Contacts of the helix formed by residues 303 - 317 (chain A) in PDB entry 2C17
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 LEU 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A GLU* 3.6 24.7 - - + +
288A ASN* 3.7 25.8 - - - +
289A VAL* 4.1 14.8 - - + -
298A SER 3.9 2.7 - - - +
299A ASP* 3.7 17.6 + - - +
302A ARG* 1.3 77.2 + - - +
304A LEU* 1.3 62.5 + - - +
306A LEU* 3.9 19.7 - - + -
307A GLU* 4.0 16.7 - - - +
406A PHE* 3.7 56.9 - - + -
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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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284A GLU* 2.8 18.5 + - - +
302A ARG* 4.3 18.6 - - + +
303A LEU* 1.3 77.0 - - - +
305A LEU* 1.3 65.3 + - + +
306A LEU 3.4 0.6 - - - +
307A GLU* 3.4 2.1 + - - +
308A ALA* 2.8 31.3 + - - +
371A LEU* 4.3 30.5 - - + -
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Residues in contact with LEU 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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280A LYS* 3.8 51.6 - - + +
281A LEU* 3.5 14.4 - - + -
283A GLU* 4.0 22.4 - - + +
284A GLU* 3.0 15.3 + - + +
302A ARG* 4.9 0.4 - - - +
304A LEU* 1.3 78.3 - - + +
306A LEU* 1.3 55.9 + - - +
308A ALA* 3.9 2.9 - - + +
309A THR* 2.6 38.2 + - - +
367A PRO* 5.0 10.5 - - + +
368A GLU* 5.3 0.9 - - - +
371A LEU* 3.7 27.6 - - + -
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Residues in contact with LEU 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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267A THR* 6.0 1.3 - - + -
271A LEU* 5.7 0.7 - - + -
281A LEU* 3.5 29.3 - - + +
284A GLU* 2.8 18.1 + - + +
285A ILE* 4.3 24.2 - - + -
289A VAL* 5.6 0.2 - - + -
303A LEU* 3.9 22.7 - - + -
305A LEU* 1.3 76.1 - - - +
307A GLU* 1.3 59.8 + - - +
309A THR* 3.6 3.5 + - - -
310A ILE* 3.2 35.8 + - + +
406A PHE* 4.0 36.8 - - + +
409A MET* 4.3 22.9 - - + -
410A ALA* 4.7 3.8 - - + +
413A LEU* 5.3 0.2 - - + -
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Residues in contact with GLU 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 LEU* 4.0 17.4 - - - +
304A LEU 3.4 8.6 + - - +
305A LEU 3.4 0.2 - - - -
306A LEU* 1.3 76.0 - - - +
308A ALA* 1.3 54.3 + - - +
310A ILE* 3.0 8.9 + - + +
311A ARG* 2.6 68.7 + - + +
402A ARG* 2.7 31.6 + - + +
406A PHE* 3.5 38.1 - - + -
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Residues in contact with ALA 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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304A LEU 2.8 22.5 + - - +
305A LEU* 4.0 6.3 - - - +
307A GLU* 1.3 70.5 - - - +
309A THR* 1.3 56.1 + - - +
311A ARG* 3.4 14.3 + - - +
312A GLU* 2.9 28.8 + - - +
367A PRO* 3.8 17.5 - - + +
370A PHE* 4.1 5.3 - - - +
371A LEU* 3.8 33.2 - - + +
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Residues in contact with THR 309 (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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267A THR* 4.5 14.4 - - + -
271A LEU* 4.2 25.6 - - + -
277A VAL* 4.0 9.9 - - + +
281A LEU* 3.9 12.9 - - + +
305A LEU* 2.6 24.7 + - - +
306A LEU* 3.6 7.0 - - - -
308A ALA* 1.3 75.4 - - - +
310A ILE* 1.3 57.5 + - - +
312A GLU* 3.3 8.0 + - - +
313A VAL* 2.9 27.8 + - + +
365A PHE* 4.5 14.8 - - + -
367A PRO* 3.9 15.5 - - + +
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Residues in contact with ILE 310 (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 VAL* 4.0 12.1 - - + -
267A THR* 4.0 23.1 - - + +
306A LEU* 3.2 22.4 + - + +
307A GLU* 3.0 12.4 + - + +
309A THR* 1.3 73.6 - - - +
311A ARG* 1.3 59.1 + - + +
313A VAL* 3.3 8.5 + - - +
314A LEU* 2.9 48.5 + - + +
388A PHE* 5.7 3.6 - - + -
405A LEU* 4.3 28.3 - - + -
406A PHE* 4.2 23.3 - - + -
409A MET* 4.9 11.4 - - + -
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Residues in contact with ARG 311 (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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307A GLU* 2.6 53.4 + - + +
308A ALA* 3.6 12.1 - - - +
310A ILE* 1.3 72.0 - - + +
312A GLU* 1.3 55.9 + - - +
314A LEU* 3.2 4.9 + - + -
315A ARG* 3.0 24.6 + - - +
370A PHE* 3.7 32.6 + - + -
385A TYR* 2.8 59.4 + - + -
387A PRO* 5.4 3.7 - - + +
402A ARG* 2.9 32.8 - - - +
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Residues in contact with GLU 312 (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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308A ALA 2.9 17.0 + - - +
309A THR* 3.3 8.0 + - - +
311A ARG* 1.3 71.3 - - - +
313A VAL* 1.3 64.4 + - - +
315A ARG* 2.7 40.9 + - - +
316A LEU* 3.1 27.5 + - + +
365A PHE* 3.7 27.8 - - + -
366A MET 2.9 24.0 + - - +
367A PRO* 4.4 6.3 - - + -
369A ARG* 2.7 31.6 + - - -
370A PHE* 3.5 16.4 - - + -
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Residues in contact with VAL 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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263A VAL* 5.0 4.5 - - + +
266A TRP* 4.1 23.6 - - + -
267A THR* 3.9 39.9 - - + +
270A PHE* 4.0 9.0 - - + -
309A THR* 2.9 21.6 + - + +
310A ILE 3.3 8.3 + - - +
312A GLU* 1.3 69.8 - - - +
314A LEU* 1.3 58.6 + - + +
316A LEU* 3.1 10.6 + - - +
317A ARG 2.8 37.9 + - - +
365A PHE* 4.0 22.4 - - + -
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Residues in contact with LEU 314 (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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395 HEM 4.5 4.0 - - + -
263A VAL* 3.9 30.7 - - + -
310A ILE* 2.9 42.9 + - + +
311A ARG* 3.5 5.6 - - + +
313A VAL* 1.3 70.1 - - + +
315A ARG* 1.3 63.0 + - - +
317A ARG 4.0 14.1 - - - +
318A PRO* 3.6 23.7 - - + +
319A VAL* 4.5 3.4 - - + +
353A HIS* 4.2 0.2 + - - -
385A TYR* 4.0 3.1 - - + -
386A LEU 3.4 18.6 + - - +
387A PRO* 3.7 48.5 - - + +
388A PHE* 4.7 9.2 - - + -
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Residues in contact with ARG 315 (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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311A ARG 3.0 6.5 + - - -
312A GLU* 2.7 48.4 + - - +
314A LEU* 1.3 74.7 - - - +
316A LEU* 1.3 81.8 + - - +
317A ARG 3.4 0.7 + - - -
318A PRO* 3.4 2.8 - - - +
353A HIS* 2.7 69.1 + - + +
354A HIS* 4.7 0.4 - - - +
359A TRP* 3.4 41.1 - - - +
362A PRO* 2.7 38.0 + - - +
364A GLN 4.7 0.4 + - - -
369A ARG* 3.1 13.6 - - - +
370A PHE* 3.8 11.9 - - + -
384A SER 3.8 8.1 - - - +
385A TYR* 3.6 15.2 - - + +
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Residues in contact with LEU 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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7A PHE* 4.8 1.0 - - - -
270A PHE* 4.6 17.3 - - + -
312A GLU* 3.1 19.9 + - + +
313A VAL* 3.5 6.1 - - - +
315A ARG* 1.3 89.9 - - - +
317A ARG* 1.3 68.2 + - - +
318A PRO* 4.2 2.1 - - - +
350A TRP* 4.3 6.9 - - - -
354A HIS* 3.5 33.5 + - + +
362A PRO 3.3 26.9 - - - +
363A ASP* 3.8 18.4 - - - +
365A PHE* 3.3 46.4 - - + -
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Residues in contact with ARG 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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4A ASN* 2.8 26.9 + - - +
7A PHE* 3.8 23.0 - - + -
266A TRP* 3.3 50.7 - - + +
270A PHE* 4.5 15.3 - - + -
313A VAL* 2.8 21.5 + - + +
314A LEU* 4.0 7.4 - - - +
316A LEU* 1.3 76.7 - - + +
318A PRO* 1.3 66.3 - - - +
319A VAL 4.0 0.2 + - - -
350A TRP* 3.2 48.6 - - - +
429A LEU 5.2 8.3 + - - -
431A GLY* 5.8 1.6 - - - +
437A PHE* 3.3 20.2 - - - -
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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