Contacts of the helix formed by residues 318 - 337 (chain A) in PDB entry 1OJ7
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 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A GLY* 1.3 76.2 - - - +
319A ASP* 1.3 65.8 + - - +
320A ASP* 3.5 10.5 + - - +
321A GLU* 3.1 36.7 + - - +
322A ARG* 3.0 21.2 + - - +
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 3.7 30.1 + - + -
305A LEU* 3.6 31.0 - - + +
318A SER* 1.3 73.3 - - - +
320A ASP* 1.3 58.0 + - - +
322A ARG* 3.3 15.0 + - - +
323A ILE* 2.9 38.3 + - + +
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Residues in contact with ASP 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG* 2.9 31.8 + - - +
318A SER* 3.2 8.4 + - - +
319A ASP* 1.3 80.2 - - - +
321A GLU* 1.3 62.4 + - - +
323A ILE* 4.7 1.6 - - - +
324A ASP* 2.9 43.5 - - - +
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Residues in contact with GLU 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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316A GLU 4.8 2.5 - - - +
317A GLY* 3.3 12.7 - - - -
318A SER* 3.1 38.3 + - - +
320A ASP* 1.3 82.2 + - - +
322A ARG* 1.3 58.4 + - - +
324A ASP* 3.7 7.2 - - - +
325A ALA* 3.0 30.0 + - - +
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 3.7 43.8 + - + +
308A ALA* 4.0 5.0 - - + +
309A GLU* 4.2 16.8 + - - -
314A ILE* 3.9 27.4 + - + +
315A THR* 3.6 28.5 + - - +
316A GLU 3.3 19.5 - - - +
317A GLY 3.5 20.2 + - - -
318A SER 3.0 13.0 + - - +
319A ASP* 3.8 12.9 + - - +
321A GLU* 1.3 75.7 - - - +
323A ILE* 1.3 58.9 + - - +
325A ALA* 3.4 2.1 + - - +
326A ALA* 3.0 28.9 + - - +
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Residues in contact with ILE 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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297A ARG* 3.8 42.8 - - + +
298A ASP* 6.1 0.4 - - - +
301A ARG* 3.9 34.1 - - + +
304A LEU* 3.9 29.2 - - + -
305A LEU* 4.0 13.5 - - + +
308A ALA* 5.6 0.2 - - - -
319A ASP* 2.9 25.7 + - + +
320A ASP* 4.9 0.9 - - - +
322A ARG* 1.3 74.1 - - - +
324A ASP* 1.3 65.9 - - - +
326A ALA* 3.2 5.4 + - - +
327A ILE* 2.9 37.5 + - + +
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Residues in contact with ASP 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG* 2.6 38.1 + - - +
320A ASP* 2.9 38.7 - - - +
321A GLU* 3.7 8.4 - - - +
323A ILE* 1.3 75.1 - - - +
325A ALA* 1.3 58.5 + - - +
327A ILE* 3.5 4.9 + - - +
328A ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 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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314A ILE* 3.7 22.5 - - + +
321A GLU 3.0 18.3 + - - +
322A ARG 3.7 4.0 - - - +
323A ILE 3.1 0.2 - - - -
324A ASP* 1.3 75.8 - - - +
326A ALA* 1.3 59.0 + - - +
328A ALA* 3.4 7.1 + - - +
329A ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 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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304A LEU* 4.6 5.6 - - + +
307A TYR* 4.1 17.9 - - + -
308A ALA* 3.7 27.6 - - + -
312A TRP* 4.5 1.3 + - + -
314A ILE* 3.7 8.7 - - + +
322A ARG 3.0 17.5 + - - +
323A ILE* 3.2 6.3 + - - +
325A ALA* 1.3 74.3 - - - +
327A ILE* 1.3 64.5 + - + +
329A ALA* 3.4 4.7 + - - +
330A THR* 2.8 30.2 + - - -
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Residues in contact with ILE 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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290A PRO* 3.9 31.3 - - + +
293A TRP* 3.9 22.9 - - + -
294A ASN* 3.7 34.8 - - + +
297A ARG* 3.9 9.2 - - - +
304A LEU* 5.0 3.1 - - + -
323A ILE* 2.9 38.3 + - + +
324A ASP* 3.8 5.2 - - - +
326A ALA* 1.3 75.2 - - - +
328A ALA* 1.3 58.4 + - - +
330A THR* 3.2 8.2 + - - -
331A ARG* 2.9 33.0 + - - +
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Residues in contact with ALA 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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324A ASP 2.9 18.4 + - - +
325A ALA* 3.7 7.9 - - - +
326A ALA 3.2 0.2 - - - -
327A ILE* 1.3 77.1 - - - +
329A ALA* 1.3 57.4 + - - +
331A ARG* 3.7 9.1 - - - +
332A ASN* 3.0 30.4 + - - +
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Residues in contact with ALA 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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312A TRP* 3.8 39.2 - - + -
314A ILE* 4.7 4.3 - - + -
325A ALA 2.9 18.0 + - - +
326A ALA* 3.7 4.9 - - - +
327A ILE 3.3 0.2 - - - -
328A ALA* 1.3 74.0 - - - +
330A THR* 1.3 60.6 + - - +
332A ASN* 3.5 7.8 + - - +
333A PHE* 3.0 28.4 + - - +
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Residues in contact with THR 330 (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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196A PHE* 4.0 8.5 - - + -
289A LEU* 4.3 4.3 - - + -
290A PRO* 6.0 4.7 - - + -
293A TRP* 3.5 19.1 - - + -
307A TYR* 2.5 32.7 + - - +
312A TRP* 3.8 4.6 + - - -
326A ALA 2.8 20.6 + - - -
327A ILE 3.2 5.1 + - - -
329A ALA* 1.3 74.3 - - - +
331A ARG* 1.3 64.0 + - - +
333A PHE* 3.2 7.7 + - - +
334A PHE* 3.2 49.3 + - + -
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Residues in contact with ARG 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ILE 5.2 0.6 + - - -
290A PRO* 3.3 38.8 - - + +
291A ALA* 4.4 4.8 - - - +
327A ILE* 2.9 22.0 + - - +
328A ALA* 3.7 7.9 - - - +
330A THR* 1.3 78.0 - - - +
332A ASN* 1.3 56.4 + - - +
334A PHE* 3.3 7.9 + - - +
335A GLU* 3.0 36.3 + - + +
341A THR* 3.0 56.5 + - + +
342A HIS* 3.4 30.8 + - - -
385A ALA 5.7 2.8 + - - -
386A ALA* 6.3 0.4 - - - +
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Residues in contact with ASN 332 (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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328A ALA 3.0 18.6 + - - +
329A ALA* 3.7 8.5 + - - +
331A ARG* 1.3 73.5 - - - +
333A PHE* 1.3 63.0 + - - +
335A GLU* 3.3 6.6 + - - +
336A GLN* 2.8 55.9 + - - +
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Residues in contact with PHE 333 (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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192A VAL* 3.9 10.1 - - + -
196A PHE* 3.7 33.9 - + + -
224A LEU 3.6 18.8 - - - -
225A ILE* 3.7 28.7 - - + -
229A PRO* 3.9 22.9 - - + -
312A TRP* 3.9 13.5 - + + -
329A ALA 3.0 19.2 + - - +
330A THR* 3.2 5.1 + - - +
332A ASN* 1.3 80.3 - - - +
334A PHE* 1.3 80.5 + + - +
336A GLN* 3.3 5.7 + - + +
337A LEU* 3.1 49.5 + - + +
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Residues in contact with PHE 334 (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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193A VAL* 3.8 21.1 - - + -
196A PHE* 3.9 29.4 - + + -
197A VAL* 4.0 12.3 - - + -
286A ALA* 3.7 36.6 - - + -
289A LEU* 4.0 24.0 - - + -
290A PRO* 5.1 2.2 - - + -
330A THR* 3.2 30.4 + - + -
331A ARG* 3.6 7.2 - - - +
333A PHE* 1.3 93.7 - + - +
335A GLU* 1.3 62.2 + - - +
337A LEU* 3.1 15.5 + - - +
338A GLY 3.4 0.3 + - - -
339A VAL* 3.0 34.3 + - + +
341A THR* 4.0 5.8 - - + -
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Residues in contact with GLU 335 (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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331A ARG* 3.0 27.0 + - + +
332A ASN* 3.7 7.6 - - - +
334A PHE* 1.3 77.0 - - - +
336A GLN* 1.3 67.1 + - - +
338A GLY* 3.0 19.6 + - - -
339A VAL 3.7 4.7 + - - -
340A PRO* 3.6 21.2 - - - +
341A THR* 2.7 35.7 + - + +
342A HIS* 4.5 3.8 + - - -
345A ASP* 4.2 5.4 - - - +
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Residues in contact with GLN 336 (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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229A PRO* 6.6 0.7 - - + -
232A LEU* 4.8 0.7 - - - +
332A ASN* 2.8 45.2 + - - +
333A PHE* 3.8 6.7 - - + +
334A PHE 3.2 0.2 - - - -
335A GLU* 1.3 85.2 + - - +
337A LEU* 1.3 60.5 + - - +
338A GLY 3.2 1.2 + - - -
52C ASP* 4.7 13.3 - - - +
55C LYS* 4.2 20.3 + - - -
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Residues in contact with LEU 337 (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 PRO* 5.0 0.9 - - - +
189A ALA* 3.3 28.2 - - + +
192A VAL* 3.7 29.4 - - + -
193A VAL* 3.9 20.6 - - + -
228A GLY 4.1 5.2 - - - +
229A PRO* 3.9 33.0 - - + -
232A LEU* 3.6 31.1 - - + +
333A PHE* 3.1 34.5 + - + +
334A PHE* 3.1 10.8 + - - +
336A GLN* 1.3 76.7 - - - +
338A GLY* 1.3 57.5 + - - +
339A VAL* 4.3 2.0 - - + -
55C LYS* 5.7 1.3 - - - -
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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
------------------------------------------------------------
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