Contacts of the strand formed by residues 610 - 619 (chain A) in PDB entry 4X61
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 LYS 610 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A MET* 6.3 0.4 - - + -
606A SER* 3.3 2.3 - - - -
607A ASN* 3.0 45.6 + - - +
608A SER 3.8 0.4 - - - -
609A LYS* 1.3 85.7 - - + +
611A VAL* 1.3 64.8 + - - +
612A TRP* 3.5 11.4 - - + -
629A THR 5.2 4.7 - - - -
630A GLY 5.7 1.2 + - - -
634A THR* 3.4 38.3 + - + +
635A ILE 3.3 14.1 - - - +
636A GLY* 4.2 2.7 - - - -
637A LEU* 4.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU* 3.5 33.0 - - + -
448A GLU* 4.1 9.6 - - + -
604A ARG* 3.8 28.0 - - + +
605A CYS 3.3 13.5 - - - +
606A SER* 3.8 13.2 - - - -
610A LYS* 1.3 79.2 - - - +
612A TRP* 1.3 66.2 + - - +
613A TYR* 6.3 1.1 - - + -
635A ILE* 2.7 44.1 + - + +
637A LEU* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ARG* 3.7 2.3 - - - +
605A CYS* 2.7 55.1 + - + +
606A SER* 3.7 19.5 - - - -
607A ASN* 3.8 14.8 - - + -
610A LYS* 3.5 29.6 - - + -
611A VAL* 1.3 84.1 - - - +
613A TYR* 1.3 74.1 + - - +
614A GLU* 2.8 30.5 + - + +
627A ASN* 4.0 0.9 - - - +
629A THR* 3.4 25.8 - - + -
630A GLY* 3.3 21.3 - - - +
633A TYR* 3.5 28.3 - - + +
634A THR* 3.9 11.7 - - + -
635A ILE* 4.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PHE* 3.6 23.9 - + + -
442A ASP* 2.7 26.2 + - - -
443A ASN* 3.3 34.3 + - + +
501A PRO* 5.0 1.1 - - + -
519A PHE* 4.1 17.3 - + - -
582A ILE* 5.9 0.2 - - + -
584A PHE* 3.8 30.7 - + + -
602A PHE* 4.7 5.8 - + + -
603A TRP 3.2 12.6 - - - +
604A ARG* 3.7 26.7 - - + -
611A VAL* 6.3 0.9 - - + -
612A TRP* 1.3 78.0 - - - +
614A GLU* 1.3 62.9 + - - +
615A TRP* 3.7 10.6 - - + -
627A ASN* 3.1 26.2 + - - +
633A TYR* 3.1 30.3 - - + -
635A ILE* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A PHE* 3.5 1.9 - - - -
603A TRP* 2.7 53.4 + - + +
605A CYS* 3.5 16.4 - - - -
612A TRP* 2.8 30.4 + - - +
613A TYR* 1.3 71.9 - - - +
615A TRP* 1.3 63.2 + - - +
625A ILE* 4.2 10.7 - - + +
626A HIS 3.4 10.1 - - - +
627A ASN 3.3 15.9 - - - +
628A PRO* 3.8 9.7 - - - +
629A THR* 3.0 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A PHE 3.7 20.0 - - - -
499A GLU* 3.5 25.1 - - - -
500A MET* 3.6 7.0 - - - -
501A PRO* 4.9 2.7 - - + -
551A PHE* 5.6 1.8 - + - -
584A PHE* 3.7 40.9 - + + +
585A PRO* 2.9 25.4 + - + -
586A ILE* 4.3 12.3 - - + +
600A VAL* 5.0 2.9 - - + -
601A ARG 3.2 12.3 - - - +
602A PHE* 3.6 28.9 - + + -
603A TRP* 3.9 5.1 - - - -
613A TYR* 3.7 19.3 - - + -
614A GLU* 1.3 84.2 - - - +
616A ALA* 1.3 66.1 + - - +
617A VAL* 6.0 0.2 - - + -
625A ILE* 3.6 0.9 - - - +
626A HIS* 2.7 58.5 + + + +
627A ASN* 4.1 8.7 - - + -
633A TYR* 4.9 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A VAL* 3.4 5.9 - - - +
601A ARG* 2.8 37.8 + - + +
603A TRP* 3.9 16.8 - - + -
615A TRP* 1.3 79.7 - - - +
617A VAL* 1.3 67.9 + - - +
618A THR* 5.1 4.5 - - + -
623A SER* 3.6 12.3 - - - +
624A ALA 4.2 1.1 - - - +
625A ILE* 4.1 20.9 - - + +
626A HIS* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A LEU* 4.3 13.9 - - + -
551A PHE* 3.8 31.2 - - + -
586A ILE* 4.3 14.4 - - + -
590A ILE* 3.8 19.3 - - + -
598A ILE* 4.6 2.0 - - + -
599A CYS 3.4 6.7 - - - +
600A VAL* 4.5 1.1 - - + -
615A TRP* 6.0 0.2 - - + -
616A ALA* 1.3 76.4 - - - +
618A THR* 1.3 63.9 + - - +
619A ALA 3.4 22.0 - - - +
620A PRO* 5.0 1.3 - - + -
621A VAL 3.5 10.1 - - - +
622A CYS* 3.0 5.0 - - - +
623A SER* 2.7 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A CYS* 2.8 37.7 + - - +
601A ARG* 3.2 39.1 + - + +
616A ALA* 5.0 5.6 - - + +
617A VAL* 1.3 77.0 - - - +
619A ALA* 1.3 61.2 + - - +
620A PRO 4.4 1.2 - - - +
621A VAL* 3.2 13.4 - - - +
622A CYS* 3.8 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A GLU* 6.1 0.2 - - - +
597A THR* 3.5 12.6 - - + +
598A ILE* 3.3 2.8 - - - -
599A CYS* 2.9 38.4 + - + -
617A VAL* 3.4 10.2 - - - +
618A THR* 1.3 81.5 + - - +
620A PRO* 1.3 72.0 - - + +
621A VAL 3.2 4.6 + - - -
----------------------------------------------------------
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