Contacts of the helix formed by residues 417 - 426 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A GLY 5.5 0.4 - - - -
361A MET* 3.2 15.1 - - - +
400B GLY 4.4 1.1 - - - +
415B VAL* 3.6 19.7 - - + +
416B CYS* 1.3 76.2 - - - +
418B PRO* 1.4 75.0 - - + +
419B GLU* 3.3 14.0 + - - +
420B ALA* 2.8 35.5 + - - +
421B LEU 3.1 15.6 + - - -
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Residues in contact with PRO 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A VAL* 5.0 0.7 - - - +
346A ASP* 4.6 4.8 - - - +
356A TRP* 3.4 62.4 - - + +
360A GLY 4.5 8.7 - - - +
361A MET* 3.7 8.9 - - + -
417B ASP* 1.4 88.7 - - + +
419B GLU* 1.4 56.6 + - - +
421B LEU* 3.5 1.8 + - + +
422B PHE* 3.0 29.3 + - - +
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Residues in contact with GLU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ASP* 5.3 2.9 - - - -
398B GLU 4.3 5.4 - - - +
399B LYS 3.6 20.2 - - - +
400B GLY* 3.8 12.1 - - - -
417B ASP* 3.2 15.5 + - - +
418B PRO* 1.4 74.9 - - - +
420B ALA* 1.4 65.0 + - - +
422B PHE* 3.3 7.3 + - - +
423B SER* 3.1 27.1 + - - +
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Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B GLY 3.3 28.8 + - - +
401B ILE* 4.0 9.8 - - - +
415B VAL 3.2 27.1 - - - +
417B ASP* 2.8 19.3 + - - +
419B GLU* 1.4 70.8 - - - +
421B LEU* 1.4 57.6 + - - +
423B SER* 3.2 5.0 + - - -
424B MET* 2.9 40.6 + - + +
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Residues in contact with LEU 421 (chain B).
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* 4.6 1.6 - - + -
342A VAL* 3.4 30.7 - - + -
356A TRP* 3.8 7.4 - - + -
361A MET* 3.6 18.2 - - + -
414A PHE* 3.5 34.8 - - + -
415A VAL 6.1 0.2 - - - +
424A MET* 3.7 36.8 - - + -
417B ASP 3.1 17.0 + - - +
418B PRO 3.7 5.2 - - - +
420B ALA* 1.4 76.1 - - - +
422B PHE* 1.3 55.7 + - - +
424B MET* 3.4 12.1 + - + +
425B ALA* 2.9 31.2 + - - +
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Residues in contact with PHE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A VAL* 3.7 14.1 - - + +
343A ALA* 4.4 8.1 - - + -
346A ASP* 3.3 49.1 - - + +
418B PRO 3.0 17.2 + - - +
419B GLU* 3.6 6.3 - - - +
420B ALA 3.3 0.2 - - - -
421B LEU* 1.3 75.5 - - - +
423B SER* 1.4 62.5 + - - +
425B ALA 3.3 0.3 + - - -
426B PHE* 2.9 68.7 + + + +
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Residues in contact with SER 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B GLN* 5.2 6.1 + - - -
399B LYS* 2.8 36.6 + - - +
401B ILE* 3.7 31.9 - - - +
419B GLU* 3.1 10.5 + - - +
420B ALA 3.7 3.4 - - - -
422B PHE* 1.4 79.7 - - - +
424B MET* 1.3 60.1 + - - +
426B PHE 3.0 22.4 - - - +
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Residues in contact with MET 424 (chain B).
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* 4.8 7.5 - - + -
421A LEU* 3.5 34.3 - - + -
424A MET* 4.5 7.9 - - + +
336B GLN* 5.7 1.2 + - - -
338B TRP* 3.8 48.0 + - + +
401B ILE* 4.1 27.8 - - + +
414B PHE* 4.6 3.1 - - - -
415B VAL 4.8 6.3 - - - +
416B CYS* 6.4 0.7 - - - -
420B ALA* 2.9 33.5 + - + +
421B LEU* 3.8 21.5 - - + +
423B SER* 1.3 76.5 - - - +
425B ALA* 1.3 63.0 + - - +
426B PHE 3.6 1.6 + - - -
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Residues in contact with ALA 425 (chain B).
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* 3.6 30.9 - - + -
339A GLN* 3.2 27.8 + - + -
342A VAL* 4.2 8.3 - - + -
421B LEU 2.9 18.8 + - - +
422B PHE 3.7 4.0 - - - +
424B MET* 1.3 78.3 - - - +
426B PHE* 1.4 80.7 + - + +
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Residues in contact with PHE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A LEU* 3.6 28.9 - - + -
339A GLN* 3.3 31.9 - - + -
342A VAL* 4.3 0.9 - - + -
343A ALA* 3.6 23.6 - - + -
336B GLN* 6.1 2.7 - - - -
399B LYS* 6.1 1.4 - - - -
422B PHE* 2.9 51.6 + + + +
423B SER* 3.0 23.9 - - - +
424B MET 4.8 1.1 - - - -
425B ALA* 1.4 95.5 - - + +
403C GLN* 4.3 22.0 - - - +
413C LYS* 6.1 0.7 - - - -
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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