Contacts of the helix formed by residues 295 - 308 (chain A) in PDB entry 4RQO
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 GLY 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A TYR 4.8 0.2 - - - +
272A ALA* 3.8 12.5 - - - -
275A VAL* 3.6 17.9 - - - -
276A ASN* 3.0 23.4 + - - -
294A ALA* 1.3 78.3 - - - +
296A ILE* 1.3 66.0 + - - +
298A PRO* 3.3 2.8 - - - +
299A ALA* 3.1 25.8 + - - +
400A ASN* 3.0 1.7 + - - -
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Residues in contact with ILE 296 (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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293A ALA 4.3 0.9 - - - +
294A ALA 3.3 0.6 - - - -
295A GLY* 1.3 78.5 - - - +
297A ILE* 1.3 66.4 + - - +
299A ALA* 3.5 3.1 - - - +
300A VAL* 3.1 24.1 + - - +
347A VAL* 3.6 40.8 - - + +
350A ALA* 3.9 20.6 - - + +
351A SER* 3.8 23.1 - - - +
354A ALA* 4.1 8.1 - - + -
400A ASN* 3.2 41.7 + - - +
403A GLY* 4.0 19.3 - - - +
404A ALA* 4.0 6.1 - - - +
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Residues in contact with ILE 297 (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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9A PHE* 4.2 14.1 - - + -
218A MSE 4.0 20.9 - - + -
288A ALA* 3.9 28.3 - - + +
293A ALA 4.9 0.4 + - - -
294A ALA 4.4 0.8 + - - -
296A ILE* 1.3 78.9 - - - +
298A PRO* 1.3 67.0 - - + +
301A LEU* 3.0 14.6 + - - +
319A TYR* 2.7 39.1 + - + +
320A PHE* 4.2 7.9 - - + -
323A ALA* 4.3 6.5 - - + -
350A ALA* 3.9 10.1 - - + +
353A MSE 4.1 11.7 - - + -
354A ALA* 3.8 31.2 - - + +
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Residues in contact with PRO 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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218A MSE 4.0 37.5 - - + -
222A ILE* 3.9 19.9 - - + +
275A VAL* 4.1 13.0 - - + -
288A ALA* 5.1 0.2 - - + -
294A ALA 3.1 29.4 - - - +
295A GLY* 3.3 13.5 - - - +
297A ILE* 1.3 92.2 - - + +
299A ALA* 1.3 52.8 + - - +
301A LEU* 3.2 7.2 + - + +
302A LYS* 2.8 35.5 + - - +
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Residues in contact with ALA 299 (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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222A ILE* 4.5 0.6 - - - +
268A LEU* 3.7 12.6 - - - +
271A TYR* 3.6 22.6 - - + -
272A ALA 3.7 21.8 - - - +
295A GLY 3.1 18.8 + - - +
296A ILE 3.2 4.2 + - - +
298A PRO* 1.3 78.9 - - - +
300A VAL* 1.3 62.5 + - - +
302A LYS 3.5 0.2 + - - -
303A TYR* 3.0 24.3 + - - +
404A ALA* 4.0 13.5 - - + -
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Residues in contact with VAL 300 (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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268A LEU* 4.2 5.8 - - + -
296A ILE 3.1 15.2 + - - +
299A ALA* 1.3 74.8 - - - +
301A LEU* 1.3 59.2 + - - +
303A TYR* 3.4 2.9 + - - +
304A CYS* 2.8 27.5 + - - +
319A TYR* 3.4 23.3 - - + +
354A ALA* 3.9 28.9 - - + +
358A LEU* 4.2 22.0 - - + -
404A ALA* 3.9 30.7 - - + +
407A ALA* 4.1 5.6 - - + -
408A VAL* 4.3 7.2 - - + -
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Residues in contact with LEU 301 (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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215A ALA* 4.3 15.7 - - + +
218A MSE 5.3 4.9 - - + -
297A ILE* 3.0 18.3 + - + +
298A PRO* 3.6 7.0 - - + +
300A VAL* 1.3 76.1 - - - +
302A LYS* 1.3 64.0 + - - +
304A CYS* 3.1 8.0 + - + +
305A GLN* 2.9 38.3 + - - +
311A MSE 3.8 31.6 - - + -
316A ILE* 4.7 3.1 - - + -
319A TYR* 3.4 33.3 + - + -
320A PHE* 3.8 29.4 - - + -
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Residues in contact with LYS 302 (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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219A ASP* 4.7 14.8 - - - +
222A ILE* 4.1 27.9 - - + +
223A ASN* 4.4 10.7 + - - -
226A CYS* 5.8 1.4 - - - -
246A TYR* 5.7 7.1 - - - -
271A TYR* 3.6 50.1 + - + +
298A PRO 2.8 19.3 + - - +
301A LEU* 1.3 74.7 - - - +
303A TYR* 1.3 61.6 + - - +
305A GLN* 3.2 14.0 + - - +
306A GLN* 3.1 37.7 + - + +
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Residues in contact with TYR 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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264A ILE* 3.1 37.5 - - + +
267A HIS* 5.9 3.6 - - + -
268A LEU* 3.5 26.7 - - + +
271A TYR* 4.0 10.9 - - + -
299A ALA 3.0 9.0 + - - +
300A VAL 3.8 6.1 - - - +
302A LYS* 1.3 71.6 - - - +
304A CYS* 1.3 76.3 + - + +
306A GLN* 3.0 16.0 + - + +
307A ALA* 3.1 33.1 + - + +
308A HIS* 4.5 5.9 + - - -
358A LEU* 4.3 15.3 - - + -
362A LEU* 6.3 0.7 - - + -
408A VAL* 4.1 28.1 - - + +
412A ARG* 3.5 19.9 + - - -
261B GLN* 3.9 15.6 + - + -
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Residues in contact with CYS 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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300A VAL* 2.8 15.2 + - + +
301A LEU* 3.4 13.2 - - + +
303A TYR* 1.3 87.2 - - - +
305A GLN* 1.3 61.7 + - - +
306A GLN 3.4 0.2 + - - -
307A ALA 3.6 1.2 + - - -
308A HIS* 3.5 32.0 + - - +
309A ASP 5.4 0.2 - - - +
311A MSE 4.2 17.0 - - - +
319A TYR* 5.9 2.7 - - + -
358A LEU* 3.5 26.9 - - + -
361A VAL* 4.0 25.8 - - - -
362A LEU* 4.8 0.9 - - - -
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Residues in contact with GLN 305 (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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215A ALA* 5.6 2.4 - - - +
219A ASP* 4.5 11.3 - - - +
301A LEU* 2.9 41.3 + - - +
302A LYS* 3.7 16.0 - - + +
303A TYR 3.2 0.4 - - - -
304A CYS* 1.3 76.7 - - - +
306A GLN* 1.3 65.9 + - + +
308A HIS 3.5 15.1 - - - +
309A ASP 4.5 4.4 - - - +
310A ARG* 4.9 4.4 + - - -
311A MSE 3.5 33.3 - - + +
316A ILE* 4.3 16.0 - - - +
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Residues in contact with GLN 306 (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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271A TYR* 4.2 18.3 + - - +
302A LYS* 3.1 33.9 + - + +
303A TYR* 3.0 8.1 + - + +
305A GLN* 1.3 83.6 - - + +
307A ALA* 1.3 59.2 + - - +
308A HIS 3.5 2.4 - - - +
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Residues in contact with ALA 307 (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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303A TYR* 3.1 38.3 + - + +
305A GLN 3.4 0.2 - - - -
306A GLN* 1.3 76.3 - - + +
308A HIS* 1.3 86.0 + - + +
261B GLN* 4.9 6.2 + - - +
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Residues in contact with HIS 308 (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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303A TYR* 4.5 7.7 + - - -
304A CYS* 3.5 27.8 + - - +
305A GLN 3.5 10.5 - - - +
306A GLN 3.5 2.1 - - - +
307A ALA* 1.3 98.8 + - + +
309A ASP* 1.3 69.4 + - - +
310A ARG* 3.6 5.9 + - - -
311A MSE 6.5 0.4 - - + -
362A LEU* 3.6 22.4 - - + +
258B VAL* 3.5 48.7 + - + +
261B GLN* 3.6 13.4 + - - -
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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