Contacts of the strand formed by residues 578 - 590 (chain A) in PDB entry 2VWJ
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 GLU 578 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU* 3.4 5.7 - - - +
404A ASP* 2.8 44.0 + - + +
407A SER* 2.9 31.0 + - - +
460A ARG* 3.0 33.3 + - - -
464A LYS* 5.1 3.8 - - - -
487A LYS* 3.3 16.1 + - - -
564A LEU* 4.4 7.6 - - - -
576A GLU* 4.9 5.8 - - + +
577A LEU* 1.3 80.0 - - - +
579A TYR* 1.3 60.9 + - - +
580A GLU* 3.4 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A VAL* 3.8 28.8 - - + +
402A TYR 4.5 0.9 - - - -
403A LEU* 3.6 20.4 - - + -
557A LYS* 4.1 14.2 - - + +
560A ALA* 4.2 13.5 - - + -
561A LYS* 4.4 31.6 - - + -
564A LEU* 3.7 24.7 - - + +
578A GLU* 1.3 70.6 - - - +
580A GLU* 1.3 61.7 + - - +
581A GLY* 3.6 18.9 + - - -
582A PHE* 3.5 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A TYR* 3.1 36.9 + - + +
404A ASP* 3.3 37.9 - - + +
406A ARG* 4.0 9.4 + - - +
487A LYS* 3.4 18.1 + - - -
578A GLU* 3.4 8.6 + - - +
579A TYR* 1.3 76.4 - - - +
581A GLY* 1.3 54.1 + - - +
583A TYR* 4.6 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A VAL* 3.5 4.7 - - - +
402A TYR* 2.8 32.4 + - - +
579A TYR* 3.5 20.1 + - - -
580A GLU* 1.3 79.1 - - - +
582A PHE* 1.3 56.9 + - - -
583A TYR* 4.2 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ASN* 3.5 51.1 - - + -
400A ILE 3.3 14.6 - - - -
401A VAL* 3.9 13.9 - - + -
553A ALA* 3.7 13.0 - - + -
556A VAL* 4.4 4.7 - - + -
557A LYS* 3.6 26.9 - - + -
579A TYR* 3.5 15.0 - - + +
581A GLY* 1.3 73.4 - - - -
583A TYR* 1.3 79.1 + - - +
584A LYS* 4.3 2.9 - - + -
598A ASP* 4.2 10.7 - - - +
599A GLU* 3.4 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ASN* 3.5 2.6 - - - -
400A ILE* 2.7 53.6 + - + +
402A TYR* 3.9 25.9 - - + +
545A PHE* 4.2 22.2 - + - -
580A GLU 4.6 8.3 + - - -
581A GLY* 4.2 7.1 - - - -
582A PHE* 1.3 89.2 - - - +
584A LYS* 1.3 62.0 + - - +
585A ARG 3.5 4.2 + - - +
596A VAL* 3.6 37.0 - - + -
597A ILE 3.5 19.3 - - - +
598A ASP* 4.1 12.1 - - + +
604A THR* 4.6 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLU* 3.4 8.5 - - - +
399A ASN* 2.8 28.2 + - - +
582A PHE* 4.3 8.3 - - + -
583A TYR* 1.3 70.1 - - - +
585A ARG* 1.3 88.3 + - - +
597A ILE* 2.8 20.6 + - + +
598A ASP* 4.0 18.9 - - - +
599A GLU* 4.3 19.3 - - + +
601A ASP* 4.5 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 3.8 29.4 - - + -
397A TRP 3.0 22.0 - - - +
398A GLU* 2.9 34.7 + - + -
400A ILE* 3.8 9.2 - - - -
583A TYR* 4.2 1.7 - - - +
584A LYS* 1.3 108.4 + - - +
586A GLY* 1.3 57.6 + - - +
596A VAL* 3.6 2.9 - - - +
597A ILE* 3.0 31.3 + - + +
601A ASP* 5.9 0.4 + - - -
631A LEU* 3.0 26.2 + - - +
632A LYS* 3.2 23.0 + - - +
633A HIS* 4.9 1.8 - - - +
634A GLY* 4.0 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLY 4.0 0.2 - - - +
396A LEU* 3.5 6.0 - - - +
397A TRP* 3.1 27.9 + - - +
400A ILE* 3.5 9.2 - - - +
585A ARG* 1.3 79.5 - - - +
587A PHE* 1.3 61.5 + - - +
588A PHE* 3.9 10.7 - - - -
595A ALA 3.1 13.7 - - - -
596A VAL* 3.9 5.2 - - - -
631A LEU* 3.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLY 3.5 18.4 - - - +
396A LEU* 4.3 1.6 - - - -
586A GLY* 1.3 74.2 - - - +
588A PHE* 1.3 72.1 + - - +
589A VAL* 3.4 28.3 - - + -
594A TYR* 3.3 3.6 - - - +
595A ALA* 2.8 48.8 + - + +
608A LEU* 4.4 5.4 - - + -
627A LEU* 4.2 8.3 - - + -
630A ILE* 3.7 36.1 - - + -
631A LEU* 3.7 15.9 - - + -
744A ILE* 3.5 31.9 - - + -
747A ALA* 4.8 3.6 - - + -
748A PHE* 3.7 21.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A PRO* 3.8 23.1 - - + +
393A GLU 3.5 20.0 + - - +
394A ARG* 4.9 3.5 - - - -
395A GLY 4.6 1.4 + - - +
397A TRP* 4.5 7.6 - + - -
400A ILE* 4.0 13.0 - - + -
537A LEU* 3.8 25.6 - - + +
538A TYR* 3.4 23.8 - + + -
545A PHE* 3.5 50.9 - + + -
586A GLY 3.9 6.7 - - - -
587A PHE* 1.3 89.5 - - - +
589A VAL* 1.3 63.9 + - - +
590A THR 3.8 0.7 - - - -
593A LYS 3.7 0.2 - - - -
594A TYR* 3.3 27.4 - - + -
596A VAL* 3.9 14.8 - - + -
747A ALA* 5.2 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A PRO* 4.1 5.3 - - - +
587A PHE* 3.4 33.9 - - + -
588A PHE* 1.3 74.1 - - - +
590A THR* 1.3 74.1 + - + +
593A LYS* 2.8 23.8 + - + +
594A TYR* 4.8 0.2 - - - -
608A LEU* 4.1 19.1 - - + -
743A ARG* 3.7 47.2 + - + +
744A ILE* 4.6 0.4 - - - -
747A ALA* 4.4 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A GLU* 5.6 0.7 - - - -
392A PRO* 3.8 14.1 - - - +
538A TYR* 3.4 13.5 - - - -
589A VAL* 1.3 94.6 - - + +
591A LYS* 1.3 60.9 + - - +
592A LYS* 2.7 24.4 + - - +
593A LYS* 3.3 31.6 + - + +
743A ARG* 3.9 26.9 - - - +
----------------------------------------------------------
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