Contacts of the strand formed by residues 620 - 625 (chain A) in PDB entry 5H65
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 ILE 620 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU 5.9 1.3 - - - +
354A GLN 3.6 23.8 - - - +
355A LYS* 4.2 4.0 - - + -
356A ALA* 3.8 22.9 - - + +
609A SER* 3.8 5.6 - - - -
610A TYR 3.6 8.7 - - - +
611A ASN* 3.9 17.3 - - - +
619A GLN* 1.3 77.1 + - - +
621A CYS* 1.3 74.1 + - - +
622A TYR* 3.7 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A GLU 5.4 0.4 - - - -
558A TYR* 4.2 13.0 - - + -
609A SER* 3.4 4.5 - - - -
610A TYR* 3.0 61.8 + - + +
612A VAL* 4.8 7.2 - - - -
619A GLN* 3.8 14.5 + - - -
620A ILE* 1.3 76.7 - - - +
622A TYR* 1.3 66.7 + - - +
312B MET* 3.6 35.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ILE* 3.5 30.8 + - + -
352A LEU* 3.9 22.2 + - + +
354A GLN 5.1 0.7 + - - -
360A TYR* 5.4 0.7 - + - -
555A LEU* 3.7 34.8 - - + -
556A GLU 3.6 23.1 + - - +
557A ALA* 3.5 4.2 - - + -
558A TYR* 2.9 30.9 + - - -
607A ILE* 4.2 13.5 - - + -
608A LYS 3.3 7.0 - - - +
609A SER* 3.6 29.8 - - - -
610A TYR* 3.8 1.6 - - - -
620A ILE* 3.7 32.3 - - + +
621A CYS* 1.3 74.6 - - - +
623A GLN* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ALA* 4.5 0.6 - - - +
558A TYR* 3.4 18.4 - - + +
560A MET* 4.1 29.2 + - - +
607A ILE* 3.3 4.1 - - - -
608A LYS* 2.9 50.8 + - + +
610A TYR* 3.7 15.7 + - + -
622A TYR* 1.3 77.6 - - - +
624A ILE* 1.3 77.5 + - - +
313B LEU* 3.9 11.8 - - - +
314B CYS* 3.0 46.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A PHE* 3.5 37.7 - - + -
548A LEU* 5.1 2.5 - - + -
557A ALA* 4.5 8.5 - - + -
558A TYR 2.9 18.5 + - - +
559A LEU* 4.4 14.6 - - + +
560A MET 5.3 4.9 + - - +
565A PHE* 4.3 14.6 - - + -
603A LEU* 4.9 6.5 - - + -
605A CYS* 4.5 6.3 - - + -
606A PHE 3.4 7.9 - - - +
607A ILE* 3.9 16.6 - - + -
623A GLN* 1.3 86.7 + - - +
625A PHE* 1.3 65.4 + - - +
627A THR* 3.6 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLN* 3.4 43.3 - - + -
606A PHE* 3.3 47.1 + + + +
607A ILE 3.5 18.6 - - - -
608A LYS* 3.6 36.3 - - + +
623A GLN 4.1 1.1 - - - +
624A ILE* 1.3 75.6 - - - +
626A ASP* 1.3 85.7 + - + +
627A THR* 2.7 26.4 + - - -
----------------------------------------------------------
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