Contacts of the strand formed by residues 615 - 621 (chain B) in PDB entry 2H5G
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 LEU 615 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B CYS* 3.8 7.4 - - - +
585B HIS 3.9 1.3 - - - -
586B MSE 3.4 26.9 - - + +
601B VAL* 3.9 32.1 - - + +
604B SER* 2.8 37.4 + - - +
605B LYS* 2.7 41.3 + - + +
613B ASN 3.5 2.2 + - - -
614B ALA* 1.3 70.1 - - - +
616B GLU* 1.3 57.5 + - - +
617B THR 3.2 28.9 - - - +
618B LEU* 4.1 9.9 - - + +
673B LEU* 3.8 18.2 - - + -
725B THR* 3.6 5.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B GLY 3.5 22.8 - - - +
583B ILE* 4.2 5.6 - - + -
584B CYS 2.9 15.2 + - - +
605B LYS* 3.5 8.7 + - - +
609B PRO 4.4 0.3 - - - +
611B ALA 4.9 1.2 - - - +
614B ALA* 3.6 14.6 - - - +
615B LEU* 1.3 80.2 - - - +
617B THR* 1.3 64.4 + - - +
666B THR 3.7 13.5 - - - +
667B GLU* 3.4 16.2 - - - +
668B TYR* 2.8 45.4 + - - +
669B GLY* 3.4 17.7 + - - -
673B LEU* 3.5 7.4 - - - +
674B CYS* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 617 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B ILE* 4.9 2.8 - - - +
584B CYS 3.2 5.0 + - - -
585B HIS* 3.2 34.0 + - + +
586B MSE 3.2 22.3 + - - -
615B LEU* 3.2 4.9 - - - +
616B GLU* 1.3 83.8 + - - +
618B LEU* 1.3 63.4 + - - +
619B LEU* 3.7 21.2 + - + -
664B LEU* 4.3 13.8 + - + +
666B THR 5.2 2.3 + - - -
668B TYR* 5.6 0.3 - - - -
674B CYS* 3.3 29.4 - - - +
676B GLU* 4.6 0.9 - - + -
687B HIS* 3.9 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B MSE 3.5 24.7 - - + +
588B VAL* 3.7 21.3 - - + -
601B VAL* 3.9 26.0 - - + -
615B LEU* 4.3 5.6 - - + -
617B THR* 1.3 72.1 - - - +
619B LEU* 1.3 60.0 + - - +
620B ILE* 3.7 25.5 + - + -
633B ILE* 4.1 25.8 - - + -
673B LEU* 3.8 14.5 - - + +
674B CYS 2.7 12.6 + - - +
675B ILE* 3.4 17.8 - - + +
676B GLU 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 619 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B HIS* 4.0 11.7 - - + -
586B MSE 2.9 14.2 + - - +
587B TYR* 3.4 15.1 - - + -
588B VAL* 2.7 32.1 + - - +
617B THR* 3.7 11.4 - - + -
618B LEU* 1.3 72.5 - - - +
620B ILE* 1.3 59.9 + - - +
676B GLU* 3.2 11.4 - - + +
678B VAL* 4.0 15.3 - - + -
684B ALA* 3.8 28.9 - - + +
687B HIS* 3.7 46.9 - - + +
688B ILE* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 620 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B VAL* 4.0 11.4 - - + -
618B LEU* 3.7 25.6 - - + -
619B LEU* 1.3 80.6 - - - +
621B HIS* 1.4 73.5 + - - +
624B LEU* 4.2 13.0 - - + -
625B LEU* 4.2 8.1 - - + -
629B LEU* 6.5 0.2 - - + -
630B PHE* 3.4 44.0 - - + -
633B ILE* 5.1 5.2 - - + -
675B ILE* 3.4 26.7 - - + -
676B GLU 2.8 11.4 + - - +
677B VAL* 3.1 12.5 - - + +
678B VAL* 2.7 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 621 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B TYR* 3.4 21.4 + - - +
588B VAL 3.2 20.9 + - - +
589B ASP* 5.0 0.7 - - - -
590B SER* 3.6 35.8 + - - +
620B ILE* 1.4 74.2 - - - +
622B ARG* 1.3 85.0 + - + +
623B ASP* 3.3 38.2 + - + -
624B LEU* 3.0 20.9 + - + +
625B LEU* 3.5 7.3 - - - +
678B VAL* 3.6 6.5 - - - -
679B ASP 3.2 25.1 + - - -
680B ASN* 3.9 11.2 - - + -
681B VAL* 6.4 0.2 - - + -
----------------------------------------------------------
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