Contacts of the helix formed by residues 369 - 385 (chain A) in PDB entry 2W7J
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 369 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ARG* 6.2 2.7 - - - -
288A ASN* 3.4 12.1 - - - -
367A GLY 3.6 2.7 + - - -
368A PHE* 1.3 73.5 - - - +
370A LEU* 1.3 65.6 + - - -
371A GLU 3.4 2.9 - - - -
372A GLU* 2.7 18.8 + - - +
373A MET* 3.0 24.1 + - - +
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Residues in contact with LEU 370 (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 ASP* 4.0 19.7 - - + +
288A ASN* 3.7 15.3 - - - +
291A ARG* 3.7 54.7 - - + +
369A GLY* 1.3 71.2 - - - -
371A GLU* 1.3 67.5 + - + +
373A MET* 3.1 5.2 + - - +
374A ASP* 3.0 25.5 + - - +
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Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 3.9 17.2 + - - -
369A GLY 3.4 0.4 - - - -
370A LEU* 1.3 77.8 - - + +
372A GLU* 1.3 73.6 + - - +
374A ASP* 3.3 11.8 + - - +
375A GLU* 3.1 22.0 + - - +
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Residues in contact with GLU 372 (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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367A GLY 4.8 1.5 - - - +
368A PHE* 3.7 37.7 - - + -
369A GLY* 2.7 34.0 + - - +
371A GLU* 1.3 83.9 + - - +
373A MET* 1.3 62.1 + - - +
375A GLU* 3.2 3.0 + - - +
376A ILE* 2.8 34.7 + - - +
403A LEU* 3.7 26.4 - - + +
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Residues in contact with MET 373 (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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288A ASN* 3.4 47.3 - - + +
291A ARG* 3.8 13.2 - - + -
292A LEU* 3.4 29.5 - - - +
295A ALA* 4.7 1.8 - - - -
360A THR* 4.1 13.2 - - - -
363A VAL* 3.9 11.2 - - + -
368A PHE* 3.7 25.6 - - + -
369A GLY 3.0 21.8 + - - +
370A LEU* 3.1 9.2 + - - +
372A GLU* 1.3 77.2 - - - +
374A ASP* 1.3 62.8 + - - +
376A ILE* 3.4 18.3 + - + -
377A ALA* 3.0 22.0 + - - +
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Residues in contact with ASP 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 2.8 48.5 + - - +
295A ALA* 3.7 18.9 - - - +
299A GLU* 5.2 0.7 - - - +
370A LEU 3.0 8.9 + - - -
371A GLU* 3.4 17.1 - - - +
372A GLU 3.3 0.2 - - - -
373A MET* 1.3 75.8 - - - +
375A GLU* 1.3 57.8 + - - +
377A ALA* 3.4 3.3 + - - +
378A ALA* 3.0 28.1 + - - +
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLU 3.1 10.5 + - - +
372A GLU* 3.2 8.3 + - - +
374A ASP* 1.3 77.3 - - - +
376A ILE* 1.3 60.4 + - - +
378A ALA* 3.1 4.3 + - - +
379A ILE* 2.8 43.5 + - + +
399A ARG* 2.8 58.8 + - - +
403A LEU* 3.7 21.1 - - + -
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Residues in contact with ILE 376 (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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26A ILE* 4.0 21.3 - - + -
28A LEU* 3.9 25.6 - - + -
292A LEU* 4.0 9.9 - - + -
336A ILE* 4.8 4.4 - - + +
363A VAL* 4.7 0.7 - - + -
368A PHE* 3.8 24.5 - - + -
372A GLU 2.8 24.7 + - - +
373A MET* 3.7 21.8 - - + +
375A GLU* 1.3 72.5 - - - +
377A ALA* 1.3 56.9 + - - +
379A ILE* 3.3 9.4 + - - +
380A ILE* 2.9 47.4 + - + +
403A LEU* 3.9 15.5 - - + -
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 3.9 8.9 - - + +
295A ALA* 3.4 46.0 - - + +
296A LEU* 3.7 18.6 - - + +
299A GLU* 3.5 11.1 - - + +
373A MET 3.0 11.0 + - - +
374A ASP 3.6 1.8 - - - +
376A ILE* 1.3 75.7 - - - +
378A ALA* 1.3 58.2 + - - +
380A ILE* 3.3 2.8 + - - +
381A GLY 2.9 23.7 + - - -
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Residues in contact with ALA 378 (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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299A GLU* 3.6 22.1 + - - +
374A ASP 3.0 18.1 + - - +
375A GLU* 3.1 6.9 + - - +
377A ALA* 1.3 76.0 - - - +
379A ILE* 1.3 58.2 + - - +
381A GLY* 3.4 1.4 + - - -
382A LEU* 2.9 29.5 + - - +
399A ARG* 3.5 23.4 + - - +
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Residues in contact with ILE 379 (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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26A ILE* 4.9 1.3 - - + -
336A ILE* 3.6 22.4 - - + -
375A GLU* 2.8 51.2 + - + +
376A ILE* 3.7 5.6 - - - +
378A ALA* 1.3 73.4 - - - +
380A ILE* 1.3 58.6 + - - +
382A LEU* 3.3 6.8 + - - +
383A VAL* 2.9 30.8 + - + +
396A ALA* 3.8 24.7 - - + -
399A ARG* 3.7 31.6 - - + +
400A VAL* 4.0 10.5 - - + +
403A LEU* 3.9 16.8 - - + -
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Residues in contact with ILE 380 (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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28A LEU* 4.2 8.1 - - + -
292A LEU* 5.2 0.7 - - + -
296A LEU* 4.0 22.7 - - + -
301A PHE* 4.1 4.3 - - + -
315A VAL* 6.2 1.3 - - + -
331A LEU* 4.1 25.6 - - + -
336A ILE* 4.2 10.3 - - + -
356A ILE* 5.0 4.5 - - + -
358A ILE* 4.0 25.8 - - + -
376A ILE* 2.9 37.7 + - + +
377A ALA 3.7 4.3 - - - +
379A ILE* 1.3 75.0 - - - +
381A GLY* 1.3 58.3 + - - +
383A VAL* 3.3 1.4 + - - -
384A LEU* 2.9 53.4 + - + +
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Residues in contact with GLY 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLU* 4.4 6.3 - - - -
301A PHE* 3.6 20.8 - - - -
377A ALA 2.9 13.5 + - - -
378A ALA 3.7 3.4 - - - -
379A ILE 3.3 0.2 - - - -
380A ILE* 1.3 77.0 - - - +
382A LEU* 1.3 61.7 + - - +
385A LYS* 3.0 45.2 + - - +
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Residues in contact with LEU 382 (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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299A GLU* 5.3 0.2 + - - -
378A ALA 2.9 13.8 + - - +
379A ILE* 3.5 8.3 - - - +
381A GLY* 1.3 74.4 - - - +
383A VAL* 1.3 62.2 + - - +
386A ASN* 2.8 40.0 + - - +
392A ALA* 3.7 34.9 - - + +
395A GLU* 3.6 32.1 - - + +
396A ALA* 3.9 17.5 - - + +
399A ARG* 3.7 14.1 - - - +
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Residues in contact with VAL 383 (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 VAL* 3.7 39.9 - - + +
331A LEU* 4.0 17.5 - - + -
334A VAL* 3.9 17.9 - - + -
379A ILE* 2.9 21.9 + - + +
380A ILE 3.8 3.4 - - - +
382A LEU* 1.3 77.5 - - - +
384A LEU* 1.3 59.8 + - + +
386A ASN 3.1 17.7 + - - +
387A VAL* 3.2 14.6 + - - +
392A ALA* 5.9 0.2 - - - -
393A LEU* 3.9 11.0 - - + -
396A ALA* 3.4 28.9 - - + -
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Residues in contact with LEU 384 (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 PHE* 3.8 26.9 - - + -
315A VAL* 5.7 0.2 - - + -
317A LEU* 3.8 20.2 - - + -
320A GLN* 5.2 4.3 - - + +
322A LEU* 3.6 27.8 - - + +
327A ALA* 3.8 23.6 - - + +
330A VAL* 3.8 27.6 - - + -
331A LEU* 4.3 4.3 - - + -
356A ILE* 4.5 8.3 - - + -
380A ILE* 2.9 41.9 + - + +
383A VAL* 1.3 76.0 - - + +
385A LYS* 1.3 61.6 + - - +
386A ASN 3.3 0.4 - - - -
387A VAL* 3.6 9.0 - - + +
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Residues in contact with LYS 385 (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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299A GLU* 2.9 41.7 + - - +
301A PHE* 5.2 6.3 - - + -
320A GLN* 5.5 8.5 - - + -
381A GLY* 3.0 36.5 + - - +
382A LEU* 5.1 0.4 - - - +
384A LEU* 1.3 78.5 - - - +
386A ASN* 1.3 73.1 + - - +
387A VAL 3.9 1.1 - - - -
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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