Contacts of the helix formed by residues 298 - 316 (chain F) in PDB entry 5ZCS
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 ILE 298 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F TYR* 6.6 0.2 - - + -
293F ARG 3.9 7.0 + - - +
296F ALA* 5.0 8.7 - - + -
297F GLY* 1.3 78.3 - - - +
299F ILE* 1.3 59.8 + - - +
300F ASN* 4.4 3.1 - - + +
301F LEU* 3.9 24.2 - - + +
302F CYS* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 299 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297F GLY 4.2 0.8 + - - -
298F ILE* 1.3 70.4 - - - +
300F ASN* 1.3 60.4 + - - +
302F CYS* 3.8 5.8 - - - +
303F LYS* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 300 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F THR* 5.7 7.0 - - - -
261F HIS* 3.5 22.8 - - + +
298F ILE* 3.3 2.8 - - + +
299F ILE* 1.3 80.5 - - - +
301F LEU* 1.3 59.8 + - - +
303F LYS* 4.3 3.8 - - - +
304F PRO* 3.3 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F TYR* 5.3 15.9 - - + +
261F HIS* 4.7 4.0 - - - +
289F ILE 5.1 3.9 - - - +
290F ALA* 5.5 1.7 - - - -
293F ARG* 4.0 22.1 - - + +
296F ALA* 6.2 1.1 - - + -
298F ILE* 3.6 22.7 + - + +
299F ILE 3.3 0.2 - - - -
300F ASN* 1.3 76.3 - - - +
302F CYS* 1.3 63.4 + - - +
304F PRO* 4.0 4.9 - - - +
305F GLY* 3.4 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 302 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293F ARG* 4.3 12.3 - - + +
298F ILE 3.1 17.6 + - - +
299F ILE* 3.3 7.2 + - - +
301F LEU* 1.3 77.4 - - - +
303F LYS* 1.3 64.2 + - - +
305F GLY* 3.8 0.9 + - - -
306F ASN* 3.3 22.5 + - - +
343F THR* 6.2 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 303 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F ILE 2.9 17.5 + - - +
300F ASN* 4.3 4.9 - - - +
302F CYS* 1.3 76.1 - - - +
304F PRO* 1.3 58.0 - - - +
306F ASN* 3.5 5.7 + - - +
307F SER* 2.9 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 304 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F HIS* 4.2 16.8 - - + +
264F HIS* 4.0 31.6 - - + +
265F SER 5.7 0.2 - - - +
300F ASN 3.3 18.5 - - - +
301F LEU* 4.2 5.6 - - - +
302F CYS 3.4 0.2 - - - -
303F LYS* 1.3 77.0 - - - +
305F GLY* 1.3 59.8 + - - +
307F SER* 3.4 6.3 + - - -
308F GLY* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 305 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290F ALA* 4.8 19.4 - - - +
301F LEU 3.4 13.1 + - - -
302F CYS* 3.8 1.3 + - - -
303F LYS 3.4 0.4 - - - -
304F PRO* 1.3 79.3 - - - +
306F ASN* 1.3 57.0 + - - +
308F GLY* 3.4 1.4 + - - -
309F ILE* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 306 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F CYS 3.3 19.0 + - - +
303F LYS* 3.8 6.1 - - - +
305F GLY* 1.3 72.8 - - - +
307F SER* 1.3 60.6 + - - +
309F ILE* 3.4 6.6 + - - +
310F GLN* 2.9 29.1 + - - +
350F LEU* 5.5 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F HIS 6.1 1.3 - - - -
265F SER* 6.3 2.9 - - - -
268F THR* 4.6 9.1 - - - -
303F LYS 2.9 18.1 + - - -
304F PRO* 3.7 7.6 - - - -
305F GLY 3.3 0.2 - - - -
306F ASN* 1.3 78.1 - - - +
308F GLY* 1.3 55.8 + - - +
310F GLN* 3.4 6.2 + - - +
311F SER* 2.9 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 308 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F HIS* 5.6 3.5 + - - -
268F THR* 5.1 5.8 - - - -
304F PRO 2.9 16.8 + - - -
305F GLY* 3.8 2.0 - - - -
307F SER* 1.3 75.2 - - - +
309F ILE* 1.3 58.4 + - - +
311F SER* 3.4 5.9 + - - -
312F LEU* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F GLY 2.9 17.9 + - - +
306F ASN* 3.8 7.9 - - - +
308F GLY* 1.3 75.5 - - - +
310F GLN* 1.3 57.8 + - - +
312F LEU* 3.4 6.2 + - - +
313F ILE* 2.9 30.5 + - - +
350F LEU* 6.1 2.2 - - + +
354F ASP* 5.1 6.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 310 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ASN 2.9 18.1 + - - +
307F SER* 3.7 7.4 - - - +
309F ILE* 1.3 77.1 - - - +
311F SER* 1.3 57.7 + - - +
313F ILE* 3.3 5.1 + - - +
314F GLY* 2.9 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 311 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F THR* 3.8 33.4 - - - -
307F SER 2.9 17.8 + - - -
308F GLY* 3.8 4.9 - - - -
309F ILE 3.3 0.2 - - - -
310F GLN* 1.3 76.4 - - - +
312F LEU* 1.3 60.9 + - - +
314F GLY* 5.3 0.7 - - - -
315F VAL* 3.5 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 312 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F GLY 2.9 19.0 + - - +
309F ILE* 3.8 6.3 - - - +
310F GLN 3.3 0.2 - - - -
311F SER* 1.3 77.0 - - - +
313F ILE* 1.3 59.2 + - - +
315F VAL* 4.3 3.3 - - - +
316F LEU 3.1 22.9 + - - +
320F ASN* 4.1 16.9 - - + +
323F ILE* 5.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 313 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F ILE 2.9 17.3 + - - +
310F GLN* 4.0 5.2 - - - +
312F LEU* 1.3 79.0 - - - +
314F GLY* 1.3 60.9 + - - +
315F VAL 3.4 0.6 + - - -
316F LEU 3.9 11.3 + - - +
317F CYS* 5.7 1.9 - - - +
353F VAL 5.1 2.0 - - - +
354F ASP* 3.8 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F GLN 2.9 16.3 + - - -
311F SER* 4.5 0.9 - - - -
313F ILE* 1.3 76.5 - - - +
315F VAL* 1.3 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 315 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F GLY 5.2 9.2 - - - +
311F SER 3.5 18.3 + - - +
312F LEU* 4.5 3.1 - - - +
313F ILE 3.4 0.6 - - - -
314F GLY* 1.3 80.8 - - - +
316F LEU* 1.3 66.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F LEU 3.1 19.9 + - - +
313F ILE* 3.9 9.4 - - - +
314F GLY 3.7 0.4 - - - -
315F VAL* 1.3 83.2 - - + +
317F CYS* 1.3 62.6 + - - +
318F ILE* 4.6 1.3 - - + +
319F PRO* 4.5 21.1 - - + -
320F ASN* 3.9 8.6 - - + +
----------------------------------------------------------
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