Contacts of the strand formed by residues 305 - 310 (chain A) in PDB entry 4ZCH
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 CYS 305 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ILE* 4.3 4.5 - - + -
292A LEU* 3.5 31.2 - - - -
303A GLN 3.8 7.0 - - - -
304A ASP* 1.3 76.7 - - - +
306A LEU* 1.3 63.0 + - - +
331A PHE* 3.5 31.9 - - + -
332A LYS* 3.5 1.7 - - - +
333A ARG* 2.8 45.8 + - - +
337A LEU* 3.8 7.1 - - - +
440A ALA 3.2 16.4 - - - +
441A LEU* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A CYS* 1.3 75.5 - - - +
307A GLN* 1.3 63.0 + - - +
308A LEU* 3.8 31.6 - - + -
329A LEU* 4.1 8.3 - - + -
331A PHE* 3.4 12.1 - - - +
332A LYS* 3.7 27.6 - - + -
337A LEU* 3.8 17.2 - - + +
338A GLU* 3.7 9.4 - - - -
339A GLU* 3.7 27.6 - - + +
344A ILE* 4.1 20.6 - - + -
355A TYR* 4.5 0.8 + - - -
439A GLY* 3.2 2.8 - - - -
440A ALA* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 4.0 12.4 - - - -
257A GLY* 3.9 2.8 - - - -
258A ILE 2.9 38.5 + - - +
306A LEU* 1.3 74.0 - - - +
308A LEU* 1.3 76.4 + - - +
309A ILE* 4.8 5.2 - - - +
329A LEU* 4.0 1.4 - - - +
330A SER* 2.9 45.0 + - - -
331A PHE* 2.9 33.4 + - + +
355A TYR* 2.9 32.1 + - + +
437A PHE* 4.9 3.3 - - + -
438A PHE 3.5 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU* 3.8 16.4 - - + -
307A GLN* 1.3 80.3 - - - +
309A ILE* 1.3 65.0 + - - +
327A TRP* 3.9 39.5 - - + -
328A LEU 3.4 15.7 - - - +
329A LEU* 4.0 9.9 - - + -
330A SER 4.0 0.2 - - - +
339A GLU* 3.6 31.0 - - + -
342A ASN 4.9 0.4 - - - +
343A LYS 4.7 4.7 - - - -
344A ILE* 3.7 26.0 - - + -
437A PHE* 3.3 7.3 - - - +
438A PHE* 2.7 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 6.3 1.3 - - + -
307A GLN* 4.8 4.9 - - - +
308A LEU* 1.3 80.7 - - - +
310A ALA* 1.3 64.0 + - - +
327A TRP* 3.6 5.3 - - - -
328A LEU* 2.8 65.0 + - + +
329A LEU 4.9 0.2 - - - +
330A SER* 3.8 28.9 - - - +
433A GLY* 3.3 34.3 - - - +
436A THR 3.8 3.6 - - - -
437A PHE* 3.9 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ILE* 1.3 77.3 - - - +
311A ASP* 1.3 59.7 + - - +
312A SER* 3.6 2.0 + - - -
325A VAL* 3.8 8.7 - - + -
326A PRO 3.4 7.2 - - - -
327A TRP* 3.6 5.4 - - - -
328A LEU* 4.6 2.3 - - - +
431A LEU* 3.5 39.5 - - + +
432A ASP 4.3 0.9 - - - +
433A GLY* 4.2 8.2 + - - -
436A THR* 3.0 35.6 + - + +
----------------------------------------------------------
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