Contacts of the helix formed by residues 295 - 309 (chain A) in PDB entry 2ZB8
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 LYS 295 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 4.2 20.8 - - + +
145A GLN* 6.4 0.7 - - + -
146A GLU* 3.1 33.7 - - - +
292A TYR* 2.8 25.2 + - + +
294A ASP* 1.3 101.8 + - - +
296A PHE* 1.3 66.9 + - - +
297A GLU 3.3 2.7 - - - -
298A PRO* 3.2 11.8 - - + +
299A GLY* 2.9 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 5.1 12.1 - + - -
135A MET* 6.4 1.1 - - + -
138A LEU* 3.6 28.2 - - + +
142A ILE* 4.0 5.4 - - + -
289A VAL* 3.4 43.7 - - + -
290A LEU* 4.2 10.8 - - + -
292A TYR 3.1 20.4 - - - -
293A LYS* 3.4 43.5 - - + +
294A ASP 3.3 1.0 - - - -
295A LYS* 1.3 79.7 - - - +
297A GLU* 1.3 58.0 + - - +
299A GLY* 3.8 0.2 - - - -
300A ILE* 2.9 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LYS 4.8 1.0 + - - -
294A ASP 4.7 1.9 + - - +
296A PHE* 1.3 79.2 - - - +
298A PRO* 1.3 73.0 - - + +
300A ILE* 3.8 3.9 - - - +
301A LEU* 3.0 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASP 3.9 7.2 - - - +
295A LYS* 3.2 31.2 - - + +
297A GLU* 1.3 101.1 - - + +
299A GLY* 1.3 59.5 + - - -
301A LEU* 4.0 8.4 - - + +
302A GLN* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.8 13.9 - - - -
141A LEU* 3.5 19.4 - - - +
142A ILE* 5.5 2.2 - - - -
295A LYS 2.9 17.9 + - - -
296A PHE 3.8 0.7 - - - -
298A PRO* 1.3 79.5 - - - +
300A ILE* 1.3 52.2 + - - +
302A GLN* 3.2 3.8 + - - +
303A LEU* 2.8 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.2 24.9 - - + -
129A PHE* 5.4 2.9 - - + -
133A ILE* 3.6 40.4 - - + +
134A GLY* 3.8 5.2 - - - +
138A LEU* 3.7 29.8 - - + +
296A PHE* 2.9 22.2 + - + +
297A GLU* 3.8 4.5 - - - +
299A GLY* 1.3 71.2 - - - +
301A LEU* 1.3 63.8 + - + +
303A LEU* 3.8 5.9 - - + +
304A SER* 2.8 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.0 25.8 - - + -
297A GLU* 3.0 39.6 + - + +
298A PRO* 4.0 7.4 - - + +
299A GLY 3.2 0.2 - - - -
300A ILE* 1.3 77.8 - - + +
302A GLN* 1.3 57.9 + - - +
304A SER* 3.4 4.2 + - - -
305A GLN* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 4.1 9.2 - - + -
298A PRO 3.1 20.0 + - - +
299A GLY 3.5 4.3 - - - +
301A LEU* 1.3 75.4 - - - +
303A LEU* 1.3 64.5 + - - +
305A GLN* 3.3 14.5 + - - +
306A TRP* 3.0 75.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA 3.4 20.6 - - - +
133A ILE* 3.6 21.8 - - + +
137A GLY 3.6 26.5 - - - +
138A LEU* 3.7 15.9 - - + +
141A LEU* 4.0 6.3 - - + -
170A VAL* 4.4 2.9 - - + -
174A ILE* 4.0 26.5 - - + -
299A GLY 2.8 21.6 + - - +
300A ILE* 3.8 12.3 - - + +
302A GLN* 1.3 76.0 - - - +
304A SER* 1.3 65.5 + - - +
306A TRP* 3.3 11.0 + - + +
307A PHE* 3.1 17.2 + - - +
312A LEU* 3.8 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 2.7 53.0 + - - +
133A ILE* 3.8 13.5 - - - +
300A ILE 2.8 19.5 + - - -
301A LEU* 3.6 5.2 - - - -
303A LEU* 1.3 76.6 - - - +
305A GLN* 1.3 56.6 + - - +
307A PHE* 3.1 4.5 + - - +
308A LYS* 2.8 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU 3.0 17.8 + - - +
302A GLN* 3.5 18.2 - - - +
303A LEU 3.2 0.2 - - - -
304A SER* 1.3 76.2 - - - +
306A TRP* 1.3 58.6 + - - +
308A LYS* 3.2 12.9 + - - +
309A GLU* 2.8 80.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.8 26.0 - - + -
174A ILE* 3.8 24.7 - - + -
177A PHE* 3.5 35.7 - + + +
178A LEU* 4.0 20.0 - - + -
302A GLN* 3.0 59.6 + - + +
303A LEU* 3.3 14.1 + - + +
305A GLN* 1.3 77.2 - - + +
307A PHE* 1.3 60.1 + - - +
309A GLU* 3.6 12.2 + - - +
310A GLY 3.4 1.7 + - - -
311A LYS* 2.9 41.8 + - + +
312A LEU* 2.9 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU 4.3 12.8 - - - -
122A VAL* 3.7 23.6 - - - -
123A ASP* 3.5 25.1 - - - -
125A HIS* 4.5 7.4 - + - -
128A TYR* 3.8 21.5 - + - -
133A ILE* 4.3 4.9 - - + -
303A LEU 3.1 13.0 + - - +
304A SER 3.1 9.4 + - - +
306A TRP* 1.3 75.1 - - - +
308A LYS* 1.3 71.0 + - + +
310A GLY* 3.0 13.9 + - - -
312A LEU* 3.8 19.4 - - + +
314A ILE* 3.3 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLN* 3.1 39.2 + - - +
121A LEU* 4.1 3.1 - - - +
123A ASP* 2.7 40.8 + - - +
304A SER* 2.8 33.3 + - - +
305A GLN* 3.7 13.7 - - - +
307A PHE* 1.3 83.8 - - + +
309A GLU* 1.3 57.8 + - - +
310A GLY* 3.1 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLN* 2.8 50.1 + - - +
306A TRP* 3.9 16.2 - - - +
307A PHE 3.2 0.2 - - - -
308A LYS* 1.3 75.5 - - - +
310A GLY* 1.3 59.6 + - - +
311A LYS* 3.2 34.0 + - + +
----------------------------------------------------------
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