Contacts of the helix formed by residues 288 - 307 (chain A) in PDB entry 5OQN
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 GLU 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ILE* 3.9 34.9 - - + +
252A ARG* 4.4 5.2 - - - +
286A ASP* 2.4 37.5 + - - +
287A ARG* 1.3 72.3 - - + +
289A LEU* 1.3 78.5 + - - +
290A SER* 3.3 5.9 + - - +
291A VAL* 3.5 20.5 + - + -
292A ARG* 3.5 10.2 + - - +
400B ARG* 2.1 41.1 + - - +
12C A 5.2 1.6 - - - +
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ARG 4.9 3.8 - - - +
288A GLU* 1.3 82.9 + - - +
290A SER* 1.3 62.4 + - - +
292A ARG* 3.0 39.0 + - - +
293A ASN* 3.4 32.0 + - - +
399B ASN* 5.8 3.1 - - - +
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Residues in contact with SER 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 4.7 13.7 - - - -
253A ARG* 2.5 41.5 + - - -
288A GLU* 3.2 4.7 + - - +
289A LEU* 1.3 81.4 - - - +
291A VAL* 1.3 62.7 + - - +
293A ASN* 3.5 5.8 + - - +
294A ALA* 3.3 20.3 + - - +
11D T 3.1 17.7 + - - -
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ALA 5.7 0.4 - - - +
249A ILE* 3.9 32.1 - - + +
252A ARG* 3.6 44.2 - - + +
253A ARG* 4.4 6.5 - - + +
256A TYR* 3.9 16.1 - - + -
283A GLY* 4.7 2.5 - - - -
286A ASP* 3.8 28.5 - - + +
288A GLU* 3.5 3.7 + - + -
289A LEU 3.4 0.4 - - - -
290A SER* 1.3 76.2 - - - +
292A ARG* 1.3 63.3 + - - +
294A ALA* 3.2 8.9 + - - +
295A CYS* 3.2 19.8 + - - +
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLY 3.3 20.4 - - - +
284A LEU 3.0 24.5 - - - +
285A GLU* 4.2 3.6 - - - +
286A ASP 2.3 41.5 + - - +
287A ARG* 4.0 8.7 + - - +
288A GLU 3.5 4.7 + - - +
289A LEU* 3.0 41.6 + - - +
290A SER 3.3 0.8 - - - -
291A VAL* 1.3 77.5 - - - +
293A ASN* 1.3 57.0 + - - +
295A CYS* 2.9 3.8 + - - +
296A LYS* 2.7 58.9 + - + +
399B ASN* 5.5 1.8 - - - +
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Residues in contact with ASN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 3.4 18.2 + - - +
290A SER* 3.9 8.3 - - - +
291A VAL 3.4 0.2 - - - -
292A ARG* 1.3 78.8 - - - +
294A ALA* 1.3 58.0 + - - +
296A LYS* 4.3 15.8 + - - +
297A ARG* 2.9 35.0 + - - +
11D T 5.4 7.7 + - - +
12D A 5.3 6.1 + - - -
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 3.8 24.7 - - + +
256A TYR* 3.9 10.6 - - + +
257A SER* 3.5 26.0 + - - +
290A SER 3.3 10.6 + - - +
291A VAL* 3.2 11.3 + - - +
292A ARG 3.1 0.8 - - - -
293A ASN* 1.3 77.6 - - - +
295A CYS* 1.3 57.2 + - - +
297A ARG* 4.6 3.6 - - - +
298A LEU* 3.2 23.9 + - - +
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Residues in contact with CYS 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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256A TYR* 4.1 24.2 - - + +
280A ILE* 4.3 9.9 - - - -
283A GLY* 4.0 25.1 - - - -
284A LEU* 3.5 26.9 - - + -
291A VAL 3.2 9.1 + - - +
292A ARG 2.9 6.1 + - - +
294A ALA* 1.3 76.8 - - - +
296A LYS* 1.3 66.2 + - - +
298A LEU* 3.2 6.9 + - - +
299A ILE* 3.0 37.5 + - - +
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 3.7 26.5 - - + -
292A ARG* 2.7 49.0 + - - +
293A ASN* 4.1 13.3 + - - +
295A CYS* 1.3 73.2 - - - +
297A ARG* 1.3 63.5 + - - +
299A ILE* 3.1 10.0 + - - +
300A ALA* 2.9 26.5 + - - +
328A LYS 5.7 0.4 - - - -
332A ALA* 3.7 30.3 - - + +
335A GLN* 5.2 9.5 - - - +
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LYS* 3.8 24.9 - - - +
293A ASN* 2.9 18.4 + - + +
294A ALA* 4.6 3.1 - - - +
296A LYS* 1.3 76.1 - - - +
298A LEU* 1.3 59.4 + - - +
300A ALA* 4.8 2.2 - - - -
301A HIS* 2.8 78.0 + - + +
302A ASP* 3.4 8.9 + - - +
336A SER* 5.9 1.3 - - - -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TYR* 3.7 28.5 - - + +
257A SER* 5.9 0.4 - - - -
260A LEU* 3.6 40.6 - - + +
261A LYS* 3.9 21.8 - - + -
294A ALA 3.2 17.8 + - - +
295A CYS* 3.2 8.9 + - - +
296A LYS 3.2 0.8 - - - -
297A ARG* 1.3 81.2 - - - +
299A ILE* 1.3 59.0 + - + +
302A ASP* 3.3 16.5 + - + +
303A TRP* 3.0 59.8 + - + +
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 4.6 9.4 - - + -
284A LEU* 3.6 30.7 - - + -
295A CYS* 3.0 24.5 + - - +
296A LYS* 3.7 6.1 - - - +
298A LEU* 1.3 79.5 - - + +
300A ALA* 1.3 66.6 + - - +
303A TRP* 3.3 49.6 - - + +
304A LEU* 3.3 4.7 + - - +
314A LEU* 4.5 14.8 - - + +
318A LEU* 4.3 19.3 - - + -
329A ALA* 4.6 18.8 - - + +
333A LEU* 5.6 4.0 - - + -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LYS 2.9 16.7 + - - +
297A ARG* 4.8 1.8 - - - -
299A ILE* 1.3 75.2 - - - +
301A HIS* 1.3 59.3 + - - +
304A LEU* 2.8 36.1 - - - +
305A ASN* 4.6 0.2 - - - +
332A ALA 4.9 1.3 - - - +
333A LEU* 4.2 30.3 - - + +
336A SER* 3.8 31.4 - - - +
337A ARG* 5.1 4.3 + - + -
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Residues in contact with HIS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LYS* 5.8 0.4 - - - -
297A ARG* 2.8 56.7 + - + +
300A ALA* 1.3 75.1 - - + +
302A ASP* 1.3 86.3 + - - +
305A ASN* 2.9 55.5 + - + +
336A SER* 5.5 4.0 - - - +
337A ARG* 5.8 2.5 - - - +
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Residues in contact with ASP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LYS* 3.1 47.7 + - + +
297A ARG* 4.2 8.8 + - - +
298A LEU* 3.3 30.4 + - + +
301A HIS* 1.3 109.3 + - - +
303A TRP* 1.3 57.5 + - + +
305A ASN* 3.6 2.5 - - - +
306A ALA* 2.7 37.5 + - - +
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Residues in contact with TRP 303 (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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260A LEU* 4.2 14.4 + - + -
264A GLY* 3.6 25.4 + - - -
267A CYS* 4.3 9.8 - - - -
268A PHE* 4.1 21.5 - + + -
276A PHE* 3.5 36.3 - + - -
280A ILE* 4.1 13.2 - - + -
298A LEU* 3.0 48.1 + - + +
299A ILE* 3.3 42.0 - - + +
302A ASP* 1.3 77.7 - - + +
304A LEU* 1.3 53.8 + - - +
306A ALA* 3.1 6.0 + - + +
307A LEU* 2.7 41.6 + - - +
314A LEU* 4.3 13.5 - - + -
318A LEU* 4.0 13.5 - - + -
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Residues in contact with LEU 304 (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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299A ILE 3.3 5.1 + - - +
300A ALA 2.8 20.8 + - - +
302A ASP 3.3 0.4 - - - -
303A TRP* 1.3 78.0 - - - +
305A ASN* 1.3 61.9 + - - +
307A LEU* 3.0 5.3 + - - -
308A ASP 2.9 5.5 + - - -
309A GLY* 2.9 50.4 + - - +
310A ASP 4.7 2.2 - - - +
311A LEU* 4.4 12.3 - - + -
314A LEU* 3.8 26.2 - - + +
333A LEU* 4.3 23.8 - - + -
337A ARG* 3.3 34.8 - - + +
340A ILE* 5.7 5.6 - - + -
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Residues in contact with ASN 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A HIS* 2.9 48.4 + - + +
302A ASP* 3.7 3.4 - - - +
304A LEU* 1.3 76.2 - - - +
306A ALA* 1.3 61.9 + - - +
308A ASP* 3.3 15.4 + - - +
309A GLY 4.8 1.6 - - - +
337A ARG* 3.9 19.6 + - - -
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLY* 5.3 7.4 - - - -
265A ARG* 3.8 32.9 - - + -
268A PHE* 5.9 0.7 - - + -
302A ASP 2.7 22.1 + - - +
303A TRP* 3.4 13.9 - - + +
305A ASN* 1.3 74.6 - - - +
307A LEU* 1.3 60.7 + - + +
308A ASP* 3.3 8.5 + - - +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ARG* 4.5 13.5 - - - +
268A PHE* 4.3 18.2 - - + -
303A TRP 2.7 18.7 + - - +
304A LEU* 3.0 4.4 + - - +
306A ALA* 1.3 77.3 - - + +
308A ASP* 1.3 73.9 + - - +
309A GLY 3.2 2.7 + - - +
310A ASP* 3.3 22.4 + - - +
313A GLU* 4.3 18.9 - - - +
314A LEU* 3.6 49.4 - - + +
317A LYS* 4.1 28.9 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
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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