* 3.3 7.6 - - - -
540A GLY* 4.0 4.4 - - - -
541A TYR* 3.5 36.8 - - - +
542A HIS* 4.5 0.2 - - + -
551A VAL* 4.0 10.8 - - + -
552A GLY 3.6 13.5 - - - +
580A SER 3.3 4.7 - - - +
581A GLU* 1.3 89.3 - - - +
583A CYS* 1.3 57.2 + - - +
584A ILE* 4.7 1.3 - - + -
593A LEU* 3.7 32.8 - - + -
594A ILE 3.3 9.0 - - - +
595A THR* 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASP* 3.6 20.2 - - - +
527A HIS* 3.8 16.2 - - - -
528A SER* 3.5 4.7 - - - -
581A GLU 4.6 0.2 - - - -
582A PRO* 1.3 72.8 - - - +
584A ILE* 1.3 59.9 + - - +
585A LYS* 5.4 0.7 - - - +
593A LEU* 3.3 4.9 - - - -
594A ILE 2.9 31.7 + - - +
630A THR* 4.1 5.6 - - - -
631A LEU 3.8 15.7 - - - +
632A PRO* 3.6 32.8 - - + -
633A PHE* 3.5 18.9 - - + +
705A GLY 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A SER* 2.9 20.2 + - - +
529A PHE 3.3 9.9 - - - +
530A ALA* 3.7 10.0 - - + +
538A ALA* 3.5 42.2 - - + +
539A MET 3.8 0.9 - - - -
540A GLY* 3.6 20.0 - - - +
553A LEU* 4.4 14.8 - - + -
582A PRO* 4.7 4.7 - - + -
583A CYS* 1.3 78.2 - - - +
585A LYS* 1.3 88.2 + - - +
591A LEU* 4.3 4.7 - - + -
592A TYR 3.3 4.5 - - - +
593A LEU* 3.6 33.9 - - + -
633A PHE* 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASP* 3.3 29.5 + - - -
528A SER* 3.5 1.4 + - - -
529A PHE 3.4 17.8 + - - +
530A ALA* 3.9 5.6 - - - +
583A CYS* 5.3 0.8 - - + +
584A ILE* 1.3 93.4 + - - +
586A TYR* 1.3 60.9 + - - +
587A TYR* 3.6 31.9 - - + +
590A VAL 3.8 0.7 - - - +
591A LEU* 3.5 6.2 - - - +
592A TYR* 2.8 34.3 + - - +
633A PHE* 3.7 39.4 + - + +
707A VAL 5.1 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ALA* 4.1 4.0 - - + +
531A THR 3.6 21.4 - - - +
532A ILE* 3.4 58.8 - - + +
585A LYS* 1.3 75.2 - - - +
587A TYR* 1.3 71.2 + - - +
588A ASP 5.3 0.4 - - - -
589A GLY* 3.4 40.4 - - - -
590A VAL 3.4 15.3 - - - -
591A LEU* 3.8 13.5 - - + -
610A SER 5.5 0.2 - - - -
611A ARG 6.4 0.4 - - - -
613A ILE* 4.8 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A LYS* 3.6 32.7 - - + +
586A TYR* 1.3 80.7 - - - +
588A ASP* 1.3 77.8 + - + +
589A GLY 3.1 2.7 - - - -
590A VAL* 2.9 25.8 + - - +
592A TYR* 4.3 12.7 + + + -
633A PHE* 4.9 2.0 - + - -
634A ALA* 3.4 17.5 - - - +
635A LYS* 3.2 67.4 + - + +
709A VAL* 5.4 0.9 - - - +
----------------------------------------------------------
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