Contacts of the helix formed by residues 369 - 383 (chain A) in PDB entry 1VCO
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
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Residue Dist Surf HB Arom Phob DC
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308A LYS* 4.8 3.1 - - - -
341A ALA* 3.6 7.3 - - - +
342A GLU* 4.0 33.7 - - - +
367A VAL 3.1 1.2 + - - -
368A ARG* 1.3 70.7 - - - +
370A ILE* 1.3 63.5 + - - +
371A GLU 3.4 1.8 - - - -
372A GLY* 3.1 4.9 + - - -
373A LYS* 2.9 30.0 + - - +
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Residues in contact with ILE 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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308A LYS* 5.5 0.2 - - + -
366A GLY 3.5 13.9 - - - +
367A VAL* 2.8 29.6 + - + +
368A ARG 3.2 1.8 - - - +
369A GLY* 1.3 77.0 - - - +
371A GLU* 1.3 69.2 + - + +
373A LYS* 3.0 8.7 + - + +
374A VAL* 2.9 37.2 + - + +
392A LEU* 3.9 24.2 - - + -
396A ILE* 4.0 13.8 - - + +
399A ILE* 5.3 1.6 - - + -
403A ARG* 6.0 0.2 - - - +
412A ASN* 4.6 5.8 - - - +
416A PHE* 3.2 54.3 - - + -
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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
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367A VAL* 4.7 4.0 + - + -
369A GLY 3.4 0.4 - - - -
370A ILE* 1.3 85.1 - - + +
372A GLY* 1.3 61.2 + - - +
374A VAL* 3.4 10.7 - - - +
375A ARG* 3.2 20.6 + - - +
403A ARG* 2.8 44.5 + - - -
412A ASN* 3.8 8.8 + - - -
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Residues in contact with GLY 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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341A ALA 3.2 25.6 - - - -
342A GLU* 5.0 3.3 - - - +
344A LEU* 3.1 35.2 - - - +
369A GLY* 3.1 6.5 + - - -
370A ILE 3.1 0.8 - - - -
371A GLU* 1.3 78.0 - - - +
373A LYS* 1.3 62.0 + - - +
375A ARG* 3.3 2.9 + - - +
376A ALA 3.3 8.5 + - - -
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Residues in contact with LYS 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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306A ALA* 3.0 28.5 + - - +
307A GLY* 3.5 11.1 - - - -
308A LYS* 3.9 25.6 - - - +
341A ALA* 3.8 12.1 - - + -
344A LEU* 4.9 1.6 - - - -
361A VAL* 3.9 16.2 - - + +
362A PRO* 3.5 23.0 + - - +
363A GLY 4.8 1.4 + - - -
369A GLY 2.9 18.7 + - - +
370A ILE* 3.0 7.8 + - - +
372A GLY* 1.3 73.8 - - - +
374A VAL* 1.3 67.1 + - - +
376A ALA* 2.9 20.3 + - - +
377A ALA* 2.9 10.9 + - - +
392A LEU* 3.8 27.6 - - + +
396A ILE* 3.8 24.5 - - + +
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Residues in contact with VAL 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 ILE* 2.9 30.0 + - + +
371A GLU* 3.4 21.1 - - - +
373A LYS* 1.3 77.0 - - - +
375A ARG* 1.3 61.8 - - - +
377A ALA* 3.3 1.1 + - - +
378A GLN* 3.0 19.3 + - + +
396A ILE* 3.7 18.8 - - + +
399A ILE* 4.4 16.8 - - + -
400A GLU* 3.4 28.9 - - + +
403A ARG* 4.1 20.2 - - - +
404A ASN* 5.4 2.7 - - - +
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Residues in contact with ARG 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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344A LEU* 4.7 7.0 - - + +
349A LEU* 3.9 24.9 - - + +
371A GLU 3.2 8.9 + - - +
372A GLY* 3.5 11.4 - - - +
373A LYS 3.1 0.6 - - - -
374A VAL* 1.3 78.2 - - - +
376A ALA* 1.3 59.1 + - - +
378A GLN* 3.4 12.4 + - - +
379A TYR* 2.9 31.7 + - - +
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Residues in contact with ALA 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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306A ALA* 4.2 13.7 - - + -
344A LEU* 3.9 15.4 - - + +
353A PHE* 3.7 33.2 - - + -
359A ILE* 4.2 12.2 - - + +
361A VAL* 4.5 3.6 - - + -
372A GLY 3.3 2.6 + - - +
373A LYS* 2.9 10.3 + - - +
375A ARG* 1.3 78.3 - - - +
377A ALA* 1.3 58.8 + - - +
379A TYR* 3.4 2.1 + - - +
380A ALA* 2.9 30.0 + - - +
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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
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373A LYS 2.9 10.8 + - - +
374A VAL 3.5 8.1 - - - +
376A ALA* 1.3 74.0 - - - +
378A GLN* 1.3 60.6 + - - +
380A ALA* 3.0 3.6 + - - +
381A ARG* 2.8 31.2 + - - +
387A TYR* 3.7 34.9 - - + +
396A ILE* 4.0 11.4 - - + -
397A ALA* 4.5 6.5 - - - -
400A GLU* 4.2 12.6 - - + +
516A PHE* 4.1 5.6 - - + -
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Residues in contact with GLN 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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349A LEU* 6.0 1.7 - - - +
374A VAL* 3.0 12.7 + - + +
375A ARG* 3.7 10.6 - - - +
377A ALA* 1.3 74.5 - - - +
379A TYR* 1.3 63.8 + - - +
381A ARG* 3.0 3.5 + - - +
382A GLU* 2.9 56.4 + - + +
400A GLU* 3.0 30.7 - - + +
404A ASN* 3.0 32.7 + - - +
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Residues in contact with TYR 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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349A LEU* 3.5 44.8 + - + -
350A GLU* 3.8 17.6 + - + +
353A PHE* 3.6 28.1 + + + +
359A ILE* 4.2 1.6 - - + -
375A ARG 2.9 18.4 + - - +
376A ALA* 3.7 5.4 - - - +
378A GLN* 1.3 78.1 - - - +
380A ALA* 1.3 58.2 + - - +
382A GLU* 5.0 4.7 - - - -
383A ARG* 3.0 72.8 + - + +
385A ILE* 3.3 28.5 - - + +
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Residues in contact with ALA 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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359A ILE* 4.0 16.2 - - + -
376A ALA 2.9 17.5 + - - +
377A ALA 3.0 4.2 + - - +
379A TYR* 1.3 78.2 - - - +
381A ARG* 1.3 60.4 + - - +
385A ILE* 3.1 30.9 + - + +
387A TYR* 3.7 26.0 - - + -
513A HIS* 2.8 24.2 - - - -
516A PHE* 4.5 0.9 - - - -
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Residues in contact with ARG 381 (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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377A ALA 2.8 14.7 + - - +
378A GLN* 3.0 3.0 + - - +
380A ALA* 1.3 78.2 - - - +
382A GLU* 1.3 91.4 + - - +
384A LYS* 3.8 12.0 + - - +
400A GLU* 2.8 41.9 + - - +
401A PHE* 4.5 13.4 - - - -
404A ASN* 3.8 15.8 + - - +
405A VAL* 3.7 19.8 - - - +
510A LEU* 3.4 31.6 - - + -
513A HIS* 3.5 19.3 + - - -
516A PHE* 3.8 13.2 - - + -
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Residues in contact with GLU 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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378A GLN* 2.9 43.4 + - - +
379A TYR* 4.4 3.5 - - - +
381A ARG* 1.3 99.9 + - - +
383A ARG* 1.3 67.8 + - + +
384A LYS* 3.1 20.4 + - - +
404A ASN* 5.8 0.3 - - - +
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Residues in contact with ARG 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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350A GLU* 5.4 7.3 - - - +
379A TYR* 3.0 69.4 + - + +
382A GLU* 1.3 82.5 + - + +
384A LYS* 1.3 72.4 + - - +
385A ILE* 3.1 21.3 + - + +
546A TYR* 4.4 6.1 + - - -
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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