Contacts of the helix formed by residues 354 - 362 (chain A) in PDB entry 1VPE
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 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASP* 4.5 6.4 - - - +
36A ARG* 5.1 4.5 - - - -
353A GLY* 1.3 73.2 - - - +
355A ASP* 1.3 58.8 + - - +
357A ALA* 3.4 4.7 + - - +
358A ALA* 3.2 21.0 + - - +
374A THR* 3.3 21.5 + - - +
400A ANP 3.0 16.0 + - - -
402A MG 4.5 2.2 - - - -
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Residues in contact with ASP 355 (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 PRO* 3.9 3.1 - - + -
323A PHE* 3.7 22.2 - - + -
324A GLU* 4.6 2.9 - - - +
354A GLY* 1.3 70.0 - - - -
356A SER* 1.3 55.7 - - - +
358A ALA* 3.4 9.4 - - - +
359A ALA* 2.7 35.0 + - - +
400A ANP 2.9 60.8 + - - +
402A MG 3.9 2.3 - - - -
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Residues in contact with SER 356 (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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316A TRP* 4.8 10.4 - - - -
317A ASN* 4.8 1.3 - - - -
318A GLY* 2.8 25.3 + - - -
319A PRO* 4.4 4.0 - - - +
351A VAL* 3.7 21.1 - - - -
352A GLY 3.6 7.7 + - - -
353A GLY 3.7 4.7 - - - -
354A GLY 3.3 0.6 - - - -
355A ASP* 1.3 75.8 - - - +
357A ALA* 1.3 63.7 + - - +
359A ALA* 3.1 8.8 + - - +
360A VAL* 3.0 26.9 + - - +
400A ANP 2.4 24.8 + - - -
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Residues in contact with ALA 357 (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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35A THR* 5.2 5.4 - - + +
351A VAL* 4.3 1.3 - - - +
353A GLY 2.9 17.7 + - - +
354A GLY 3.6 5.6 - - - +
356A SER* 1.3 76.6 - - - +
358A ALA* 1.3 61.7 - - - +
360A VAL* 3.2 12.4 - - - +
361A ASN* 3.0 32.5 + - - +
372A VAL* 4.0 21.0 - - + +
373A SER 4.2 2.2 - - - +
374A THR* 3.6 20.2 - - + -
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Residues in contact with ALA 358 (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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33A ASP* 3.9 19.2 + - - +
35A THR* 6.0 0.2 - - - -
323A PHE* 4.4 12.3 - - + -
354A GLY 3.2 11.2 + - - +
355A ASP* 3.4 15.7 - - - +
357A ALA* 1.3 78.4 - - - +
359A ALA* 1.3 58.0 + - - +
361A ASN* 3.2 11.5 + - - +
362A LYS* 2.9 29.6 + - - +
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Residues in contact with ALA 359 (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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316A TRP* 4.9 4.5 - - + -
319A PRO* 5.3 1.6 - - + -
323A PHE* 3.8 23.5 - - + -
332A THR* 3.8 27.8 - - + -
355A ASP 2.7 20.0 + - - +
356A SER* 3.1 9.8 + - - +
358A ALA* 1.3 70.8 - - - +
360A VAL* 1.3 67.4 + - - +
362A LYS* 3.3 9.9 + - - +
363A PHE* 2.9 22.9 + - + -
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Residues in contact with VAL 360 (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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316A TRP* 3.9 23.1 - - + -
336A ALA* 4.8 2.5 - - + -
351A VAL* 4.2 8.5 - - + -
356A SER 3.0 12.8 + - - +
357A ALA* 3.2 17.5 - - - +
359A ALA* 1.3 75.8 - - - +
361A ASN* 1.3 68.2 + - - +
363A PHE* 3.3 7.7 + - - -
364A GLY 3.2 3.3 + - - -
365A LEU* 2.9 30.3 + - + +
366A GLU* 4.2 17.0 - - + -
369A PHE* 3.6 29.6 - - + -
372A VAL* 4.4 17.5 - - + -
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Residues in contact with ASN 361 (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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33A ASP* 5.6 0.2 + - - -
35A THR* 4.2 20.6 + - - +
38A ARG* 5.2 4.4 - - - +
357A ALA* 3.0 25.2 + - - +
358A ALA* 3.4 11.0 - - - +
359A ALA 3.2 0.2 - - - -
360A VAL* 1.3 78.2 - - - +
362A LYS* 1.3 58.6 + - - +
364A GLY* 2.8 22.3 + - - -
366A GLU* 3.4 36.0 - - - +
372A VAL* 6.3 0.8 - - - +
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Residues in contact with LYS 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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323A PHE* 3.3 37.5 + - + -
324A GLU* 3.4 17.8 + - - +
326A ASP* 3.6 18.2 + - - +
329A ALA* 5.3 0.8 - - - +
358A ALA 2.9 16.7 + - - +
359A ALA* 3.6 7.9 - - - +
361A ASN* 1.3 76.9 - - - +
363A PHE* 1.3 77.8 + - + +
364A GLY 3.7 0.3 + - - -
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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