Contacts of the helix formed by residues 283 - 296 (chain A) in PDB entry 4XH9
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 ASP 283 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ILE 4.3 6.4 - - - +
280A LYS* 3.1 30.9 + - + +
281A LYS 3.3 0.2 - - - -
282A GLN* 1.3 83.0 - - + +
284A PRO* 1.3 68.2 - - - +
285A ARG* 3.0 23.9 + - - +
286A VAL* 3.2 25.4 + - + +
287A GLN* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLN 3.1 11.4 - - - +
283A ASP* 1.3 90.1 - - - +
285A ARG* 1.3 58.7 + - + +
287A GLN* 3.5 6.0 + - + +
288A ASP* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.0 22.4 + - - +
208A SER* 2.6 34.6 + - - -
209A ILE* 3.8 27.8 - - + +
283A ASP* 3.0 12.5 + - - +
284A PRO* 1.3 77.3 - - + +
286A VAL* 1.3 65.6 + - - +
288A ASP* 4.1 4.8 - - - +
289A PHE* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A MET* 5.1 5.8 - - - -
209A ILE* 3.7 29.2 - - + +
210A MET* 4.0 18.6 - - + -
277A LEU* 5.6 3.4 - - + -
280A LYS* 3.9 21.3 - - + +
283A ASP* 3.2 32.3 + - + +
285A ARG* 1.3 77.4 - - - +
287A GLN* 1.3 75.8 + - - +
289A PHE* 3.2 4.9 + - - +
290A LEU* 3.0 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU 4.7 1.4 - - - +
280A LYS* 2.9 19.9 - - - +
281A LYS* 3.3 39.7 - - - +
283A ASP 3.1 16.2 + - - +
284A PRO* 4.0 5.2 - - + +
286A VAL* 1.3 84.0 - - - +
288A ASP* 1.3 57.4 + - - +
290A LEU* 3.3 19.4 + - - +
291A GLN* 2.9 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PRO 2.9 18.8 + - - +
285A ARG* 4.1 5.2 - - - +
287A GLN* 1.3 74.4 - - - +
289A PHE* 1.3 61.4 + - - +
291A GLN* 3.3 10.7 + - - +
292A ARG* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ALA 3.5 22.4 - - - -
200A TYR* 4.0 12.1 - + - -
203A PRO* 3.8 23.8 - - + -
204A MET* 3.5 32.5 - - + -
207A LEU* 4.6 1.1 - - + -
209A ILE* 3.6 28.3 - - + -
285A ARG 3.2 18.3 + - - +
286A VAL 3.6 3.8 - - - +
288A ASP* 1.3 76.1 + - - +
290A LEU* 1.3 68.7 + - + +
292A ARG* 3.2 38.4 + - - +
293A CYS* 3.1 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A TYR* 4.5 9.6 - - + -
204A MET* 4.8 5.6 - - - -
277A LEU* 5.3 7.6 - - + -
286A VAL* 3.0 35.6 + - + +
287A GLN* 3.7 21.8 - - - +
289A PHE* 1.3 88.2 - - + +
291A GLN* 1.3 66.4 + - + +
293A CYS* 3.5 5.5 + - - +
294A LEU* 3.2 31.4 + - + +
304A LEU* 4.1 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLN* 2.9 25.7 + - + +
288A ASP* 3.5 16.2 - - - +
290A LEU* 1.3 75.9 - - - +
292A ARG* 1.3 65.4 + - - +
294A LEU* 3.1 24.1 + - - +
295A GLU* 3.1 29.4 + - - +
5B ARG* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PRO* 5.3 4.2 - - - +
207A LEU* 3.9 23.8 - - - +
288A ASP* 2.9 13.9 + - - +
289A PHE* 3.2 36.1 + - - +
291A GLN* 1.3 76.2 - - - +
293A CYS* 1.3 65.9 + - - +
295A GLU* 3.1 25.9 + - - +
296A SER* 3.4 17.9 + - - +
298A PHE* 6.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ALA 4.2 1.8 - - - -
200A TYR* 3.6 33.7 - - + +
289A PHE* 3.1 51.8 + - - -
290A LEU* 3.7 7.6 - - - +
291A GLN 3.2 0.2 - - - -
292A ARG* 1.3 78.9 - - - +
294A LEU* 1.3 61.2 + - + +
296A SER* 3.1 12.6 + - - +
298A PHE* 3.7 25.4 - - + -
299A SER* 2.8 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 3.2 18.3 + - + +
291A GLN* 3.1 23.9 + - - +
293A CYS* 1.3 79.7 - - + +
295A GLU* 1.3 60.1 + - - +
296A SER 3.5 1.7 + - - +
299A SER* 3.6 9.5 + - - -
301A LYS* 3.3 44.8 - - - +
302A LEU 3.5 21.8 - - - +
303A ASP* 3.8 16.4 - - + +
5B ARG* 3.7 42.4 + - - +
54B GLU* 5.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLN* 3.1 29.1 + - - +
292A ARG* 3.5 15.3 - - - +
293A CYS 3.1 0.6 - - - -
294A LEU* 1.3 76.9 - - - +
296A SER* 1.3 61.1 + - - +
297A PRO* 4.2 2.4 - - - +
5B ARG* 3.9 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG* 3.4 12.7 + - - +
293A CYS 3.1 3.7 + - - +
294A LEU 4.1 1.8 - - - +
295A GLU* 1.3 81.4 + - - +
297A PRO* 1.3 75.0 - - - +
298A PHE* 3.2 31.6 + - - -
299A SER* 3.0 20.3 + - - -
300A ARG 4.3 0.9 + - - -
301A LYS* 4.8 1.2 + - - +
----------------------------------------------------------
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