Contacts of the helix formed by residues 417 - 426 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400C GLY 4.3 1.4 - - - +
415C VAL* 3.6 20.7 + - + +
416C CYS* 1.3 76.8 - - - +
418C PRO* 1.4 75.3 - - + +
419C GLU* 3.3 14.8 + - - +
420C ALA* 2.8 35.9 + - - +
421C LEU 3.1 15.8 + - - -
360D GLY 5.9 0.2 - - - -
361D MET* 3.2 15.8 - - - +
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Residues in contact with PRO 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417C ASP* 1.4 87.9 - - + +
419C GLU* 1.3 55.7 + - - +
421C LEU* 3.5 2.5 + - + +
422C PHE* 3.0 28.9 + - - +
342D VAL* 4.9 0.9 - - - +
346D ASP* 4.8 5.0 - - - +
356D TRP* 3.4 60.7 - - + +
360D GLY 4.6 9.0 - - - +
361D MET* 3.6 10.5 - - + -
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Residues in contact with GLU 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C GLU 4.4 5.5 - - - +
399C LYS 3.6 22.9 - - - +
400C GLY* 4.1 7.5 + - - -
417C ASP* 3.2 13.8 + - - +
418C PRO* 1.3 75.5 - - - +
420C ALA* 1.4 65.1 + - - +
422C PHE* 3.3 7.1 + - - +
423C SER* 3.1 27.3 + - - +
346D ASP* 5.6 2.2 - - - -
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Residues in contact with ALA 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C GLY 3.3 27.9 + - - +
401C ILE* 4.0 10.9 - - - +
415C VAL 3.2 27.1 - - - +
417C ASP* 2.8 20.1 + - - +
419C GLU* 1.4 69.2 - - - +
421C LEU* 1.3 58.1 + - - +
423C SER* 3.2 3.6 + - - -
424C MET* 2.9 40.3 + - + +
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Residues in contact with LEU 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416C CYS* 6.4 0.2 - - - -
417C ASP 3.1 9.8 + - - +
418C PRO 3.7 9.0 - - - +
420C ALA* 1.3 78.6 - - - +
422C PHE* 1.3 57.5 + - - +
424C MET* 3.4 11.1 + - + +
425C ALA* 2.9 31.0 + - - +
338D TRP* 4.4 2.5 - - + -
342D VAL* 3.4 30.5 - - + -
356D TRP* 3.9 7.2 - - + -
361D MET* 3.7 17.7 - - + -
414D PHE* 3.4 35.2 - - + -
415D VAL 6.1 0.2 - - - +
424D MET* 3.5 37.9 - - + -
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Residues in contact with PHE 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418C PRO 3.0 17.4 + - - +
419C GLU* 3.6 6.3 - - - +
421C LEU* 1.3 77.3 - - - +
423C SER* 1.4 62.6 + - - +
425C ALA 3.3 0.3 + - - -
426C PHE* 2.9 69.2 + + + +
342D VAL* 3.7 15.0 - - + +
343D ALA* 4.4 7.6 - - + -
346D ASP* 3.4 48.9 - - + +
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Residues in contact with SER 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C GLN* 5.3 4.3 - - - +
338C TRP* 5.4 0.2 + - - -
399C LYS* 2.8 36.1 + - - +
401C ILE* 3.6 30.5 - - - +
419C GLU* 3.1 12.2 + - - +
420C ALA 3.7 2.7 - - - -
422C PHE* 1.4 81.0 - - - +
424C MET* 1.3 60.5 + - - +
426C PHE 2.9 23.9 - - - +
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Residues in contact with MET 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C GLN* 5.7 0.3 - - - +
338C TRP* 3.8 42.1 + - + +
401C ILE* 3.8 31.4 - - + +
414C PHE* 4.7 1.1 - - - -
415C VAL 4.8 5.4 - - - +
420C ALA* 2.9 33.7 + - + +
421C LEU* 3.8 22.9 - - + +
423C SER* 1.3 75.2 - - - +
425C ALA* 1.3 63.0 + - - +
426C PHE* 4.7 0.9 - - - -
338D TRP* 4.6 9.3 - - + -
421D LEU* 3.5 34.1 - - + -
424D MET* 4.2 9.6 - - + +
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Residues in contact with ALA 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C LEU 2.9 19.2 + - - +
422C PHE 3.3 0.6 + - - -
424C MET* 1.3 77.9 - - - +
426C PHE* 1.4 83.0 + - + +
338D TRP* 3.6 29.8 - - + -
339D GLN* 3.0 31.0 + - + +
342D VAL* 4.3 6.7 - - + -
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Residues in contact with PHE 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C GLN* 6.1 1.1 - - - -
422C PHE* 2.9 58.1 + + + +
423C SER* 2.9 24.2 - - - +
424C MET 4.8 1.1 - - - -
425C ALA* 1.4 94.3 - - + +
335D LEU* 3.5 29.4 - - + -
339D GLN* 3.3 31.0 - - + -
342D VAL* 4.4 0.7 - - + -
343D ALA* 3.7 18.2 - - + -
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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