Contacts of the strand formed by residues 302 - 308 (chain A) in PDB entry 4HXG
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 TRP 302 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 4.6 11.9 - + - -
282A GLY 3.2 23.7 + - - -
283A SER* 4.0 0.4 - - - +
284A VAL* 3.5 27.6 - - + -
301A HIS* 1.3 87.3 - - - +
303A ILE* 1.3 64.7 + - - +
304A MET* 3.4 32.6 + - + -
316A LYS* 3.6 1.7 - - - +
317A GLU* 2.8 35.0 + - + +
391A MET* 3.5 39.5 - - + -
392A TYR 4.8 1.1 - - - -
393A GLY* 4.4 0.2 - - - -
394A TYR 3.8 1.2 + - - +
395A TYR* 3.4 55.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLN* 4.9 2.4 - - - +
277A THR* 3.9 24.1 + - + +
284A VAL* 3.0 35.8 + - - +
286A LEU* 3.9 22.4 - - + +
297A ALA* 4.2 5.6 - - + +
301A HIS* 4.0 16.8 - - + +
302A TRP* 1.3 73.0 - - - +
304A MET* 1.3 62.3 + - - +
305A GLY 3.8 19.3 - - - +
306A PHE* 4.2 5.4 - - + -
314A TYR* 3.8 34.8 - - + -
315A LEU 3.4 3.1 - - - +
316A LYS* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLN* 3.7 9.0 - - - +
302A TRP* 3.7 42.6 - - + +
303A ILE* 1.3 73.2 - - - +
305A GLY* 1.3 57.2 + - - +
315A LEU* 2.9 22.7 + - + +
317A GLU* 3.7 42.6 - - + +
323A ALA* 4.4 7.2 - - + -
395A TYR* 5.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 3.8 17.5 - - - -
266A GLN* 3.7 15.9 - - - -
303A ILE* 3.3 4.0 - - - +
304A MET* 1.3 81.7 - - - +
306A PHE* 1.3 65.8 + - - -
314A TYR* 3.1 6.6 - - - +
315A LEU* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 3.7 11.1 - - - +
266A GLN* 3.7 50.5 + - + +
267A ALA* 4.1 1.6 - - - -
268A LYS* 3.0 45.4 + - + -
275A TYR* 3.6 35.2 - + + -
276A PHE* 3.9 4.9 - - - -
277A THR* 3.6 31.4 - - + -
286A LEU* 4.0 15.7 - - + -
303A ILE* 4.2 1.8 - - + -
305A GLY* 1.3 79.1 - - - +
307A ASP* 1.3 64.8 + - - +
308A ALA 5.5 0.2 - - - -
312A LEU* 4.7 4.5 - - + -
313A ILE 3.2 14.6 - - - +
314A TYR* 3.6 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO 3.8 15.5 - - - +
21A ARG* 3.4 17.8 - - - +
22A THR* 2.9 34.9 + - + +
23A ARG* 5.5 0.7 - - - -
268A LYS* 3.6 23.3 + - - +
306A PHE* 1.3 78.9 - - - +
308A ALA* 1.3 74.5 + - - +
312A LEU* 3.7 2.9 - - - +
313A ILE* 3.0 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 3.6 2.9 - - - -
268A LYS* 5.4 1.4 - - - +
270A ARG* 3.7 17.8 - - - +
275A TYR* 3.8 32.5 - - + +
306A PHE* 5.5 0.4 - - - -
307A ASP* 1.3 86.5 + - - +
309A ASP* 1.3 61.8 + - - +
311A ARG 2.9 15.7 - - - +
312A LEU* 3.7 17.9 - - + -
----------------------------------------------------------
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