Contacts of the helix formed by residues 306 - 316 (chain A) in PDB entry 1EYN
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 MET 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A ARG 5.4 0.9 - - - +
233A ILE* 3.7 33.0 - - + +
236A GLY* 3.3 35.7 - - - +
237A THR 3.6 1.3 - - - +
240A VAL* 3.8 18.2 - - + -
259A LEU* 5.5 0.2 - - + -
262A VAL* 3.9 11.7 - - + -
302A PHE* 3.7 16.2 - - + -
303A PRO* 3.0 29.5 + - + +
305A ASP* 1.3 75.2 - - - +
307A GLN* 1.3 64.9 + - - +
309A GLN* 3.2 30.8 + - + +
310A PHE* 3.0 33.2 + - + -
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Residues in contact with GLN 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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294A VAL* 5.5 0.2 - - - -
296A THR* 3.9 14.1 - - + -
302A PHE* 4.3 7.4 - - - -
303A PRO 3.7 2.0 + - - -
304A THR 3.0 14.5 + - - +
306A MET* 1.3 76.0 - - - +
308A ALA* 1.3 62.0 + - - +
310A PHE* 3.3 2.7 + - - +
311A THR* 2.8 51.8 + - - -
323A ILE* 3.5 21.8 - - + +
325A GLU* 2.9 27.6 + - + +
331A ARG* 3.1 31.5 + - - +
332A PHE* 3.6 18.7 - - + -
334A HIS* 3.1 19.0 + - - -
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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 THR 4.6 1.2 + - - -
305A ASP 5.3 0.2 - - - -
307A GLN* 1.3 80.9 + - - +
309A GLN* 1.3 69.0 + - - +
311A THR* 3.2 4.3 + - - -
312A LEU* 3.1 20.4 + - - +
331A ARG* 6.3 2.4 - - + +
334A HIS* 3.5 32.1 - - + +
369A ASP* 5.5 0.4 - - - +
371A ARG* 3.9 5.6 - - + +
372A ALA* 3.8 25.1 - - + +
375A SER* 3.3 16.8 + - - +
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Residues in contact with GLN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE* 4.0 2.0 - - - +
237A THR* 3.2 34.4 + - + +
240A VAL* 3.7 22.9 - - + +
305A ASP 3.0 21.9 + - - +
306A MET* 3.2 41.9 - - + +
308A ALA* 1.3 81.7 + - - +
310A PHE* 1.3 59.0 + - - +
312A LEU* 3.3 7.5 + - - +
313A LEU 3.1 20.8 + - - -
371A ARG* 3.9 12.4 - - - +
374A ALA* 5.8 0.2 - - + -
375A SER* 3.3 21.5 - - - +
378A LEU* 5.0 2.9 - - + -
399A TYR* 4.0 7.9 + - - -
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Residues in contact with PHE 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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240A VAL* 3.7 19.5 - - + -
262A VAL* 4.0 14.8 - - + -
265A LYS* 3.6 35.4 - - + -
266A LEU* 3.7 36.1 - - + -
292A VAL* 4.5 8.3 - - + -
294A VAL* 4.2 14.8 - - + -
302A PHE* 3.4 27.6 - + + -
306A MET* 3.0 38.8 + - + +
307A GLN* 4.0 3.1 - - - +
309A GLN* 1.3 75.7 - - - +
311A THR* 1.3 63.7 + - - +
313A LEU* 3.6 14.5 - - + +
314A ASN* 3.0 24.8 + - - +
323A ILE* 3.9 6.1 - - + +
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Residues in contact with THR 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 GLN* 2.8 34.6 + - - -
308A ALA 3.4 9.0 - - - -
310A PHE* 1.3 77.8 - - - +
312A LEU* 1.3 61.8 + - - +
314A ASN* 3.2 4.4 + - - +
315A LEU* 2.9 43.8 + - + +
323A ILE* 3.5 20.6 - - - +
334A HIS* 3.2 22.6 + - + +
335A VAL* 4.1 12.3 - - + -
352A VAL* 4.2 5.0 - - + +
354A CYS* 4.3 12.1 - - - -
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Residues in contact with LEU 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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240A VAL* 5.4 0.2 - - + -
244A ILE* 3.5 29.2 - - + -
308A ALA 3.1 12.0 + - - +
309A GLN* 3.5 11.0 - - - +
311A THR* 1.3 75.1 - - - +
313A LEU* 1.3 67.9 + - - +
315A LEU* 3.0 13.7 + - + +
316A VAL* 3.2 16.6 + - + +
338A LEU* 4.0 20.8 - - + +
360A LEU* 3.9 18.6 - - + -
375A SER* 3.4 30.1 - - - +
378A LEU* 3.8 8.3 - - + -
379A ALA* 3.7 24.7 - - + +
382A ILE* 4.7 2.2 - - + -
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Residues in contact with LEU 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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240A VAL* 4.6 4.7 - - + -
243A ALA* 4.0 16.6 - - + -
244A ILE* 3.6 21.7 - - + +
266A LEU* 3.9 27.8 - - + -
269A ALA* 4.1 25.6 - - + -
289A PRO* 4.0 15.6 - - + +
290A LYS 4.3 3.8 - - - +
292A VAL* 4.2 9.9 - - + -
309A GLN 3.1 12.2 + - - +
310A PHE* 3.3 18.1 + - + +
312A LEU* 1.3 77.1 - - - +
314A ASN* 1.3 78.2 + - - +
316A VAL* 3.2 4.7 + - - +
317A ALA* 3.1 21.2 + - + +
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Residues in contact with ASN 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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291A ALA* 3.4 6.1 - - - +
292A VAL* 2.8 55.5 + - - +
310A PHE 3.0 13.0 + - - +
311A THR 3.7 6.1 - - - +
313A LEU* 1.3 77.6 - - - +
315A LEU* 1.3 63.4 + - - +
317A ALA* 3.1 15.2 + - - +
319A GLY 4.5 1.9 - - - +
321A GLY* 3.7 18.8 + - - +
323A ILE* 3.5 22.4 - - - +
354A CYS* 3.6 19.7 - - + +
356A GLY* 3.4 14.9 + - - -
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Residues in contact with LEU 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 THR* 2.9 29.2 + - + +
312A LEU* 3.0 9.1 + - + +
314A ASN* 1.3 76.6 - - - +
316A VAL* 1.3 61.2 + - + +
317A ALA 3.5 0.2 - - - -
335A VAL* 5.5 3.8 - - + +
338A LEU* 3.7 32.8 - - + -
339A ILE* 6.1 0.2 - - + -
343A ALA* 3.8 26.4 - - + +
344A HIS 3.5 26.0 - - - +
345A ALA* 3.6 19.1 - - + -
354A CYS* 3.8 17.0 - - + -
355A HIS 4.4 1.8 - - - +
356A GLY* 3.6 4.1 - - - -
357A VAL* 3.0 29.3 + - - +
360A LEU* 4.7 1.4 - - + +
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 4.0 29.6 - - + +
288A ARG* 3.0 25.3 + - - +
289A PRO* 4.1 6.9 - - + +
312A LEU* 3.2 12.0 + - + +
313A LEU 3.6 10.5 - - - +
314A ASN 3.1 0.2 - - - -
315A LEU* 1.3 80.9 - - - +
317A ALA* 1.3 60.6 - - - +
357A VAL* 3.3 14.2 - - + +
358A GLU 5.0 5.9 - - - +
359A LYS* 5.7 0.2 - - - -
360A LEU* 3.8 33.7 - - + +
382A ILE* 3.9 18.4 - - + -
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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