Contacts of the helix formed by residues 417 - 426 (chain A) in PDB entry 4AVP
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 ASP 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A GLY 4.4 1.7 - - - +
415A VAL* 3.6 20.1 + - + +
416A CYS* 1.3 78.4 - - - +
418A PRO* 1.4 75.0 - - + +
419A GLU* 3.6 13.6 - - - +
420A ALA* 2.6 38.3 + - - +
421A LEU* 3.1 15.9 + - - +
361B MET* 3.5 15.6 - - - +
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Residues in contact with PRO 418 (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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417A ASP* 1.4 89.0 - - + +
419A GLU* 1.4 56.3 + - - +
421A LEU* 3.5 3.2 + - + +
422A PHE* 3.0 28.9 + - - +
342B VAL* 4.6 3.1 - - - +
346B ASP* 5.1 4.9 - - - +
356B TRP* 3.5 53.2 - - + +
360B GLY 4.9 6.7 - - - +
361B MET* 3.8 13.0 - - + -
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Residues in contact with GLU 419 (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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398A GLU 5.0 2.8 - - - +
399A LYS 3.8 15.1 - - - +
400A GLY* 4.2 9.8 - - - +
417A ASP* 3.2 14.0 + - - +
418A PRO* 1.4 77.2 - - - +
420A ALA* 1.4 65.3 + - - +
422A PHE* 3.3 7.0 + - + +
423A SER* 3.0 31.8 + - - +
346B ASP* 5.5 3.4 - - - -
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Residues in contact with ALA 420 (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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400A GLY 3.4 25.0 + - - +
401A ILE* 4.1 7.4 - - - +
415A VAL* 3.3 28.9 - - + +
417A ASP* 2.6 25.2 + - - +
419A GLU* 1.4 72.5 - - - +
421A LEU* 1.3 57.3 + - - +
423A SER* 3.2 3.8 + - - +
424A MET* 2.9 39.0 + - + +
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Residues in contact with LEU 421 (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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417A ASP 3.1 13.2 + - - +
418A PRO 3.7 5.2 - - - +
420A ALA* 1.3 79.7 - - - +
422A PHE* 1.3 56.4 + - - +
424A MET* 3.4 12.2 + - + +
425A ALA* 2.9 30.3 + - - +
338B TRP* 4.3 4.1 - - + -
342B VAL* 3.4 31.0 - - + -
356B TRP* 4.2 4.9 - - + -
361B MET* 3.8 16.4 - - + -
414B PHE* 3.6 33.0 - - + -
416B CYS* 6.2 3.1 - - - -
424B MET* 3.5 38.6 - - + -
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Residues in contact with PHE 422 (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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418A PRO 3.0 17.9 + - - +
419A GLU* 3.6 6.1 - - - +
421A LEU* 1.3 75.7 - - - +
423A SER* 1.3 60.2 + - - +
425A ALA* 3.3 1.0 + - - -
426A PHE* 2.9 69.1 + + + +
342B VAL* 3.6 16.5 - - + +
343B ALA* 4.1 10.3 - - + -
346B ASP* 3.8 46.7 - - + +
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Residues in contact with SER 423 (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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338A TRP* 5.7 0.5 + - - -
399A LYS* 3.1 28.7 + - - -
401A ILE* 3.7 30.8 - - - +
419A GLU* 3.0 17.5 + - - +
420A ALA* 3.2 1.5 + - - -
422A PHE* 1.3 79.1 - - - +
424A MET* 1.3 60.7 + - - +
426A PHE 3.0 24.3 - - - +
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Residues in contact with MET 424 (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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338A TRP* 3.7 47.5 - - + +
401A ILE* 3.7 27.8 - - + +
414A PHE* 4.7 2.9 - - + -
415A VAL 4.8 6.5 - - - +
420A ALA* 2.9 34.5 + - + +
421A LEU* 3.8 21.1 - - + +
423A SER* 1.3 77.0 - - - +
425A ALA* 1.4 61.6 + - - +
426A PHE 3.6 1.2 + - - -
338B TRP* 4.7 7.4 - - + -
339B GLN* 5.4 0.2 + - - -
421B LEU* 3.7 31.4 - - + -
424B MET* 4.5 8.6 - - + +
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Residues in contact with ALA 425 (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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421A LEU 2.9 18.9 + - - +
422A PHE* 3.3 5.4 + - - +
424A MET* 1.4 77.3 - - - +
426A PHE* 1.4 80.8 + - + +
338B TRP* 3.7 28.4 - - + -
339B GLN* 2.8 35.0 + - + +
342B VAL* 4.7 2.7 - - + -
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Residues in contact with PHE 426 (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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422A PHE* 2.9 51.2 + + + +
423A SER* 3.0 22.8 - - - +
424A MET 4.8 0.9 - - - -
425A ALA* 1.4 90.9 - - + +
335B LEU* 3.4 32.5 - - + -
339B GLN* 3.2 34.5 - - + -
342B VAL* 4.7 0.9 - - + -
343B ALA* 3.7 23.3 - - + -
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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