Contacts of the strand formed by residues 381 - 385 (chain K) in PDB entry 4DVQ
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 PHE 381 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K LEU* 4.7 7.4 - - + -
238K MET* 5.1 13.0 - - + -
239K PHE* 6.0 4.3 - + - -
379K GLY 3.5 0.6 - - - -
380K LEU* 1.3 89.2 - - + +
382K LEU* 1.3 71.6 + - - +
383K GLU* 3.5 28.5 - - + -
404K GLN* 3.7 20.9 - - + -
405K VAL 3.1 18.4 - - - +
406K PHE* 4.0 29.6 - + + -
407K LEU* 3.6 7.0 - - - -
485K TYR* 3.9 22.9 - + - -
487K PHE* 6.0 2.0 - + - -
602K 1CA 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K VAL* 4.9 0.9 - - + -
100K LEU* 5.9 0.9 - - + -
381K PHE* 1.3 78.3 - - - +
383K GLU* 1.3 63.7 + - - +
403K VAL 4.6 0.2 - - - -
404K GLN* 3.2 6.4 - - - -
405K VAL* 2.9 47.3 + - + +
407K LEU* 3.4 27.4 - - + -
441K VAL* 3.7 21.3 - - + +
444K GLY* 3.7 14.4 - - - -
445K PHE* 3.6 38.6 - - + -
601K HEM 3.6 34.8 - - + +
602K 1CA 4.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 383 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K LEU* 5.6 1.3 - - - +
109K CYS 4.3 2.5 - - - +
110K ARG* 3.9 21.5 + - + +
111K MET* 2.7 49.3 + - - +
381K PHE* 3.5 25.0 - - + +
382K LEU* 1.3 77.6 - - - +
384K ARG* 1.3 91.3 + - - +
402K LEU* 3.2 24.1 - - + +
403K VAL 3.6 3.6 - - - +
404K GLN* 3.5 13.7 - - + +
602K 1CA 4.7 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 384 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K LEU* 4.2 30.5 - - + +
104K ASP* 3.2 27.1 + - - +
108K PRO* 3.7 15.5 - - - +
109K CYS 3.4 14.4 - - - +
110K ARG* 4.3 5.6 - - - +
382K LEU* 5.2 0.2 - - - +
383K GLU* 1.3 103.4 + - - +
385K VAL* 1.3 65.4 + - - +
386K VAL* 3.6 5.9 + - + +
401K THR 3.4 1.7 - - - +
402K LEU* 3.5 4.6 - - - -
403K VAL* 2.9 35.8 + - - +
445K PHE* 3.3 35.4 + - + -
448K ARG* 3.5 17.2 - - - +
601K HEM 2.7 42.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 385 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K CYS* 3.0 33.8 + - + +
110K ARG* 3.8 24.2 - - - +
111K MET* 3.2 35.9 - - + +
384K ARG* 1.3 69.7 - - - +
386K VAL* 1.3 63.4 + - - +
387K SER* 3.6 2.4 + - - -
400K GLY* 4.0 27.6 - - - +
401K THR 3.6 5.6 - - - +
402K LEU* 4.1 2.7 - - + +
----------------------------------------------------------
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