Contacts of the helix formed by residues 319 - 331 (chain A) in PDB entry 1JPW
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 GLY 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A VAL* 4.5 1.6 - - - -
316A LEU 3.1 9.9 + - - -
317A ALA 3.3 2.6 + - - -
318A SER* 1.3 78.9 - - - +
320A GLY* 1.3 65.5 + - - +
321A PRO* 3.5 4.0 - - - -
322A GLN* 3.3 33.6 - - - +
323A ALA* 3.5 2.6 + - - +
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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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283A VAL* 3.8 18.2 - - - -
286A LEU* 4.9 1.3 - - - -
315A ILE* 3.1 23.0 + - - -
318A SER 3.2 2.4 + - - -
319A GLY* 1.3 77.1 - - - +
321A PRO* 1.3 69.6 - - - +
323A ALA* 2.9 14.0 + - - +
324A LEU* 3.0 22.3 + - - +
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Residues in contact with PRO 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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315A ILE* 4.8 2.0 - - + -
316A LEU* 3.3 43.5 - - + +
319A GLY* 3.5 4.9 - - - -
320A GLY* 1.3 88.7 - - - +
322A GLN* 1.3 58.2 + - - +
323A ALA 2.9 0.7 + - - -
324A LEU* 3.1 7.8 + - + +
325A VAL* 2.8 37.1 + - + +
344A LEU* 5.0 2.5 - - + -
347A LEU* 5.2 5.4 - - + -
353A ASN* 3.9 8.3 - - - +
356A ALA* 4.0 20.9 - - + -
357A ILE* 4.2 18.2 - - + -
360A ALA* 4.9 0.2 - - - -
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Residues in contact with GLN 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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319A GLY* 3.3 22.4 + - - +
321A PRO* 1.3 78.8 - - - +
323A ALA* 1.3 77.4 + - - +
325A VAL* 4.0 2.2 - - - +
326A ASN* 3.3 20.8 + - - +
329A ARG* 4.7 7.5 + - - +
356A ALA 5.0 0.4 + - - +
360A ALA* 3.8 28.1 - - + +
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Residues in contact with ALA 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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283A VAL* 5.2 3.1 - - + +
286A LEU* 3.6 29.3 - - + +
319A GLY 3.9 4.9 - - - +
320A GLY* 2.9 12.7 + - - +
322A GLN* 1.3 92.5 + - - +
324A LEU* 1.3 66.0 + - - +
326A ASN* 3.0 14.9 + - - +
327A ILE* 3.2 16.3 + - - +
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Residues in contact with LEU 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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286A LEU* 3.7 21.3 - - + -
298A THR* 4.0 17.9 - - + -
301A LEU* 4.6 7.6 - - + -
315A ILE* 5.2 2.5 - - + -
320A GLY* 3.0 22.3 + - - +
321A PRO 3.8 3.1 - - - +
323A ALA* 1.3 74.4 - - - +
325A VAL* 1.3 58.9 + - - +
327A ILE* 2.8 29.0 + - + +
328A MET* 3.1 10.7 + - - +
340A THR* 3.6 25.6 - - + +
343A VAL* 3.4 33.9 - - + -
344A LEU* 3.9 22.0 - - + -
347A LEU* 4.2 10.3 - - + -
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Residues in contact with VAL 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 PRO 2.8 24.0 + - - +
322A GLN* 4.1 7.2 - - - +
324A LEU* 1.3 79.0 - - - +
326A ASN* 1.3 58.7 + - - +
328A MET* 3.4 15.9 + - - +
329A ARG* 3.3 19.7 + - - +
344A LEU* 4.3 10.5 - - + -
357A ILE* 4.0 21.5 - - + +
360A ALA* 3.9 13.7 - - + +
361A GLY 3.8 8.5 - - - +
362A GLY* 3.6 37.7 - - - +
365A ALA* 3.8 6.7 - - + +
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Residues in contact with ASN 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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322A GLN* 3.3 15.4 + - - +
323A ALA* 3.0 8.4 + - - +
325A VAL* 1.3 76.8 - - - +
327A ILE* 1.3 67.4 + - - +
329A ARG* 2.7 52.5 + - - +
330A THR* 3.2 27.0 + - - -
331A TYR* 5.5 2.3 - - - -
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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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286A LEU* 4.1 25.1 - - + +
294A LEU* 4.2 20.6 - - + -
298A THR* 4.0 25.8 - - + -
323A ALA 3.2 14.3 + - - +
324A LEU* 2.8 17.2 + - - +
326A ASN* 1.3 80.2 - - - +
328A MET* 1.3 60.9 + - - +
329A ARG 3.2 1.4 + - - -
331A TYR* 3.2 39.5 + - + +
336A LEU* 3.9 18.8 - - + -
337A LEU* 4.2 4.9 - - + +
340A THR* 3.4 20.6 - - + +
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Residues in contact with MET 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 LEU 3.1 11.8 + - - +
325A VAL* 3.7 9.2 - - - +
326A ASN 3.2 0.2 - - - -
327A ILE* 1.3 76.9 - - - +
329A ARG* 1.3 59.2 + - - +
337A LEU* 3.7 22.9 - - + +
340A THR* 3.7 26.9 - - - -
341A SER* 3.6 30.7 - - - -
344A LEU* 3.9 15.0 - - + -
365A ALA* 3.7 20.6 - - + +
366A LEU* 3.9 20.0 - - + -
368A LEU* 3.8 5.5 - - - +
369A HIS* 2.8 35.5 + - + +
377A LEU* 4.8 0.7 - - + -
381A CYS* 4.2 11.4 - - - -
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Residues in contact with ARG 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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322A GLN* 4.7 7.9 + - - +
325A VAL* 3.3 22.1 - - - +
326A ASN* 2.7 48.0 - - - +
327A ILE 3.1 1.0 - - - -
328A MET* 1.3 79.7 - - - +
330A THR* 1.3 63.1 + - - +
331A TYR 5.2 0.6 - - - +
360A ALA* 3.3 25.5 + - - +
361A GLY* 5.2 1.7 - - - -
365A ALA* 3.9 14.6 - - + -
368A LEU* 4.0 19.3 - - + +
369A HIS* 5.9 0.2 - - - -
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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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326A ASN* 3.2 26.7 + - - -
329A ARG* 1.3 80.9 - - - +
331A TYR* 1.3 96.3 + - + +
332A THR* 4.0 7.0 + - - +
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Residues in contact with TYR 331 (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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286A LEU 6.0 0.2 - - - -
287A ASN 5.6 0.3 + - - -
288A LYS 4.1 11.9 + - - -
289A THR* 4.1 19.5 - - - +
291A VAL* 3.6 22.7 - - + -
294A LEU* 3.9 19.5 - - + -
326A ASN* 5.2 2.5 - - - -
327A ILE* 3.2 31.1 + - + +
328A MET 4.8 0.9 - - - +
329A ARG 5.2 0.3 - - - -
330A THR* 1.3 103.7 - - + +
332A THR* 1.3 64.3 + - - +
333A TYR 3.6 5.6 - - - +
336A LEU* 3.9 29.6 - - + -
337A LEU* 3.3 24.6 - - + +
369A HIS* 4.2 6.6 - - - -
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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