Contacts of the strand formed by residues 337 - 341 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D VAL 4.9 1.6 - - - +
309D VAL* 4.9 2.0 - - - -
330D GLU* 4.0 10.6 + - - +
331D VAL 3.0 17.6 + - - -
332D VAL* 3.5 28.2 - - - +
333D SER 5.3 0.2 - - - -
336D LYS* 1.3 76.2 - - - +
338D CYS* 1.4 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D LYS* 4.8 11.2 - - - -
275D ARG 6.1 0.2 - - - -
288D PHE* 5.1 2.2 - - - -
308D VAL* 3.7 31.9 - - + +
309D VAL* 5.2 0.7 - - + -
330D GLU* 3.7 4.1 - - - -
331D VAL* 2.9 45.7 + - + +
337D SER* 1.4 77.2 + - - +
339D LEU* 1.4 74.5 + - - +
340D LEU* 4.0 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D LYS* 4.0 10.5 - - - +
275D ARG* 4.0 25.4 + - + +
283D TRP* 3.7 28.3 - - + -
320D CYS* 5.1 5.2 - - - -
325D ARG* 5.3 5.2 - - + -
328D CYS* 5.0 8.1 - - + -
329D PHE 3.6 15.9 - - - +
330D GLU* 3.7 28.8 - - + +
338D CYS* 1.4 81.0 - - - +
340D LEU* 1.3 74.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D LEU* 3.8 14.4 - - + -
273D PHE 3.2 13.0 - - - +
274D LYS* 4.3 2.2 - - + +
283D TRP* 4.7 3.4 - - - -
288D PHE* 3.4 41.7 - - + -
295D LEU* 4.6 11.0 - - + -
328D CYS* 3.4 7.3 - - - +
329D PHE* 2.9 69.6 + - + +
331D VAL* 3.8 24.2 - - + -
338D CYS* 4.0 10.8 - - - -
339D LEU* 1.3 84.8 - - - +
341D GLN* 1.4 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 341 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ASN 4.9 0.2 + - - -
142C ALA* 2.8 42.4 + - - +
272D LEU* 3.9 5.9 - - - +
273D PHE* 2.9 40.5 + - + +
283D TRP* 3.4 21.4 - - + -
325D ARG* 2.8 35.9 + - - +
326D ARG* 3.0 33.4 + - - +
327D PHE* 3.9 7.8 - - - +
328D CYS* 4.5 4.0 - - + +
329D PHE* 4.8 1.1 - - - -
340D LEU* 1.4 76.6 - - - +
342D ALA* 1.3 65.6 + - - +
----------------------------------------------------------
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