Contacts of the helix formed by residues 329 - 344 (chain A) in PDB entry 1PJR
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 GLU 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ASN* 1.3 78.3 - - - +
330A ALA* 1.3 74.1 + - - +
332A GLU* 3.3 10.0 + - - +
333A ALA* 3.0 24.3 + - - +
366A VAL* 4.4 26.0 - - + +
620A ALA* 4.0 1.3 - - - +
622A MET* 3.5 4.3 + - - +
623A ARG* 3.2 34.9 - - + +
624A THR* 2.9 45.9 + - - +
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Residues in contact with ALA 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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328A ASN* 3.0 11.3 + - - +
329A GLU* 1.3 88.0 + - - +
331A ASP* 1.3 57.6 + - - +
333A ALA* 3.4 3.1 + - - +
334A GLN* 2.9 43.7 + - - +
366A VAL* 4.6 6.1 - - + -
370A MET* 3.8 22.4 - - + +
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Residues in contact with ASP 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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324A TYR* 3.0 23.2 + - - -
326A ALA* 3.3 8.2 - - - -
327A MET* 2.9 29.7 + - + +
328A ASN* 2.9 28.0 + - - +
330A ALA* 1.3 73.8 - - - +
332A GLU* 1.3 59.6 + - - +
334A GLN* 3.1 14.7 + - - +
335A PHE* 2.8 29.5 + - - +
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Residues in contact with GLU 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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324A TYR* 4.6 1.3 - - - -
326A ALA* 3.6 16.7 - - + +
328A ASN 3.1 12.7 + - - +
329A GLU* 3.3 8.8 + - - +
331A ASP* 1.3 76.0 - - - +
333A ALA* 1.3 63.4 + - - +
335A PHE* 3.2 13.8 + - - +
336A VAL* 3.2 17.3 + - - +
363A GLN* 5.9 0.2 + - - -
366A VAL* 6.0 1.2 - - - +
578A ILE* 4.0 19.2 - - + +
579A GLY* 3.1 21.8 + - - -
618A THR* 3.2 27.1 + - - +
619A SER 3.9 7.0 - - - +
620A ALA* 5.1 0.2 - - + -
623A ARG* 2.8 45.2 + - - +
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Residues in contact with ALA 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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329A GLU 3.0 16.5 + - - +
330A ALA* 3.7 2.9 - - - +
332A GLU* 1.3 77.4 - - - +
334A GLN* 1.3 61.6 + - - +
336A VAL 3.5 0.7 + - - -
337A ALA* 3.1 23.9 + - - +
366A VAL* 4.0 16.6 - - + +
367A MET* 3.6 30.2 - - - +
370A MET* 3.5 24.5 - - + +
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Residues in contact with GLN 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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330A ALA* 2.9 41.2 + - - +
331A ASP* 3.4 13.1 - - - +
333A ALA* 1.3 72.5 - - - +
335A PHE* 1.3 66.5 + - - +
337A ALA* 3.4 6.2 + - - +
338A GLY* 2.9 21.8 + - - -
370A MET* 3.9 22.9 - - - +
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Residues in contact with PHE 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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322A LEU* 4.1 20.9 - - + -
324A TYR* 3.5 67.8 - + + -
331A ASP* 2.8 6.5 + - - +
332A GLU 3.4 8.5 - - - +
334A GLN* 1.3 74.9 - - - +
336A VAL* 1.3 68.4 + - + +
338A GLY* 3.0 4.6 + - - -
339A ARG* 2.9 41.1 + - + +
576A PHE* 4.8 1.6 - + - -
616A VAL* 4.1 20.9 - - + -
618A THR* 4.1 10.1 - - + -
650A SER* 3.9 19.1 - - - -
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Residues in contact with VAL 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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332A GLU 3.2 13.5 + - - +
333A ALA 3.8 6.7 - - - +
335A PHE* 1.3 81.6 - - + +
337A ALA* 1.3 62.7 + - - +
339A ARG* 3.3 1.9 + - - +
340A ILE* 3.1 36.6 + - + +
356A VAL* 3.7 29.2 - - + -
367A MET* 3.8 14.6 - - + -
576A PHE* 3.8 32.1 - - + -
578A ILE* 3.9 23.6 - - + -
618A THR* 4.6 4.0 - - + -
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Residues in contact with ALA 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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333A ALA 3.1 17.8 + - - +
334A GLN* 3.8 4.5 - - - +
336A VAL* 1.3 75.7 - - - +
338A GLY* 1.3 57.6 + - - +
340A ILE* 3.4 0.6 + - - -
341A ARG* 2.9 32.0 + - - +
367A MET* 4.4 0.2 - - - +
370A MET* 4.5 16.8 - - + +
371A LEU* 4.1 15.0 - - + -
374A ALA* 4.5 7.2 - - + -
376A ILE* 3.4 24.6 - - + +
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Residues in contact with GLY 338 (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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334A GLN 2.9 16.3 + - - -
335A PHE* 3.4 4.0 - - - -
337A ALA* 1.3 76.0 - - - +
339A ARG* 1.3 62.8 + - - +
341A ARG* 3.1 13.6 + - - +
342A GLU* 3.0 28.6 + - - +
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Residues in contact with ARG 339 (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 LYS* 5.2 0.4 - - - +
322A LEU* 4.5 23.8 - - - +
335A PHE* 2.9 32.0 + - + +
336A VAL 3.9 6.3 - - - +
338A GLY* 1.3 71.0 - - - +
340A ILE* 1.3 62.5 + - - +
342A GLU* 3.6 16.2 + - - +
343A ALA* 3.1 35.6 + - - +
348A GLU* 4.4 10.3 + - - -
349A ARG* 5.6 0.4 - - - +
354A PHE* 4.6 15.9 - - - -
574A VAL* 4.4 7.1 - - - +
576A PHE* 4.0 21.1 - - + -
614A GLU* 2.9 35.7 + - - +
616A VAL* 4.1 20.2 - - - +
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Residues in contact with ILE 340 (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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336A VAL* 3.1 35.3 + - + +
337A ALA 3.7 3.8 - - - +
339A ARG* 1.3 74.0 - - - +
341A ARG* 1.3 64.6 + - - +
343A ALA* 3.5 0.9 + - - +
344A VAL* 3.1 28.8 + - - +
351A TYR* 4.0 13.9 - - + -
354A PHE* 4.0 25.7 - - + -
356A VAL* 4.6 2.2 - - + -
371A LEU* 4.4 12.3 - - + -
376A ILE* 4.0 7.9 - - + -
559A VAL* 3.9 45.1 - - + -
576A PHE* 4.0 20.0 - - + -
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Residues in contact with ARG 341 (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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337A ALA 2.9 18.4 + - - +
338A GLY* 3.5 9.8 + - - +
340A ILE* 1.3 74.6 - - - +
342A GLU* 1.3 64.7 + - - +
344A VAL* 3.0 7.5 + - - +
345A GLU* 3.0 45.2 + - - +
351A TYR* 5.2 4.3 - - - +
374A ALA* 3.9 36.3 + - + +
376A ILE* 4.4 13.0 - - + +
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Residues in contact with GLU 342 (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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338A GLY 3.0 17.6 + - - +
339A ARG* 3.6 18.1 + - - +
341A ARG* 1.3 80.0 - - - +
343A ALA* 1.3 62.4 + - - +
344A VAL 3.2 0.5 + - - -
345A GLU* 3.6 6.4 + - - +
346A ARG* 3.1 38.9 + - - +
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Residues in contact with ALA 343 (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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339A ARG* 3.1 25.1 + - - +
340A ILE 4.2 0.2 - - - +
341A ARG 3.5 0.2 - - - -
342A GLU* 1.3 74.5 - - - +
344A VAL* 1.3 59.2 + - - +
346A ARG* 3.7 11.6 - - - +
348A GLU* 3.1 46.0 + - + +
349A ARG* 3.2 22.6 + - + -
354A PHE* 4.0 11.9 - - + -
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Residues in contact with VAL 344 (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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340A ILE 3.1 18.6 - - - +
341A ARG* 3.0 4.5 + - - +
343A ALA* 1.3 74.0 - - - +
345A GLU* 1.3 59.1 + - - +
346A ARG 2.7 17.6 + - - -
347A GLY* 3.0 11.8 + - - -
349A ARG 3.3 21.3 - - - +
350A ARG* 4.0 13.0 - - - -
351A TYR* 3.8 48.2 - - + +
354A PHE* 4.2 6.7 - - + -
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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