Contacts of the strand formed by residues 371 - 375 (chain J) in PDB entry 6H25
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 HIS 371 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360J LEU* 3.8 22.2 - - + -
361J SER 4.9 0.2 - - - +
362J LYS* 3.8 33.6 - - + +
363J SER* 4.0 8.2 + - - +
365J ILE 5.0 4.8 + - - -
368J SER* 3.2 30.1 + - - -
369J ARG* 2.5 30.0 + - - +
370J ARG* 1.3 74.7 - - - +
372J LEU* 1.3 61.4 + - - +
384J ARG* 3.2 10.1 - - - +
385J ILE* 2.9 38.3 + - + +
387J THR* 4.1 7.6 - - + +
390J ALA* 3.5 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360J LEU* 3.4 5.4 - - - +
361J SER* 2.9 45.8 + - - +
363J SER 5.9 0.2 - - - +
371J HIS* 1.3 75.9 - - - +
373J PHE* 1.3 65.1 + - - +
374J THR* 5.3 4.9 - - + -
382J ARG* 4.1 22.4 - - + +
383J ILE 3.9 10.3 - - - +
384J ARG* 4.6 5.2 - - + +
411J TYR* 3.6 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 373 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356J TYR* 4.0 7.0 - - + -
357J CYS 3.9 5.8 - - - -
358J GLY* 3.5 45.1 - - - -
359J MET 3.1 21.1 - - - -
360J LEU* 4.3 10.1 - - + -
372J LEU* 1.3 74.9 - - - +
374J THR* 1.3 60.8 + - - +
375J PRO* 3.7 16.1 - - + +
382J ARG* 3.5 7.5 - - - +
383J ILE* 2.8 69.0 + - + +
385J ILE* 4.8 8.1 - - + -
398J ILE* 4.0 9.6 - - + -
400J VAL* 3.6 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 374 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358J GLY* 3.4 0.2 - - - -
359J MET* 2.9 37.3 + - - +
361J SER* 4.4 18.9 + - - +
372J LEU* 4.3 5.8 - - + -
373J PHE* 1.3 78.2 - - - +
375J PRO* 1.3 71.7 - - - +
382J ARG* 4.4 25.4 - - + +
919J GLN* 3.3 15.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 375 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356J TYR* 4.4 9.4 - - + -
357J CYS 3.2 11.2 - - - +
373J PHE* 3.7 23.5 - - + +
374J THR* 1.3 86.9 - - - +
376J ALA* 1.3 63.1 + - - +
377J ASP* 3.9 10.6 - - - +
378J LYS* 5.8 0.7 - - - +
380J ILE* 3.4 48.2 - - + +
381J PRO 4.3 6.5 - - - +
382J ARG* 4.5 5.6 - - + -
919J GLN* 2.6 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