Contacts of the helix formed by residues 315 - 328 (chain A) in PDB entry 4JYI
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 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A GLU 3.5 0.4 + - - +
314A MET* 1.3 74.5 - - - +
316A ASP* 1.3 60.9 + - - +
317A THR* 3.3 5.3 + - - -
318A GLU* 3.0 26.5 + - - +
319A THR* 2.9 32.2 + - - -
355A TYR* 2.7 25.4 + - - -
359A ARG* 3.4 29.9 + - - +
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Residues in contact with ASP 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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185A ARG* 4.2 6.5 - - + +
188A HIS* 3.7 26.6 + - + +
189A GLN* 2.8 49.6 + - + +
192A PHE 5.2 2.6 - - - +
194A SER* 5.0 16.1 - - - -
315A ASP* 1.3 76.1 - - - +
317A THR* 1.3 58.1 + - - +
319A THR* 4.6 0.4 - - - -
320A GLY* 2.8 28.4 + - - -
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Residues in contact with THR 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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181A THR* 3.5 34.8 - - + +
184A ILE* 4.8 1.2 - - - +
185A ARG* 3.2 33.4 - - - +
315A ASP* 3.2 2.6 + - - -
316A ASP* 1.3 78.5 - - - +
318A GLU* 1.3 58.8 + - - +
320A GLY* 3.8 0.7 - - - -
321A LEU* 2.9 36.2 + - + +
355A TYR* 3.5 44.8 + - + -
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Residues in contact with GLU 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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314A MET* 3.1 30.9 - - + +
315A ASP* 3.0 20.9 + - - +
317A THR* 1.3 73.2 - - - +
319A THR* 1.3 61.4 + - - +
321A LEU* 3.3 1.7 + - - +
322A LEU* 2.9 31.2 + - - +
352A LEU* 4.4 22.3 - - + +
355A TYR* 3.5 19.2 - - + -
356A ILE* 4.2 2.6 - - + +
359A ARG* 3.1 17.4 + - - -
360A ARG* 2.6 47.1 + - - -
370A ILE* 4.4 6.2 - - + +
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Residues in contact with THR 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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188A HIS* 3.5 29.4 - - + +
264A LEU* 4.0 19.5 - - + +
265A ARG* 5.7 1.6 - - + -
268A THR* 4.2 23.5 - - + +
314A MET* 3.6 26.0 + - - +
315A ASP 2.9 19.0 + - - -
316A ASP 4.1 0.2 - - - -
318A GLU* 1.3 76.2 - - - +
320A GLY* 1.3 57.9 + - - +
322A LEU* 3.9 3.6 - - - +
323A SER* 2.9 33.8 + - - +
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Residues in contact with GLY 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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184A ILE* 3.4 18.6 - - - +
188A HIS* 3.8 23.7 - - - -
235A PHE* 3.5 3.9 - - - -
316A ASP 2.8 19.0 + - - -
317A THR 3.8 0.9 - - - -
319A THR* 1.3 78.9 - - - +
321A LEU* 1.3 54.6 + - - +
323A SER* 3.3 5.2 + - - -
324A ALA 2.9 23.9 + - - -
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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
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180A LEU* 5.5 0.2 - - + -
181A THR* 4.6 8.3 - - + -
184A ILE* 3.4 34.3 - - + +
317A THR* 2.9 36.9 + - + +
318A GLU* 3.3 4.0 + - - +
320A GLY* 1.3 71.9 - - - +
322A LEU* 1.3 60.6 + - - +
324A ALA* 3.2 3.4 + - - +
325A ILE* 2.9 36.8 + - + +
348A LEU* 4.1 19.5 - - + +
351A ALA* 4.1 17.5 - - + +
352A LEU* 3.7 42.8 - - + +
355A TYR* 4.7 2.2 - - + -
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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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264A LEU* 4.1 24.5 - - + -
309A LEU* 6.1 0.2 - - + -
314A MET* 4.4 20.2 - - - -
318A GLU 2.9 16.3 + - - +
319A THR* 3.9 4.7 - - - +
321A LEU* 1.3 74.9 - - - +
323A SER* 1.3 56.8 + - - +
325A ILE* 3.4 5.5 + - + +
326A CYS* 3.0 34.0 + - - -
352A LEU* 4.1 22.0 - - + -
370A ILE* 3.9 26.9 - - + +
371A LEU* 4.1 4.0 - - + -
373A LYS* 4.4 12.3 - - + -
374A ILE* 3.8 30.9 - - + +
377A LEU* 5.1 2.7 - - + -
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A HIS* 4.6 5.6 + - - -
235A PHE* 3.9 18.6 - - - -
261A ILE* 3.7 25.7 - - - +
264A LEU* 3.5 16.9 - - - +
265A ARG* 5.2 3.1 + - - +
319A THR* 2.9 25.5 + - - +
320A GLY* 3.4 6.4 - - - -
321A LEU 3.2 0.2 - - - -
322A LEU* 1.3 77.0 - - - +
324A ALA* 1.3 56.6 + - - +
326A CYS* 3.2 8.9 + - - +
327A LEU* 3.0 27.9 + - - +
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Residues in contact with ALA 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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184A ILE* 4.2 5.4 - - + -
235A PHE* 4.1 1.1 - - - -
239A LEU* 3.8 35.7 - - + -
320A GLY 2.9 16.9 + - - +
321A LEU 3.2 4.2 + - - +
323A SER* 1.3 76.1 - - - +
325A ILE* 1.3 58.8 + - - +
327A LEU* 3.2 0.8 + - - +
328A ILE* 2.8 35.5 + - - +
348A LEU* 3.8 23.8 - - + -
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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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321A LEU 2.9 23.3 + - - +
322A LEU* 3.7 6.7 - - - +
324A ALA* 1.3 75.0 - - - +
326A CYS* 1.3 62.8 + - - +
328A ILE 3.4 6.1 - - - +
329A CYS* 4.1 1.9 - - - +
345A GLN* 3.1 32.2 + - + +
348A LEU* 3.7 35.0 - - + +
349A LEU* 3.8 27.6 - - + -
352A LEU* 3.8 29.2 - - + -
371A LEU* 4.2 3.4 - - + -
374A ILE* 3.6 19.5 - - + +
372B MET* 4.1 6.4 - - + +
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Residues in contact with CYS 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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257A ALA* 4.0 2.2 - - + -
260A ASP* 4.3 23.1 - - + +
261A ILE* 4.5 7.0 - - + -
264A LEU* 5.5 0.7 - - - -
322A LEU 3.0 20.8 + - - -
323A SER* 3.4 12.1 - - - +
324A ALA 3.2 0.2 - - - -
325A ILE* 1.3 79.6 - - - +
327A LEU* 1.3 61.7 + - - +
329A CYS* 3.6 7.9 - - - +
332A ARG* 3.2 22.6 + - - +
374A ILE* 4.0 25.8 - - - -
377A LEU* 3.8 28.9 - - - -
378A ARG* 5.5 2.0 + - - +
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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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232A ILE* 5.4 1.1 - - + +
235A PHE* 5.0 4.5 - - + -
236A ALA* 3.4 31.4 - - + -
239A LEU* 3.6 20.9 - - + -
242A PHE* 3.9 15.0 - - + -
253A LEU* 3.4 53.8 - - + +
254A LEU* 3.8 19.5 - - + +
257A ALA* 3.7 11.6 - - + +
261A ILE* 4.4 10.5 - - + -
323A SER 3.0 15.9 + - - +
324A ALA* 3.2 4.2 + - - +
326A CYS* 1.3 80.5 - - - +
328A ILE* 1.3 58.8 - - + +
329A CYS* 3.0 7.8 + - - +
332A ARG* 5.0 0.9 + - - -
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Residues in contact with ILE 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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239A LEU* 4.1 31.9 - - + -
240A PRO 4.8 3.4 - - - +
242A PHE* 4.7 12.1 - - + -
245A LEU* 5.6 0.7 - - + -
253A LEU* 4.5 4.3 - - + -
324A ALA 2.8 16.9 + - - +
325A ILE 3.4 2.6 - - - +
327A LEU* 1.3 72.5 - - + +
329A CYS* 1.3 58.4 + - - +
341A VAL* 3.5 31.9 - - + +
344A LEU* 3.8 34.5 - - + +
345A GLN* 3.1 32.9 + - - +
348A LEU* 3.8 23.1 - - + -
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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