Contacts of the helix formed by residues 363 - 377 (chain A) in PDB entry 3F4V
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 PRO 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A ILE* 3.9 13.2 - - + +
362A VAL* 1.3 85.5 - - + +
364A TRP* 1.3 61.3 + - + +
365A GLY 3.1 0.2 - - - -
366A MET* 3.0 28.1 + - - +
412A SER* 3.5 46.2 - - - +
413A TYR* 3.6 20.8 - - + -
416A GLN* 3.4 14.6 - - + +
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Residues in contact with TRP 364 (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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246A TRP* 3.6 26.9 - + - -
248A GLU* 3.7 35.7 - - + -
317A ALA* 4.8 0.4 - - + -
319A TYR* 4.1 11.7 - + - -
350A ILE* 3.8 30.6 + - + -
362A VAL* 3.3 24.8 - - + +
363A PRO* 1.3 84.0 - - + +
365A GLY* 1.3 57.8 + - - +
366A MET 3.2 0.4 - - - -
367A TYR* 3.3 6.5 + - + +
368A GLY* 2.9 24.0 + - - -
416A GLN* 3.6 21.2 - - - +
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Residues in contact with GLY 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP* 3.7 25.2 - - - +
314A GLN* 3.9 9.2 - - - -
316A THR 4.9 0.4 - - - -
317A ALA* 4.2 7.4 - - - -
362A VAL* 2.9 13.4 + - - +
364A TRP* 1.3 79.1 - - - +
366A MET* 1.3 59.6 + - - +
368A GLY* 3.7 0.2 - - - -
369A CYS* 2.9 35.5 + - - -
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Residues in contact with MET 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLN* 3.5 35.2 + - + +
362A VAL 4.2 0.6 + - - -
363A PRO 3.0 14.0 + - - +
365A GLY* 1.3 74.1 - - - +
367A TYR* 1.3 65.3 + - - +
369A CYS* 3.4 0.9 + - - +
370A VAL* 3.1 34.3 + - - +
384A ILE* 3.9 33.0 - - + -
387A ASN* 3.7 34.8 - - - +
413A TYR* 3.7 27.6 - - + +
416A GLN* 4.4 0.7 - - + -
417A LEU* 3.9 21.3 - - + +
430A TYR* 4.4 6.1 - - + -
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Residues in contact with TYR 367 (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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363A PRO 3.9 1.4 + - - -
364A TRP* 3.3 8.0 + - + +
366A MET* 1.3 78.8 - - - +
368A GLY* 1.3 69.3 + - - +
370A VAL 3.3 0.2 + - - -
371A ASN* 2.9 54.7 + - + +
416A GLN* 3.3 34.4 - - - +
419A LYS* 3.7 32.2 - - + -
420A ALA* 3.7 27.8 - - + -
423A GLU* 2.5 40.0 + - - -
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Residues in contact with GLY 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP* 3.4 29.9 - - - -
364A TRP* 2.9 15.3 + - - -
365A GLY 3.3 2.9 + - - -
366A MET 3.3 0.2 - - - -
367A TYR* 1.3 83.3 - - - +
369A CYS* 1.3 57.2 + - - +
371A ASN* 4.0 3.9 + - - +
372A TYR* 2.9 31.4 + - - +
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Residues in contact with CYS 369 (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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244A PHE* 3.6 40.5 - - + -
246A TRP* 3.6 22.9 - - - -
312A ILE* 5.3 3.6 - - + -
314A GLN* 3.5 30.5 - - + -
365A GLY 2.9 19.9 + - - +
366A MET 3.9 3.1 - - - +
368A GLY* 1.3 75.0 - - - +
370A VAL* 1.3 64.1 + - + +
372A TYR* 3.4 2.1 + - - +
373A ILE* 3.1 31.0 + - + +
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Residues in contact with VAL 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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312A ILE* 6.1 1.6 - - + -
366A MET* 3.1 20.2 + - - +
369A CYS* 1.3 75.7 - - + +
371A ASN* 1.3 65.9 + - - +
373A ILE* 3.4 8.6 + - + +
374A LYS* 3.0 21.3 + - - +
382A VAL* 5.2 7.2 - - + -
384A ILE* 4.0 20.4 - - + -
417A LEU* 3.9 19.5 - - + -
420A ALA* 3.6 16.4 - - + -
425A ALA* 3.5 27.1 - - + -
427A VAL* 3.6 17.3 - - + -
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Residues in contact with ASN 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A TYR* 2.9 52.3 + - + +
368A GLY* 4.0 3.2 + - - +
370A VAL* 1.3 77.0 - - - +
372A TYR* 1.3 59.8 + - - +
374A LYS* 3.3 15.3 + - - +
375A GLN* 2.9 48.9 + - - +
420A ALA* 4.5 3.5 - - + +
423A GLU* 4.3 5.0 - - - +
425A ALA* 5.6 0.4 - - - -
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Residues in contact with TYR 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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244A PHE* 3.7 20.2 - + - -
246A TRP* 3.5 15.5 - + + -
261A GLN* 2.8 32.9 + - - -
264A ARG* 3.5 30.9 - - + +
265A ASP* 3.8 4.0 + - - -
268A ILE* 4.1 20.2 - - + -
269A GLY* 6.0 0.2 - - - -
368A GLY 2.9 20.6 + - - +
369A CYS 3.6 2.5 - - - +
370A VAL 3.2 0.2 - - - -
371A ASN* 1.3 80.5 - - - +
373A ILE* 1.3 60.6 + - + +
375A GLN* 3.3 3.7 + - - +
376A LYS* 2.9 67.6 + - + +
377A TYR* 4.2 8.2 + + - -
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Residues in contact with ILE 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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244A PHE* 3.9 20.4 - - + -
268A ILE* 5.1 0.2 - - + -
272A LEU* 4.0 24.7 - - + -
310A ILE* 5.6 0.7 - - + -
312A ILE* 3.7 37.5 - - + -
369A CYS 3.1 18.7 + - - +
370A VAL* 3.9 6.1 - - + +
372A TYR* 1.3 74.9 - - + +
374A LYS* 1.3 66.9 - - - +
377A TYR* 3.0 31.5 + - + +
380A PRO* 3.6 29.3 - - + +
382A VAL* 3.9 17.7 - - + -
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Residues in contact with LYS 374 (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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370A VAL 3.0 14.8 + - - +
371A ASN* 3.4 19.3 - - - +
373A ILE* 1.3 76.4 - - - +
375A GLN* 1.3 82.2 + - - +
378A GLY* 3.8 2.8 + - - -
379A ASN* 3.0 55.9 + - + +
420A ALA 5.0 0.9 - - - +
423A GLU* 3.6 26.0 + - + -
424A GLY* 3.9 6.2 + - - -
425A ALA* 3.7 27.8 - - + +
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Residues in contact with GLN 375 (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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371A ASN* 2.9 39.4 + - - +
372A TYR* 4.0 3.8 - - + +
374A LYS* 1.3 109.6 + - + +
376A LYS* 1.3 61.5 + - - +
378A GLY 4.7 1.7 + - - -
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Residues in contact with LYS 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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261A GLN* 3.7 14.4 - - - +
265A ASP* 3.8 12.2 + - - -
273A ASP* 4.9 8.7 + - - -
277A ASN* 5.3 2.6 + - - -
372A TYR* 2.9 55.6 + - + +
375A GLN* 1.3 78.0 - - - +
377A TYR* 1.3 90.0 + - + +
378A GLY 3.5 1.6 + - - -
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Residues in contact with TYR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASP* 4.4 1.2 + - - -
268A ILE* 5.2 1.8 - - + -
269A GLY* 3.5 14.9 + - - -
272A LEU* 3.8 30.1 - - + -
273A ASP* 2.6 49.5 + - - -
276A ILE* 3.7 33.9 - - + +
277A ASN* 3.8 15.9 - - - -
372A TYR* 4.2 13.2 + + - -
373A ILE* 3.0 21.1 + - + +
376A LYS* 1.3 111.3 - - + +
378A GLY* 1.3 62.2 + - - +
379A ASN 3.3 2.0 - - - -
380A PRO* 3.3 20.5 - - + +
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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