Contacts of the helix formed by residues 281 - 295 (chain A) in PDB entry 4ZG9
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 PRO 281 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.8 8.5 - - + -
97A THR* 6.0 2.5 - - + -
101A TRP* 4.2 19.5 - - + +
278A VAL 5.3 0.4 - - - +
279A VAL 3.3 10.3 - - - +
280A ILE* 1.3 91.0 - - + +
282A HIS* 1.3 67.3 + - + +
283A GLU* 3.3 9.6 - - - +
284A ARG* 3.1 25.9 + - + -
285A ARG* 3.2 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PRO* 1.3 75.4 - - + +
283A GLU* 1.3 67.9 + - - +
285A ARG* 3.1 39.5 + - - +
286A ILE* 3.2 18.4 + - - +
306A PHE* 3.6 28.5 - + + -
307A TYR 3.9 8.5 + - - -
308A SER* 3.7 23.4 - - - -
309A GLU* 4.5 4.5 + - + -
310A GLN* 5.4 7.2 - - + -
332A ILE* 5.3 3.7 - - + +
335A ILE* 3.7 26.1 - - + +
908A 4O2 4.6 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TRP* 3.4 52.3 + - + -
281A PRO* 3.9 9.4 - - - +
282A HIS* 1.3 82.9 + - - +
284A ARG* 1.3 62.2 + - - +
286A ILE* 3.2 4.4 + - - +
287A LEU* 3.2 26.9 + - - +
335A ILE* 3.9 13.9 - - + +
338A GLN* 3.5 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 3.7 30.3 - - + -
94A CYS 3.7 16.0 + - - -
95A LEU* 4.5 8.3 - - + +
96A LYS* 3.2 26.1 + - - +
101A TRP* 3.6 24.1 - - + -
117A ALA* 3.2 27.9 + - - +
280A ILE* 3.8 17.0 - - + -
281A PRO* 3.1 24.5 + - + +
283A GLU* 1.3 76.0 - - - +
285A ARG* 1.3 61.5 + - - +
287A LEU* 3.8 20.5 - - - +
288A THR* 2.9 34.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
276A TRP* 3.7 53.1 - - + +
277A SER 3.7 5.7 + - - -
278A VAL 3.5 15.8 + - - -
280A ILE* 2.7 37.0 + - + +
281A PRO 3.2 10.9 + - - +
282A HIS* 3.1 21.3 + - - +
284A ARG* 1.3 78.0 - - - +
286A ILE* 1.3 60.1 + - - +
288A THR* 3.4 2.6 - - - -
289A ILE* 3.1 30.9 + - - +
306A PHE* 4.1 21.3 - - + -
307A TYR 3.0 23.2 + - - -
908A 4O2 2.7 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 4.9 1.8 - - + -
169A PHE* 4.4 7.0 - - + -
282A HIS 3.2 14.3 + - - +
283A GLU* 3.6 9.4 - - - +
284A ARG 3.1 0.6 - - - -
285A ARG* 1.3 75.8 - - - +
287A LEU* 1.3 66.9 + - + +
289A ILE* 2.9 22.4 + - + +
290A LEU* 2.9 24.6 + - + +
306A PHE* 3.7 27.8 - - + -
335A ILE* 3.5 23.6 - - + +
338A GLN* 4.3 10.5 - - + +
339A LEU* 3.9 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TRP* 3.9 25.1 - - + -
117A ALA 4.5 7.2 - - - +
118A CYS* 4.5 8.5 - - + -
128A GLY 5.2 0.3 - - - +
129A ASP* 6.1 2.2 - - - -
130A CYS 3.7 17.7 - - - +
131A CYS* 4.8 2.9 - - - -
132A THR* 3.4 35.2 - - + +
283A GLU 3.2 16.5 + - - +
284A ARG* 3.8 28.0 - - - +
286A ILE* 1.3 76.1 - - + +
288A THR* 1.3 52.5 + - - +
290A LEU* 3.2 8.6 + - + +
291A GLN* 2.7 40.2 + - + +
338A GLN* 5.7 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 3.7 34.5 - - + -
276A TRP* 3.6 20.5 - - + -
284A ARG* 2.9 26.1 + - - +
285A ARG* 3.4 6.9 - - - -
287A LEU* 1.3 77.6 - - - +
289A ILE* 1.3 55.5 + - - +
291A GLN* 3.5 8.5 - - - +
292A TRP* 3.1 59.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.9 31.9 - - + -
276A TRP* 4.1 21.5 - - + -
285A ARG 3.1 17.5 - - - +
286A ILE* 2.9 15.9 + - + +
288A THR* 1.3 74.8 - - - +
290A LEU* 1.3 61.3 + - + +
291A GLN 3.2 0.2 - - - -
292A TRP* 3.4 13.6 + - + +
293A LEU* 3.0 30.3 + - + +
304A TYR* 4.0 24.2 - - + -
305A ALA* 4.5 17.5 - - - +
306A PHE* 4.5 12.6 - - + +
339A LEU* 5.3 5.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
128A GLY 4.7 2.7 - - - +
130A CYS 5.8 0.9 - - - +
132A THR* 3.8 21.8 - - + -
286A ILE* 2.9 28.2 + - + +
287A LEU* 3.6 9.0 - - + +
289A ILE* 1.3 73.6 - - + +
291A GLN* 1.3 64.2 + - - +
293A LEU* 3.3 16.5 + - + +
294A THR* 3.3 19.4 + - - +
338A GLN 4.4 0.9 - - - +
339A LEU* 4.3 9.6 - - + +
342A GLY* 3.7 24.0 - - - +
343A LEU* 3.7 44.9 - - + +
345A GLN* 5.9 0.9 - - - +
346A LEU* 3.8 13.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
127A ARG 3.6 22.0 + - - -
128A GLY 3.5 21.0 + - - +
129A ASP* 4.0 16.0 + - + +
287A LEU* 2.7 23.6 + - + +
288A THR* 3.5 10.5 - - - +
290A LEU* 1.3 73.7 - - - +
292A TRP* 1.3 67.4 + - + +
294A THR* 2.8 22.7 + - - -
295A LEU* 3.6 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A CYS 5.3 0.4 + - - -
64A PHE* 2.9 35.6 + + + +
65A GLU* 5.1 5.7 - - - +
66A LEU* 5.3 7.1 - - + +
78A ASN* 4.0 11.9 - - - -
272A GLY* 4.6 4.3 - - - -
273A THR* 3.7 34.8 - - - -
276A TRP* 4.1 11.4 - + - -
288A THR* 3.1 42.1 + - + +
289A ILE* 3.8 8.1 - - + +
290A LEU 3.3 0.2 - - - -
291A GLN* 1.3 87.6 - - + +
293A LEU* 1.3 56.4 + - - +
295A LEU* 3.0 44.4 + - + +
300A ARG* 3.3 9.0 - - - +
301A PRO* 4.5 9.6 - - + -
304A TYR* 3.8 36.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 4.2 11.0 - - + -
165A PRO* 4.1 24.2 - - + -
167A ILE* 4.2 16.4 - - + -
289A ILE* 3.0 21.7 + - + +
290A LEU* 3.6 12.3 - - + +
291A GLN 3.2 0.6 - - - -
292A TRP* 1.3 76.8 - - - +
294A THR* 1.3 58.2 + - - +
295A LEU 4.0 0.2 - - - +
300A ARG* 3.4 28.4 + - - -
301A PRO 4.7 0.2 - - - +
304A TYR* 3.6 30.5 - - + +
343A LEU* 3.7 30.1 - - + -
346A LEU* 5.2 0.2 - - + -
348A LEU* 4.2 19.4 - - + +
352A VAL* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU 5.3 1.3 - - - +
126A ALA 5.2 4.5 - - - +
127A ARG 4.4 4.2 + - - -
128A GLY* 4.0 23.9 + - - +
290A LEU 3.3 12.1 + - - +
291A GLN* 2.8 20.4 + - - -
293A LEU* 1.3 73.8 - - - +
295A LEU* 1.3 68.9 + - - +
296A PRO* 4.1 2.4 - - - +
346A LEU* 3.7 32.3 - - + -
348A LEU* 5.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLN* 4.4 14.1 - - - +
292A TRP* 3.0 44.0 + - + +
293A LEU 4.0 0.2 - - - +
294A THR* 1.3 83.3 + - - +
296A PRO* 1.3 79.8 - - + +
299A GLU* 4.4 16.4 - - + -
300A ARG* 3.3 32.8 + - - +
301A PRO* 5.5 1.8 - - + -
----------------------------------------------------------
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