Contacts of the helix formed by residues 318 - 328 (chain A) in PDB entry 5HOO
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 318 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ALA 4.5 3.5 - - - +
317A LYS* 1.3 81.0 - - - +
319A ASP* 1.3 65.6 + - - +
320A GLU* 3.8 26.9 - - + +
321A PHE* 3.5 17.9 - - + +
322A TYR* 3.4 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLN 4.1 2.0 - - - +
200A SER* 4.0 21.0 - - - +
317A LYS 5.1 0.7 - - - +
318A ASP* 1.3 72.2 - - - +
320A GLU* 1.3 59.7 + - + +
321A PHE 3.0 4.0 - - - -
322A TYR* 2.9 25.3 + - - +
323A TRP* 3.2 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASP* 4.1 19.8 - - + +
319A ASP* 1.3 78.8 - - + +
321A PHE* 1.3 56.3 + - - +
323A TRP* 4.1 12.2 - - + +
324A ARG* 3.0 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A HIS* 3.1 52.5 + + - -
287A LEU* 4.5 7.4 - - + -
290A SER* 3.7 34.3 - - - -
317A LYS* 3.3 49.1 - - + -
318A ASP* 3.5 23.1 + - + +
319A ASP 2.9 1.0 + - - -
320A GLU* 1.3 76.2 - - - +
322A TYR* 1.3 73.0 + + - +
324A ARG* 3.2 21.1 + - - +
325A GLY 3.3 1.2 + - - -
5E G 5.4 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TRP* 3.6 35.0 - + + -
198A ASP 4.1 2.9 - - - +
199A GLN 3.5 13.9 - - - +
200A SER 3.8 5.4 - - - -
201A GLY* 3.6 21.1 - - - -
202A VAL* 3.8 24.1 + - + +
286A HIS* 4.6 0.4 - - - -
287A LEU* 4.4 5.4 - - + -
314A PHE* 3.0 32.3 + - - +
317A LYS* 3.0 40.4 + - - -
318A ASP 3.4 26.0 - - - -
319A ASP* 2.9 7.1 + - - +
321A PHE* 1.3 78.8 - + - +
323A TRP* 1.3 67.3 + - - +
325A GLY 3.1 11.1 + - - -
326A ILE* 3.2 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A HIS* 4.6 3.2 + - - -
199A GLN* 3.1 48.2 + - - +
319A ASP 3.2 11.7 + - - +
320A GLU* 4.1 11.9 - - + +
322A TYR* 1.3 77.6 - - - +
324A ARG* 1.3 86.4 + - + +
326A ILE* 3.2 3.3 + - - +
327A HIS* 2.9 75.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A HIS* 4.2 15.7 - - + +
320A GLU* 3.0 28.5 + - - +
321A PHE* 3.5 10.6 - - - +
322A TYR 3.1 1.4 + - - -
323A TRP* 1.3 94.8 - - + +
325A GLY* 1.3 58.2 + - - +
327A HIS* 3.4 1.7 + - - +
328A LYS* 2.9 37.2 + - + +
4E G 3.2 40.9 + - - -
5E G 4.0 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TRP* 4.8 4.3 - - - -
282A PRO* 4.4 1.2 - - - +
285A TYR* 2.9 27.6 + - - -
286A HIS* 3.4 35.2 - - - -
321A PHE 3.3 4.2 + - - -
322A TYR 3.1 6.8 + - - -
324A ARG* 1.3 75.7 - - - +
326A ILE* 1.3 64.6 + - - +
328A LYS* 3.6 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 3.7 33.6 - - + +
152A ILE* 4.3 20.6 - - + -
154A THR* 4.3 9.6 - - - +
197A TRP* 3.6 35.0 - - + +
198A ASP 4.7 1.1 - - - -
199A GLN* 3.8 27.4 - - + +
282A PRO* 4.2 10.5 - - + -
322A TYR 3.2 14.0 + - - +
323A TRP 3.2 5.3 + - - +
325A GLY* 1.3 75.4 - - - +
327A HIS* 1.3 59.8 + - + +
329A LEU* 3.1 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 5.3 6.0 + - - -
147A SER* 4.2 9.0 - - - -
149A LEU* 3.9 23.9 - - + +
150A HIS* 3.4 27.1 + + - -
199A GLN* 3.0 26.0 + - - -
323A TRP* 2.9 64.8 + + + +
324A ARG 3.7 2.7 - - - +
326A ILE* 1.3 78.9 - - + +
328A LYS* 1.3 55.7 + - - +
329A LEU 3.2 1.3 - - - -
330A PRO* 3.2 17.9 - - - +
331A GLU* 5.0 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A TYR* 3.9 26.6 + - - +
286A HIS* 3.9 24.5 - - - +
324A ARG* 2.9 20.7 + - + +
325A GLY* 3.7 7.2 - - - +
326A ILE 3.1 0.8 + - - -
327A HIS* 1.3 75.1 - - - +
329A LEU* 1.3 65.1 + - - +
330A PRO* 3.6 0.9 - - - -
331A GLU* 3.3 41.5 - - - +
332A ARG* 3.4 19.0 + - - +
4E G 4.9 15.0 + - - -
----------------------------------------------------------
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