Contacts of the strand formed by residues 337 - 341 (chain B) in PDB entry 4CKG
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 SER 337 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B VAL 4.9 1.6 - - - +
309B VAL* 5.0 2.2 - - - -
330B GLU* 4.0 9.9 + - - +
331B VAL 3.0 18.1 + - - -
332B VAL* 3.5 28.1 - - - +
336B LYS* 1.3 75.7 - - - +
338B CYS* 1.4 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LYS* 4.8 11.0 - - - -
288B PHE* 5.1 2.2 - - - -
308B VAL* 3.7 31.2 - - + -
309B VAL* 5.2 0.7 - - + -
330B GLU* 3.7 4.9 - - - -
331B VAL* 2.9 44.7 + - + +
337B SER* 1.4 76.8 + - - +
339B LEU* 1.4 74.8 + - - +
340B LEU* 4.0 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LYS* 4.0 10.3 - - - -
275B ARG* 4.0 25.0 + - + +
283B TRP* 3.7 28.3 - - + -
320B CYS* 5.1 5.2 - - - -
325B ARG* 5.3 4.5 - - + -
328B CYS* 5.0 8.7 - - + -
329B PHE 3.6 16.4 - - - +
330B GLU* 3.7 27.5 - - + +
338B CYS* 1.4 80.5 - - - +
340B LEU* 1.3 74.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.8 13.9 - - + -
273B PHE 3.2 13.7 - - - +
274B LYS* 4.3 3.1 - - + +
283B TRP* 4.7 2.9 - - - -
288B PHE* 3.4 41.7 - - + -
295B LEU* 4.6 11.2 - - + -
328B CYS* 3.4 7.3 - - - +
329B PHE* 2.9 70.2 + - + +
331B VAL* 3.8 23.6 - - + -
338B CYS* 4.0 10.1 - - - -
339B LEU* 1.3 84.0 - - - +
341B GLN* 1.4 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 2.8 42.1 + - - +
272B LEU* 3.9 5.6 - - - +
273B PHE* 2.9 42.0 + - + +
283B TRP* 3.4 20.8 - - + -
285B ARG* 5.3 0.2 + - - -
325B ARG* 2.8 35.5 + - - +
326B ARG* 3.0 34.3 + - - +
327B PHE* 3.9 7.8 - - - +
328B CYS* 4.1 4.7 - - + +
329B PHE* 4.8 1.1 - - - -
340B LEU* 1.4 75.5 - - - +
342B ALA* 1.3 67.0 + - - +
----------------------------------------------------------
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