Contacts of the strand formed by residues 335 - 342 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D VAL* 6.2 2.7 - - - -
552D LYS* 4.7 2.0 - - - +
300E PHE* 3.4 10.5 - - - -
304E SER* 6.4 2.2 - - - -
330E SER* 4.5 0.4 - - - -
331E SER 3.0 35.6 + - - -
332E SER 4.5 2.6 + - - -
333E ALA 3.4 2.2 - - - -
334E LEU* 1.3 79.6 - - - +
336E PHE* 1.3 65.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 336 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300E PHE* 3.8 1.3 - - - -
301E PRO* 3.4 19.9 - - - +
304E SER* 6.2 3.6 - - - -
307E TYR* 3.4 35.5 - + + +
329E GLU 3.9 3.1 - - - -
330E SER* 3.7 25.6 - - - +
335E GLY* 1.3 74.3 - - - -
337E GLY* 1.3 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 337 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E LEU 3.3 11.4 - - - -
300E PHE* 3.4 12.9 - - - -
301E PRO* 4.4 2.2 - - - -
307E TYR* 4.2 3.8 - - - -
328E PRO* 3.6 2.6 - - - +
329E GLU 2.7 45.5 + - - +
336E PHE* 1.3 75.4 - - - +
338E PHE* 1.3 71.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 338 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E GLY* 3.7 0.5 - - - -
299E LEU* 2.8 41.6 + - - +
300E PHE* 4.7 0.8 - - - -
307E TYR* 3.4 35.2 - + - -
310E PHE* 3.5 25.4 - + + -
311E ARG* 3.4 47.8 - - + -
314E LEU* 3.6 18.6 - - + -
326E TYR* 4.0 17.9 - + - -
327E GLU 3.3 6.3 - - - +
328E PRO* 3.7 31.0 - - + -
329E GLU* 4.4 4.0 - - - -
337E GLY* 1.3 72.8 - - - -
339E ARG* 1.3 60.7 + - - +
340E CYS* 3.8 11.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 339 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E TYR* 3.2 34.1 - - + +
297E ALA 4.0 9.2 - - - +
298E GLY* 4.5 1.1 - - - -
325E PHE* 3.5 28.1 - - - -
326E TYR* 3.2 2.8 - - - -
327E GLU* 2.7 69.7 + - - +
329E GLU* 3.5 32.1 - - + +
338E PHE* 1.3 71.4 - - - +
340E CYS* 1.3 62.1 + - - +
385E ASP* 3.3 34.8 + - - +
386E SER* 4.0 23.6 - - - +
389E LYS* 4.9 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 340 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E TYR* 3.2 9.7 - - - +
297E ALA 2.9 37.6 + - - +
299E LEU* 3.7 23.3 - - + -
314E LEU* 4.5 7.9 - - - -
324E LEU* 5.0 1.1 - - + -
325E PHE* 3.2 7.6 - - - +
326E TYR* 3.7 19.1 - - - -
338E PHE* 3.8 16.8 - - - -
339E ARG* 1.3 80.7 - - - +
341E GLY* 1.3 58.8 + - - +
342E PHE* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 341 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293E PRO* 3.7 17.9 - - - -
295E VAL 3.2 7.2 - - - -
296E TYR* 3.7 11.7 - - - -
323E SER 4.1 0.7 - - - +
324E LEU* 4.0 1.9 - - - +
325E PHE* 2.8 42.7 + - - +
340E CYS* 1.3 71.8 - - - +
342E PHE* 1.3 70.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 342 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293E PRO* 3.3 4.4 - - - +
294E GLN 2.8 28.8 + - - -
295E VAL* 2.7 27.8 + - + +
297E ALA* 4.5 7.6 - - + -
299E LEU* 4.2 15.7 - - + -
314E LEU* 6.5 0.2 - - + -
323E SER 5.0 1.8 - - - -
324E LEU* 4.2 10.5 - - + -
340E CYS* 3.6 33.4 - - + -
341E GLY* 1.3 78.1 - - - -
343E LEU* 1.3 55.6 + - - +
344E GLY 3.3 14.6 - - - +
347E HIS* 3.4 11.7 - + + -
348E MET* 3.6 48.5 - - + +
351E ILE* 3.8 39.3 - - + -
352E GLN* 5.6 1.1 - - + -
----------------------------------------------------------
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