Contacts of the helix formed by residues 286 - 298 (chain A) in PDB entry 2OZL
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 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ARG* 2.9 33.5 + - - -
260A TYR* 3.0 19.5 + - - +
281A VAL 3.6 1.2 + - - -
282A ARG* 3.2 26.9 + - + +
284A LYS 3.9 0.6 - - - -
285A SER* 1.3 72.5 - - - +
287A PRO* 1.3 64.7 - - - +
288A ILE* 3.1 13.7 + - - +
289A MET* 2.9 39.6 + - + +
290A LEU* 2.9 30.2 + - - +
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Residues in contact with PRO 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 4.0 9.9 - - - +
43A ARG* 3.9 4.9 - - - +
67A GLY 3.7 24.9 - - - +
69A GLU* 3.8 22.4 - - + +
70A ALA* 3.8 23.1 - - + +
228A MET* 3.4 29.0 - - + +
230A ILE* 5.3 2.6 + - - +
260A TYR* 4.0 2.0 - - - +
285A SER 3.0 6.4 - - - +
286A ASP* 1.3 89.8 - - - +
288A ILE* 1.3 62.0 + - - +
290A LEU* 3.5 3.3 + - + +
291A LEU* 3.2 21.8 + - - +
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 3.5 30.4 - - + +
39A MET* 3.7 45.3 - - + +
40A GLN* 3.5 31.0 - - + +
43A ARG* 3.7 32.8 - - + +
69A GLU* 4.8 2.5 - - + -
286A ASP* 3.1 8.1 + - - +
287A PRO* 1.3 75.5 - - + +
289A MET* 1.3 67.0 + - - +
291A LEU* 3.3 1.9 + - - +
292A LYS* 2.9 23.9 + - + +
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Residues in contact with MET 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ARG 4.4 5.4 - - - +
283A SER* 3.6 36.1 - - - +
284A LYS 5.1 1.8 - - - -
286A ASP* 2.9 27.1 + - + +
288A ILE* 1.3 77.8 - - - +
290A LEU* 1.3 64.5 + - - +
292A LYS* 3.4 9.2 + - + +
293A ASP* 3.0 47.7 + - - +
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASP* 5.9 1.3 - - - +
228A MET* 3.4 30.7 - - + +
229A ASP* 4.8 7.4 - - + +
284A LYS 4.0 19.5 - - - +
285A SER* 3.5 20.0 - - - +
286A ASP 2.9 17.2 + - - +
287A PRO 3.8 3.8 - - - +
288A ILE 3.2 0.2 - - - -
289A MET* 1.3 85.1 - - + +
291A LEU* 1.3 61.2 + - - +
293A ASP* 3.5 7.4 + - - +
294A ARG* 3.2 34.2 + - - +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.1 19.5 - - + -
32A GLY* 4.1 4.5 - - - +
35A TYR* 4.0 11.7 - - + -
36A TYR* 3.6 33.7 - - + +
39A MET* 3.5 26.9 - - + -
230A ILE* 4.0 20.8 - - + +
231A LEU* 5.2 1.6 - - + -
287A PRO 3.2 14.3 + - - +
288A ILE* 3.9 3.1 - - - +
290A LEU* 1.3 75.8 - - - +
292A LYS* 1.3 67.8 + - - +
294A ARG* 3.1 14.9 + - + +
295A MET* 2.9 40.2 + - + +
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Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 4.2 19.4 - - + +
288A ILE* 2.9 18.6 + - + +
289A MET* 3.6 9.0 - - + +
291A LEU* 1.3 77.5 - - - +
293A ASP* 1.3 70.7 + - - +
295A MET* 3.3 2.2 + - - +
296A VAL* 3.0 34.3 + - + +
303A VAL* 4.4 23.2 - - - +
306A LEU* 3.6 29.2 - - + -
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Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A MET* 3.0 39.5 + - - +
290A LEU* 3.8 8.4 - - + +
291A LEU 3.3 0.2 - - - -
292A LYS* 1.3 85.5 - - - +
294A ARG* 1.3 57.7 + - + +
296A VAL* 4.1 3.5 - - - +
297A ASN* 3.0 43.8 + - - +
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Residues in contact with ARG 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.6 38.9 - - + +
8A GLU 3.1 26.0 + - - -
9A ILE* 3.8 3.6 - - - +
10A LYS* 5.7 2.4 - - - +
27A LEU* 6.0 0.2 - - + -
229A ASP* 2.7 45.3 + - - -
230A ILE* 4.7 4.6 - - - +
231A LEU* 3.5 26.6 - - - +
290A LEU* 3.2 20.2 + - - +
291A LEU* 3.1 17.5 + - + +
293A ASP* 1.3 79.8 - - + +
295A MET* 1.3 58.1 + - + +
297A ASN* 4.0 3.4 - - - +
298A SER* 2.8 32.8 + - - -
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Residues in contact with MET 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.6 2.7 - - + -
29A ARG 4.2 3.4 - - - +
32A GLY* 3.4 44.4 - - - +
33A LEU* 3.5 24.0 - - + +
36A TYR* 4.5 7.2 - - - -
291A LEU* 2.9 38.9 + - + +
292A LYS 3.9 3.6 - - - +
294A ARG* 1.3 74.3 - - + +
296A VAL* 1.3 63.5 + - - +
298A SER* 3.7 4.5 - - - -
299A ASN 3.2 1.4 + - - -
300A LEU* 2.8 50.6 + - + +
301A ALA* 3.3 18.9 + - + -
306A LEU* 4.6 10.5 - - + -
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LYS* 3.0 26.5 + - + +
293A ASP* 4.1 4.5 - - - +
295A MET* 1.3 74.1 - - - +
297A ASN* 1.3 74.7 + - - +
299A ASN* 3.1 13.7 + - - +
301A ALA 3.6 12.9 - - - +
302A SER* 5.5 0.4 - - - -
303A VAL* 4.3 26.2 - - + +
306A LEU* 3.9 20.0 - - + -
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ASP* 3.0 27.5 + - - +
294A ARG* 4.0 4.3 - - - +
296A VAL* 1.3 86.3 - - - +
298A SER* 1.3 60.5 + - - +
299A ASN* 3.2 2.5 + - - +
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Residues in contact with SER 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 3.8 13.7 - - - +
5A ALA* 3.8 15.0 - - - +
7A PHE* 3.5 18.5 - - - -
294A ARG 2.8 22.0 + - - -
295A MET 3.5 2.3 + - - -
297A ASN* 1.3 74.9 - - - +
299A ASN* 1.3 69.5 + - - +
300A LEU* 3.2 24.8 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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