Contacts of the helix formed by residues 312 - 327 (chain A) in PDB entry 4RWN
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 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A LYS* 5.4 1.2 - - - +
296A PRO* 6.3 0.2 - - - -
309A GLY 4.7 1.6 + - - +
310A GLY* 3.2 7.6 - - - +
311A GLY* 1.3 76.7 - - - +
313A THR* 1.3 63.6 + - - +
314A HIS* 3.2 23.3 + - - +
315A SER* 2.4 44.7 + - - +
316A TRP* 3.5 13.7 - - - -
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Residues in contact with THR 313 (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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265A HIS* 4.8 4.7 + - + -
266A GLN* 4.7 13.9 - - - +
294A PRO* 5.6 7.4 - - + -
295A ARG 4.3 17.5 - - - +
296A PRO* 5.6 1.8 - - + -
311A GLY 3.8 7.9 + - - +
312A ASP* 1.3 70.8 + - - +
314A HIS* 1.3 73.3 + - - +
316A TRP* 3.1 10.0 + - - +
317A GLN* 2.9 27.8 + - - +
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Residues in contact with HIS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ASP* 3.2 14.0 + - - +
313A THR* 1.3 91.2 + - - +
315A SER* 1.3 62.6 + - - +
317A GLN* 3.3 20.6 + - - +
318A ARG* 3.0 35.8 + - + +
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Residues in contact with SER 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LYS* 3.1 27.8 + - - +
226A LEU* 3.7 4.3 + - - +
227A PRO* 3.3 34.4 - - - +
312A ASP* 2.4 41.1 + - - +
314A HIS* 1.3 80.1 - - - +
316A TRP* 1.3 56.4 + - - +
318A ARG* 3.5 2.9 + - - +
319A LEU 3.2 19.9 + - - -
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Residues in contact with TRP 316 (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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227A PRO* 3.5 26.7 - - + +
231A ALA* 4.1 13.2 - - + -
232A LEU* 4.3 8.1 - - + -
235A LEU* 4.7 9.2 - - + -
262A VAL* 4.4 21.3 - - + -
265A HIS* 3.5 38.9 + + + -
268A LEU* 5.1 2.0 - - + -
296A PRO* 3.3 30.3 - - + +
298A ILE* 3.9 30.3 - - + -
309A GLY 2.9 24.9 + - - -
311A GLY 5.7 0.2 - - - -
312A ASP 3.5 17.5 - - - -
313A THR* 3.1 6.5 + - - +
315A SER* 1.3 75.3 - - - +
317A GLN* 1.3 61.4 + - - +
319A LEU* 3.8 20.3 - - + +
320A ALA* 2.9 32.6 + - - +
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Residues in contact with GLN 317 (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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265A HIS* 4.3 9.5 + - - +
313A THR 2.9 12.5 + - - +
314A HIS* 3.4 30.7 + - - +
316A TRP* 1.3 78.0 - - - +
318A ARG* 1.3 63.4 + - + +
320A ALA* 3.3 3.4 + - - +
321A GLN* 3.1 47.0 + - + +
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Residues in contact with ARG 318 (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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221A THR* 5.2 2.0 + - - +
222A HIS* 3.0 47.4 + - + +
225A LYS* 3.3 54.3 - - - +
226A LEU* 4.2 6.3 - - + -
314A HIS* 3.0 21.2 + - + +
315A SER 3.9 4.0 - - - +
316A TRP 3.3 0.2 - - - -
317A GLN* 1.3 76.1 - - + +
319A LEU* 1.3 67.3 + - - +
321A GLN* 3.3 18.6 + - - +
322A GLU* 3.3 22.7 + - - +
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Residues in contact with LEU 319 (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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214A TRP* 3.7 26.2 - - + -
215A TYR* 4.6 7.0 - - + -
218A CYS* 4.4 13.5 - - + -
226A LEU* 4.1 22.6 - - + +
227A PRO* 4.0 11.4 - - + -
232A LEU* 3.7 39.5 - - + -
262A VAL* 3.9 8.3 - - + -
315A SER 3.2 17.6 + - - +
316A TRP* 3.9 21.5 - - + +
317A GLN 3.4 0.2 - - - -
318A ARG* 1.3 76.0 - - - +
320A ALA* 1.3 57.7 + - - +
322A GLU* 3.0 7.1 + - - +
323A ALA* 2.8 25.1 + - - +
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Residues in contact with ALA 320 (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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262A VAL* 3.8 16.5 - - - +
263A LEU* 3.3 25.1 - - + +
265A HIS* 4.1 17.9 - - + -
316A TRP 2.9 18.4 + - - +
317A GLN* 3.6 4.7 - - - +
319A LEU* 1.3 74.0 - - - +
321A GLN* 1.3 60.4 + - - +
323A ALA* 4.1 0.4 - - - -
324A ARG* 2.9 27.4 + - - +
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Residues in contact with GLN 321 (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 HIS* 4.2 10.9 - - - -
317A GLN* 3.1 42.4 + - + +
318A ARG* 3.5 18.9 - - - +
320A ALA* 1.3 76.6 - - + +
322A GLU* 1.3 66.5 + - - +
324A ARG* 3.6 6.6 + - - +
325A VAL* 3.2 27.6 + - - +
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Residues in contact with GLU 322 (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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214A TRP* 4.3 1.3 - - + -
218A CYS* 3.6 32.0 - - + -
221A THR* 4.2 12.3 + - - +
222A HIS* 2.6 42.7 + - + +
318A ARG 3.3 4.7 + - - +
319A LEU* 3.0 10.4 + - - +
321A GLN* 1.3 79.2 - - - +
323A ALA* 1.3 59.8 + - - +
325A VAL* 3.1 11.8 + - - +
326A TRP* 2.9 50.8 + - + -
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Residues in contact with ALA 323 (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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214A TRP* 3.9 11.1 - - + -
259A LEU* 3.5 38.6 - - + +
262A VAL* 4.0 12.3 - - + -
263A LEU* 4.0 6.3 - - + -
319A LEU 2.8 13.5 + - - +
320A ALA 3.2 7.6 + - - +
322A GLU* 1.3 75.4 - - - +
324A ARG* 1.3 61.7 + - - +
326A TRP* 3.4 1.4 + - - +
327A LEU* 3.1 31.5 + - - +
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Residues in contact with ARG 324 (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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263A LEU* 3.5 36.1 - - + +
320A ALA 2.9 16.3 + - - +
321A GLN* 3.7 9.0 - - - +
322A GLU 3.2 0.2 - - - -
323A ALA* 1.3 78.3 - - - +
325A VAL* 1.3 62.1 + - + +
327A LEU* 3.5 22.3 + - - +
328A GLY* 4.0 2.9 + - - -
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Residues in contact with VAL 325 (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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321A GLN 3.2 13.9 + - - +
322A GLU* 3.1 19.4 + - - +
324A ARG* 1.3 79.5 - - + +
326A TRP* 1.3 62.8 + - + +
328A GLY* 3.1 19.4 + - - -
329A TYR* 3.2 38.8 + - + +
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Residues in contact with TRP 326 (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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3A LEU* 3.7 35.0 - - + -
4A ARG* 3.7 35.0 - - + -
214A TRP* 3.4 38.0 - + - +
217A THR* 4.0 28.5 - - + -
218A CYS* 4.5 4.6 - - - -
255A PHE* 4.4 5.2 - + - -
259A LEU* 4.3 14.6 - - + +
322A GLU* 2.9 43.9 + - + +
323A ALA 4.1 3.6 - - - +
325A VAL* 1.3 75.6 - - + +
327A LEU* 1.3 60.4 + - - +
328A GLY 3.0 5.8 - - - -
329A TYR* 3.2 47.8 + + - +
331A CYS* 3.9 18.6 - - - +
332A CYS* 4.9 1.7 - - - -
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Residues in contact with LEU 327 (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 GLN* 3.7 33.9 - - + +
259A LEU* 3.8 26.0 - - + -
260A GLU* 4.4 13.2 - - + +
263A LEU* 3.7 27.8 - - + -
323A ALA 3.1 22.7 + - - +
324A ARG* 3.7 16.4 - - - +
325A VAL 3.2 0.6 - - - -
326A TRP* 1.3 77.1 - - - +
328A GLY* 1.3 56.9 + - - +
329A TYR 3.4 1.4 - - - +
332A CYS* 4.5 6.1 - - + -
333A LYS* 4.2 2.1 - - - -
339A LEU* 3.5 32.0 - - + +
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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