Contacts of the helix formed by residues 361 - 375 (chain A) in PDB entry 3FVS
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 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359A ASP 3.3 9.8 - - - +
360A GLU* 1.3 90.8 - - + +
362A TYR* 1.3 67.6 + - - +
363A ASP* 3.3 17.5 - - - +
364A ARG* 3.1 27.9 + - + +
365A ARG* 3.3 8.8 + - - +
382A SER* 3.7 17.9 - - - +
390A GLN* 3.9 27.6 - - + +
391A LYS* 6.0 1.8 - - - -
394A ASP* 4.3 11.9 - - + -
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Residues in contact with TYR 362 (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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344A ILE* 3.8 26.0 - - + -
347A PHE* 3.1 17.3 + - - +
348A LYS* 3.5 45.5 - - + -
351A MET* 2.7 31.5 + - - +
352A PRO 3.8 17.7 - - - -
354A LEU* 3.7 26.9 - - + +
360A GLU 3.5 2.7 + - - -
361A PRO* 1.3 71.1 - - - +
363A ASP* 1.3 57.9 + - - +
365A ARG* 3.0 13.1 + - + +
366A PHE* 2.7 36.0 + + + -
394A ASP* 3.7 25.3 + - - +
395A HIS* 5.4 0.2 - - - -
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Residues in contact with ASP 363 (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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344A ILE* 3.9 16.6 - - + -
361A PRO* 3.3 9.7 - - - +
362A TYR* 1.3 75.6 - - - +
364A ARG* 1.3 63.3 + - - +
366A PHE* 3.3 0.7 + - - +
367A VAL* 2.9 34.5 + - - +
380A PRO* 3.6 7.9 - - + -
381A VAL* 3.0 9.0 + - - +
382A SER* 2.7 49.5 + - - -
393A PHE 4.4 0.5 - - - +
394A ASP 3.0 24.4 + - - +
396A TYR 3.2 18.8 + - - +
397A ILE* 4.1 2.0 - - + +
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Residues in contact with ARG 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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15A TYR* 5.5 9.7 - - - -
17A PRO* 5.8 2.2 - - - +
21A PHE* 5.8 3.3 - - + -
360A GLU* 3.7 21.1 - - + +
361A PRO* 3.1 23.9 + - + +
363A ASP* 1.3 83.1 + - - +
365A ARG* 1.3 62.8 + - - +
367A VAL* 3.5 2.5 + - - +
368A LYS* 3.2 29.1 + - - +
380A PRO* 3.6 22.4 - - + -
382A SER* 2.9 34.1 + - - +
383A ILE* 3.6 20.5 - - - +
390A GLN* 3.2 37.8 + - - +
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Residues in contact with ARG 365 (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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354A LEU* 2.9 43.3 + - + +
355A PRO* 3.6 18.6 - - - +
356A GLY* 3.8 13.9 + - - +
357A ALA 2.6 30.3 + - - -
358A VAL* 4.4 1.2 - - - +
359A ASP* 4.2 4.6 - - - +
360A GLU* 2.9 41.3 + - - +
361A PRO 3.6 9.2 - - - +
362A TYR* 3.0 14.7 + - - +
364A ARG* 1.3 77.0 - - - +
366A PHE* 1.3 61.6 + - - +
368A LYS* 3.4 7.5 + - - +
369A TRP* 3.0 23.0 + - - +
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Residues in contact with PHE 366 (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 LEU* 4.4 3.4 - - + -
344A ILE* 3.7 24.9 - - + -
347A PHE* 3.5 49.8 - + + -
351A MET* 5.6 1.3 - - - -
354A LEU* 3.6 10.0 - - + +
362A TYR* 2.7 39.6 + + + +
363A ASP 3.6 4.7 - - - +
365A ARG* 1.3 72.0 - - - +
367A VAL* 1.3 62.4 + - - +
369A TRP* 3.1 29.4 + + - +
370A MET* 2.7 41.4 + - - +
397A ILE* 3.9 27.8 - - + -
418A TRP* 4.4 4.5 - + - -
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Residues in contact with VAL 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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21A PHE* 6.0 4.3 - - + -
24A LEU* 5.9 0.2 - - + -
363A ASP 2.9 19.4 + - - +
364A ARG 3.9 4.7 - - - +
365A ARG 3.4 0.2 - - - -
366A PHE* 1.3 80.4 - - + +
368A LYS* 1.3 57.4 + - + +
370A MET* 3.3 6.0 + - + +
371A ILE* 2.9 47.3 + - + +
378A ALA* 3.1 35.7 - - + +
380A PRO* 3.9 20.4 - - + -
397A ILE* 3.5 27.4 - - + -
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Residues in contact with LYS 368 (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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20A GLU* 4.4 23.6 - - - -
24A LEU* 3.7 30.1 - - + -
355A PRO 5.0 2.5 + - - +
356A GLY* 4.9 5.1 - - - -
360A GLU* 2.5 38.4 + - - -
364A ARG* 3.2 15.3 + - - +
365A ARG* 3.8 8.6 - - - +
367A VAL* 1.3 76.7 - - + +
369A TRP* 1.3 62.8 + - - +
371A ILE* 3.4 1.2 + - - +
372A LYS* 3.0 44.4 + - - +
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Residues in contact with TRP 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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347A PHE* 4.6 2.9 - + - -
351A MET* 3.7 37.0 - - + -
354A LEU* 3.8 24.9 - - + -
355A PRO* 5.9 3.4 - - + -
365A ARG 3.0 14.1 + - - +
366A PHE* 3.4 43.1 - + - +
368A LYS* 1.3 76.5 - - - +
370A MET* 1.3 75.5 + - - +
372A LYS* 3.9 10.2 - - - +
373A ASN* 2.9 64.6 + - + +
374A LYS* 3.5 31.0 - - + -
418A TRP* 3.9 18.4 - + - -
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Residues in contact with MET 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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329A LEU* 4.9 1.8 - - - -
366A PHE* 2.7 31.6 + - + +
367A VAL* 3.8 8.7 - - - +
369A TRP* 1.3 83.3 - - + +
371A ILE* 1.3 60.7 + - - +
374A LYS* 2.9 30.7 + - + -
375A GLY 3.0 7.6 + - - -
376A LEU* 3.4 30.0 + - + +
378A ALA* 3.8 32.1 - - + +
397A ILE* 4.0 9.6 - - + -
399A PHE* 4.1 13.9 - - + -
418A TRP* 3.8 39.0 - - + -
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Residues in contact with ILE 371 (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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21A PHE* 5.5 2.5 - - - +
24A LEU* 3.9 46.4 - - + +
25A ALA* 4.5 4.5 - - + +
28A HIS* 4.1 16.0 + - + +
30A VAL* 3.9 17.4 - - + +
367A VAL* 2.9 37.1 + - + +
368A LYS 3.8 4.0 - - - +
370A MET* 1.3 76.3 - - - +
372A LYS* 1.3 63.1 + - - +
375A GLY* 3.3 19.9 + - - +
376A LEU 3.5 19.1 - - - +
377A VAL* 4.0 25.1 - - + -
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Residues in contact with LYS 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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24A LEU* 4.4 14.8 - - + -
28A HIS* 3.4 43.2 + - + +
355A PRO* 5.5 9.1 - - - +
368A LYS* 3.0 43.1 + - - +
369A TRP* 3.9 9.0 - - - +
371A ILE* 1.3 77.0 - - + +
373A ASN* 1.3 69.2 + - - +
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Residues in contact with ASN 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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369A TRP* 2.9 56.5 + - + +
372A LYS* 1.3 88.7 - - - +
374A LYS* 1.3 77.8 + - + +
422A LEU* 6.1 1.2 - - - +
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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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369A TRP* 3.5 36.6 - - + -
370A MET* 2.9 14.4 + - + +
373A ASN* 1.3 90.1 + - + +
375A GLY* 1.3 63.6 + - - +
376A LEU* 3.5 1.9 + - + +
414A LYS* 3.6 27.0 - - - +
418A TRP* 3.5 75.7 + - + +
421A GLU 5.6 2.8 + - - -
422A LEU* 6.0 5.5 - - - +
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Residues in contact with GLY 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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29A ASP 3.6 18.2 - - - -
30A VAL* 3.3 7.1 - - - -
31A VAL 2.8 24.8 + - - -
370A MET 3.0 4.4 + - - -
371A ILE 3.3 14.9 + - - -
373A ASN 3.8 0.4 - - - -
374A LYS* 1.3 79.2 - - - +
376A LEU* 1.3 59.9 + - - +
414A LYS* 3.6 15.7 - - - +
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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