Contacts of the helix formed by residues 317 - 326 (chain A) in PDB entry 4X4W
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 LEU 317 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP* 3.0 12.4 + - - +
316A PRO* 1.3 79.3 - - - +
318A LYS* 1.3 65.0 + - - +
319A PRO* 3.3 2.2 - - - -
320A TYR* 2.9 27.9 + - + +
321A GLN* 3.0 28.3 + - + +
340A LEU* 4.3 2.9 - - + -
348A LEU* 4.0 38.6 - - + +
351A GLU* 4.1 29.6 - - + +
352A MET* 3.4 38.1 - - + +
355A TRP* 5.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ALA* 5.3 1.8 - - + -
313A SER* 5.5 1.3 - - - +
315A ASP* 3.0 29.3 + - + +
317A LEU* 1.3 76.2 - - - +
319A PRO* 1.4 69.4 - - + +
320A TYR 3.1 0.2 + - - -
321A GLN* 3.1 11.0 + - - +
322A ASP* 2.8 55.2 + - - +
390A LYS* 2.9 42.3 - - - +
391A LYS* 4.5 9.2 - - - +
393A GLY* 4.2 13.7 - - - +
394A TYR* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.5 22.5 - - + +
308A ILE 3.4 26.2 - - - +
310A ALA* 3.9 18.4 - - + +
316A PRO 3.5 14.4 - - - +
317A LEU 3.5 1.3 - - - -
318A LYS* 1.4 93.0 - - + +
320A TYR* 1.3 60.0 + - + +
322A ASP* 3.6 11.0 + - + +
323A PHE* 3.1 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.6 33.0 - - + -
308A ILE* 3.3 17.9 - - - -
309A LYS* 3.4 28.4 + - + -
316A PRO 4.3 0.9 - - - -
317A LEU* 2.9 25.8 + - + +
319A PRO* 1.3 77.3 - - + +
321A GLN* 1.3 65.8 + - - +
323A PHE* 3.2 5.7 + - - +
324A ILE* 3.0 26.0 + - - +
336A VAL* 3.9 21.2 - - + +
339A LEU* 4.2 7.0 - - + -
340A LEU* 3.4 23.4 - - + +
343A GLN* 2.6 29.1 + - - -
345A GLU* 4.4 5.7 + - - +
348A LEU* 4.2 3.6 - - + -
352A MET* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP* 2.6 35.5 + - - +
317A LEU* 3.0 32.3 + - + +
318A LYS* 3.3 11.3 - - - +
320A TYR* 1.3 73.0 - - - +
322A ASP* 1.3 53.2 + - - +
324A ILE* 3.1 4.4 + - - +
325A ILE* 2.8 37.9 + - - +
352A MET* 4.1 5.4 - - + -
355A TRP* 3.3 59.1 - - + +
393A GLY 4.0 10.2 + - - +
394A TYR* 3.9 12.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS* 2.8 53.5 + - - +
319A PRO* 3.7 8.9 - - + +
321A GLN* 1.3 68.9 - - - +
323A PHE* 1.3 68.8 + - - +
325A ILE* 3.9 0.2 - - - -
326A ASP* 2.9 38.9 + - - +
390A LYS* 3.9 9.5 - - - +
394A TYR* 2.4 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PHE* 3.2 34.8 - + - -
303A ASN* 5.0 7.6 - - - -
307A LEU* 4.2 22.4 - - + -
319A PRO 3.1 11.9 + - - +
320A TYR* 3.2 8.0 + - - +
322A ASP* 1.3 79.9 - - - +
324A ILE* 1.3 64.7 + - - +
326A ASP* 3.6 4.1 + - - +
327A SER 3.1 40.5 + - - -
332A ALA* 4.0 12.6 - - + -
335A ARG* 4.4 9.9 - - - -
336A VAL* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR 3.0 15.2 + - - +
321A GLN 3.1 6.9 + - - +
323A PHE* 1.3 76.8 - - - +
325A ILE* 1.3 66.7 + - - +
327A SER* 3.1 13.9 + - - -
332A ALA* 4.3 12.9 - - + +
333A THR* 3.6 34.1 - - + +
336A VAL* 3.9 18.6 - - + -
352A MET* 3.4 34.3 - - + -
355A TRP* 4.2 9.4 - - + -
357A ILE* 3.8 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLN 2.8 16.6 + - - +
322A ASP 4.1 2.2 - - - +
324A ILE* 1.3 74.0 - - - +
326A ASP* 1.3 69.2 + - - +
327A SER* 3.2 4.9 + - - -
355A TRP* 3.8 18.2 - - + -
357A ILE* 4.2 16.6 - - + -
358A PRO* 4.6 4.9 - - + +
389A TRP* 4.4 14.6 - - + -
394A TYR* 3.2 58.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASP* 2.9 26.8 + - - +
323A PHE* 4.1 4.0 - - - +
325A ILE* 1.3 86.0 - - - +
327A SER* 1.3 68.7 + - - +
390A LYS* 4.2 18.5 + - - -
394A TYR* 5.0 1.6 + - - -
----------------------------------------------------------
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