Contacts of the strand formed by residues 335 - 342 (chain D) in PDB entry 3CB4
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 GLY 335 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D PHE* 3.6 5.1 - - - -
304D SER* 6.5 0.4 - - - -
330D SER* 3.5 2.8 - - - -
331D SER 2.9 38.1 + - - -
332D SER 4.9 2.0 - - - -
333D ALA 3.4 2.6 - - - -
334D LEU* 1.3 80.5 - - - +
336D PHE* 1.3 66.8 + - - -
337D GLY 3.6 1.2 + - - -
549E VAL* 6.3 2.0 - - - -
552E LYS* 5.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D PHE* 4.0 1.6 - - - -
301D PRO* 3.2 21.8 - - - +
304D SER* 6.1 6.8 - - - -
307D TYR* 3.2 37.7 - + + +
329D GLU 3.9 2.9 - - - -
330D SER* 3.7 25.1 - - - -
334D LEU 4.2 0.2 + - - -
335D GLY* 1.3 72.5 - - - -
337D GLY* 1.3 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D LEU 3.3 12.8 - - - -
300D PHE* 3.4 11.9 - - - -
301D PRO* 4.2 4.3 - - - -
307D TYR* 4.1 10.0 + - - -
328D PRO* 3.8 2.3 - - - +
329D GLU 2.8 33.8 + - - +
336D PHE* 1.3 74.3 - - - +
338D PHE* 1.3 73.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D GLY* 4.5 1.6 - - - -
299D LEU 2.8 39.4 + - - +
300D PHE* 4.4 1.2 - - - -
307D TYR* 3.4 35.9 - + - -
310D PHE* 3.5 17.7 - + + -
311D ARG* 3.5 44.9 - - + -
314D LEU* 3.5 21.1 - - + -
326D TYR* 4.0 22.4 - + + -
327D GLU 3.4 7.9 - - - +
328D PRO* 3.7 27.4 - - + -
329D GLU* 4.1 2.9 - - - +
337D GLY* 1.3 74.1 - - - -
339D ARG* 1.3 61.7 + - - +
340D CYS* 3.6 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D TYR* 3.3 32.7 - - + +
297D ALA 3.9 10.3 - - - +
298D GLY* 4.3 1.1 - - - -
325D PHE* 3.4 31.3 - - - -
326D TYR* 3.5 1.9 - - - -
327D GLU* 2.8 65.7 + - - +
329D GLU* 3.5 33.9 - - + +
338D PHE* 1.3 71.4 - - - +
340D CYS* 1.3 62.3 + - - +
369D THR* 5.9 0.2 - - - +
385D ASP* 3.2 37.6 + - - +
386D SER* 3.7 26.5 - - - +
389D LYS* 5.3 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D TYR* 3.1 13.0 - - - -
297D ALA 2.8 36.6 + - - +
299D LEU* 4.2 19.1 - - + -
314D LEU* 4.2 12.3 - - - -
324D LEU* 4.9 0.9 - - + -
325D PHE* 3.2 7.0 - - - +
326D TYR* 3.8 19.3 - - - -
338D PHE* 3.7 18.8 - - - -
339D ARG* 1.3 79.0 - - - +
341D GLY* 1.3 59.1 + - - +
342D PHE* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 341 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D PRO* 3.7 7.9 - - - -
295D VAL 3.2 7.9 - - - -
296D TYR* 3.7 13.5 - - - -
323D SER 3.8 3.8 - - - +
324D LEU* 3.9 0.7 - - - -
325D PHE* 2.7 46.5 + - - +
340D CYS* 1.3 74.6 - - - +
342D PHE* 1.3 69.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D PRO* 3.2 5.5 - - - +
294D GLN 2.7 31.8 + - - -
295D VAL* 2.8 23.9 + - + +
296D TYR* 5.0 0.9 - - - -
297D ALA* 4.6 8.3 - - + -
299D LEU* 4.7 10.5 - - + -
323D SER 5.0 1.8 - - - -
324D LEU* 4.1 8.1 - - + -
340D CYS* 3.6 34.3 - - + -
341D GLY* 1.3 79.2 - - - -
343D LEU* 1.3 54.8 + - - +
344D GLY 3.3 15.7 - - - +
347D HIS* 3.4 10.5 - + + -
348D MET* 3.5 45.8 - - + -
351D ILE* 3.6 46.0 - - + -
352D GLN* 6.0 0.4 - - + -
----------------------------------------------------------
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