Contacts of the helix formed by residues 310 - 329 (chain A) in PDB entry 2J6U
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 SER 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A TYR* 3.3 2.8 + - - -
308A GLY 4.1 2.6 + - - -
309A ILE* 1.3 79.6 - - - +
311A LYS* 1.3 66.8 + - - +
312A GLU* 3.6 9.4 + - - +
313A THR* 3.1 29.1 + - - -
314A ALA 2.8 18.2 + - - -
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Residues in contact with LYS 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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272A ILE* 4.6 0.4 - - + -
273A GLU* 3.1 36.2 + - - +
276A TYR* 3.5 57.8 + - + +
277A TYR 5.7 0.4 - - - +
310A SER* 1.3 74.0 - - - +
312A GLU* 1.3 67.8 + - + +
314A ALA* 3.0 3.8 + - - +
315A TYR* 2.9 44.0 + - + -
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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
----------------------------------------------------------
310A SER* 3.2 9.2 + - - +
311A LYS* 1.3 81.7 - - + +
313A THR* 1.3 65.3 + - - +
315A TYR* 3.1 13.6 + - - +
316A SER* 3.0 22.9 + - - -
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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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305A PHE* 4.3 28.0 - - + -
307A HIS* 5.3 8.1 - - + -
309A ILE* 3.5 20.0 - - + -
310A SER* 3.1 22.5 + - - -
312A GLU* 1.3 79.6 - - - +
314A ALA* 1.3 56.7 + - - +
316A SER* 3.4 5.8 + - - +
317A GLU* 2.9 29.7 + - + +
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Residues in contact with ALA 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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272A ILE* 4.3 8.1 - - + -
276A TYR* 4.0 9.4 - - + -
287A ILE* 3.8 8.4 - - + +
309A ILE* 3.6 7.3 - - + +
310A SER 2.8 14.0 + - - +
311A LYS 3.0 9.4 + - - +
313A THR* 1.3 77.7 - - - +
315A TYR* 1.3 56.4 - - - +
317A GLU* 4.8 0.2 - - - -
318A SER* 2.9 34.8 + - - -
340A PHE* 3.7 34.1 - - + -
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Residues in contact with TYR 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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269A PHE* 3.3 55.2 + + + +
272A ILE* 3.6 24.5 - - + -
273A GLU* 2.2 47.4 + - + +
311A LYS* 2.9 37.8 + - + -
312A GLU* 3.1 15.2 + - - +
314A ALA* 1.3 75.9 - - - +
316A SER* 1.3 61.2 + - - +
318A SER* 2.6 23.0 + - - -
319A VAL* 3.3 15.2 + - - +
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Residues in contact with SER 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU 3.0 12.2 + - - -
313A THR* 3.9 5.8 - - - -
315A TYR* 1.3 82.1 - - - +
317A GLU* 1.3 62.5 + - - +
319A VAL* 3.5 7.2 + - - +
320A LYS* 3.4 38.2 + - - +
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Residues in contact with GLU 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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287A ILE* 4.0 22.7 - - + -
303A ARG* 3.3 33.5 + - + +
305A PHE* 3.4 27.4 - - + -
309A ILE* 6.1 0.2 - - + -
313A THR* 2.9 23.0 + - + +
314A ALA* 4.2 1.8 - - - +
316A SER* 1.3 71.1 - - - +
318A SER* 1.3 67.0 + - - +
320A LYS* 3.0 24.4 + - - +
321A LEU* 2.9 48.7 + - + +
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Residues in contact with SER 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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268A LEU* 3.6 15.8 - - - +
269A PHE* 4.1 1.0 - - - -
272A ILE* 3.5 22.3 - - - +
287A ILE* 4.4 7.5 - - - +
289A VAL* 3.5 26.5 - - - +
314A ALA 2.9 16.3 + - - -
315A TYR* 2.6 22.3 + - - -
317A GLU* 1.3 77.1 - - - +
319A VAL* 1.3 60.2 + - - +
321A LEU 3.3 0.5 + - - -
322A LEU* 2.8 31.0 + - - +
338A VAL* 4.5 0.4 - - - -
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Residues in contact with VAL 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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261A LEU* 4.5 4.5 - - + -
265A LYS* 4.1 27.4 - - + +
268A LEU* 4.5 4.5 - - + -
269A PHE* 3.8 28.7 - - + -
315A TYR 3.3 15.6 + - - +
316A SER* 3.7 8.3 - - - +
317A GLU 3.2 0.4 - - - -
318A SER* 1.3 82.6 + - - +
320A LYS* 1.3 63.3 + - + +
322A LEU* 3.3 7.0 + - - +
323A GLN* 3.0 49.1 + - + +
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Residues in contact with LYS 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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303A ARG* 5.5 4.9 - - - +
316A SER* 3.4 29.9 + - - +
317A GLU* 3.0 29.9 + - - +
319A VAL* 1.3 79.2 - - + +
321A LEU* 1.3 57.8 + - + +
323A GLN* 3.3 19.0 + - - +
324A LYS* 2.9 27.0 + - - +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ILE* 3.9 13.7 - - + +
289A VAL* 3.7 25.8 - - + +
301A ARG* 3.4 25.4 - - + +
302A GLY* 3.7 34.5 - - - +
303A ARG* 4.8 0.9 - - + -
317A GLU* 2.9 47.3 + - + +
320A LYS* 1.3 73.2 - - - +
322A LEU* 1.3 64.8 + - - +
324A LYS* 3.2 16.5 + - + +
325A ILE* 3.0 27.7 + - - +
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Residues in contact with LEU 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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261A LEU* 3.4 29.2 - - + +
264A ILE* 3.9 24.5 - - + -
265A LYS* 4.8 4.0 - - + +
268A LEU* 3.9 22.0 - - + -
289A VAL* 4.3 8.9 - - + +
318A SER 2.8 17.2 + - - +
319A VAL* 3.6 5.8 - - - +
321A LEU* 1.3 75.8 - - - +
323A GLN* 1.3 58.3 - - - +
325A ILE* 3.0 7.6 + - + +
326A LEU* 2.9 32.1 + - + +
333A ILE* 4.1 19.1 - - + -
336A ILE* 4.0 23.6 - - + -
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Residues in contact with GLN 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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261A LEU* 3.7 33.0 - - + +
319A VAL* 3.0 35.2 + - - +
320A LYS* 3.4 20.8 - - - +
321A LEU 3.2 0.2 - - - -
322A LEU* 1.3 75.2 - - - +
324A LYS* 1.3 60.1 + - - +
326A LEU* 3.9 8.4 - - + +
327A GLU* 2.8 34.5 + - - +
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Residues in contact with LYS 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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301A ARG* 3.6 19.1 - - + +
320A LYS 2.9 14.0 + - - +
321A LEU* 3.2 24.2 + - + +
323A GLN* 1.3 75.8 - - - +
325A ILE* 1.3 58.0 + - - +
327A GLU* 4.2 7.2 - - + -
328A GLU* 2.9 57.6 + - - +
8P G 2.9 27.9 + - - +
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Residues in contact with ILE 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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289A VAL* 3.8 35.9 - - + +
291A ALA* 4.2 8.7 - - + -
299A VAL* 3.7 37.2 - - + +
300A SER* 4.3 1.3 - - - -
301A ARG* 3.4 26.2 - - + +
321A LEU 3.0 18.6 + - - +
322A LEU* 3.0 10.7 + - + +
324A LYS* 1.3 75.2 - - - +
326A LEU* 1.3 66.8 + - - +
328A GLU* 3.3 2.3 + - - -
329A ASP* 3.0 28.1 + - + +
333A ILE* 4.3 19.3 - - + -
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Residues in contact with LEU 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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259A ARG* 2.6 75.8 + - - +
261A LEU* 4.2 28.3 - - + -
264A ILE* 4.2 5.8 - - + -
322A LEU* 2.9 27.1 + - + +
323A GLN* 3.9 6.3 - - + +
325A ILE* 1.3 76.1 - - - +
327A GLU* 1.3 59.5 + - - +
329A ASP 2.8 7.4 - - - +
331A ARG 5.1 0.9 - - - +
333A ILE* 3.6 27.6 - - + -
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Residues in contact with GLU 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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323A GLN 2.8 18.9 + - - +
324A LYS* 3.8 5.6 - - + +
326A LEU* 1.3 80.5 - - - +
328A GLU* 1.3 73.3 + - + +
329A ASP 3.7 0.5 + - - -
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Residues in contact with GLU 328 (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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301A ARG* 2.7 50.2 + - - +
324A LYS* 2.9 39.6 + - - +
325A ILE 3.3 0.6 + - - +
327A GLU* 1.3 89.5 - - + +
329A ASP* 1.3 60.4 + - - +
330A GLU* 4.9 1.4 - - - +
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Residues in contact with ASP 329 (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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259A ARG* 2.5 30.0 + - - -
293A THR* 3.9 8.4 - - - +
299A VAL* 4.5 14.1 - - + +
301A ARG* 6.0 0.7 - - - +
325A ILE* 3.0 18.3 + - + +
326A LEU* 2.8 8.4 - - - +
327A GLU 3.4 1.2 - - - -
328A GLU* 1.3 82.5 - - - +
330A GLU* 1.3 77.9 + - - +
331A ARG* 2.7 61.8 + - - +
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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