Contacts of the helix formed by residues 367 - 379 (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 GLU 367 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352B HIS* 3.3 35.6 - - - +
353B PHE* 3.0 23.6 + - + +
366B ILE* 1.3 81.1 - - + +
368B PRO* 1.3 67.6 - - - +
369B GLU 3.2 3.4 - - - +
370B GLU* 3.0 27.4 + - + +
371B VAL* 3.1 13.9 + - - +
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Residues in contact with PRO 368 (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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365B LEU* 3.4 23.6 - - + +
366B ILE 3.4 5.2 - - - +
367B GLU* 1.3 86.6 - - - +
369B GLU* 1.3 65.8 + - + +
371B VAL* 3.3 6.4 + - + +
372B ALA* 3.1 25.3 + - - +
386B TYR* 3.5 33.3 - - + +
389B LEU* 4.1 5.2 - - - +
410B TYR* 3.7 35.4 - - + +
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Residues in contact with GLU 369 (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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367B GLU 3.2 0.8 - - - -
368B PRO* 1.3 79.7 - - + +
370B GLU* 1.3 59.3 + - - +
372B ALA* 3.4 5.1 + - - +
373B ARG* 2.9 27.9 + - - +
385B ASN* 4.6 6.2 - - - +
386B TYR* 3.4 37.1 + - - +
410B TYR* 5.5 1.9 + - - -
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Residues in contact with GLU 370 (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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352B HIS* 5.6 0.9 - - - +
353B PHE* 3.8 24.7 - - + -
367B GLU* 3.0 32.1 + - + +
369B GLU* 1.3 75.0 - - - +
371B VAL* 1.3 66.8 + - - +
373B ARG* 2.7 48.9 + - - +
374B ARG* 2.8 49.5 + - - +
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Residues in contact with VAL 371 (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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340B PHE* 4.3 2.5 - - + -
341B LEU* 3.7 29.6 - - + -
344B LEU* 4.6 6.5 - - + -
353B PHE* 3.6 40.2 - - + +
354B ILE* 3.9 13.7 - - + -
365B LEU* 4.3 11.9 - - + -
367B GLU 3.1 9.2 + - - +
368B PRO* 3.3 9.6 + - + +
370B GLU* 1.3 77.2 - - - +
372B ALA* 1.4 55.3 + - - +
374B ARG* 3.4 5.1 + - - +
375B TRP* 2.9 26.9 + - - +
389B LEU* 3.8 19.1 - - + -
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Residues in contact with ALA 372 (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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368B PRO 3.1 11.8 + - - +
369B GLU* 3.5 10.3 - - - +
370B GLU 3.3 0.2 - - - -
371B VAL* 1.4 73.0 - - - +
373B ARG* 1.3 54.9 + - - +
375B TRP 3.2 0.5 + - - -
376B GLY 2.8 29.8 + - - -
384B MET* 3.2 14.4 - - + +
385B ASN* 3.4 40.2 - - - +
386B TYR* 3.5 6.7 - - - +
389B LEU* 4.1 13.4 - - + +
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Residues in contact with ARG 373 (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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369B GLU 2.9 17.6 + - - +
370B GLU* 2.7 44.9 + - - +
372B ALA* 1.3 73.4 - - - +
374B ARG* 1.3 75.2 + - - +
376B GLY* 3.1 4.6 + - - -
377B ILE* 3.0 55.9 + - + +
384B MET* 4.9 5.8 + - - -
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Residues in contact with ARG 374 (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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340B PHE* 3.5 20.8 - - + -
344B LEU* 4.8 9.5 - - + +
350B ASN* 3.9 8.7 + - - -
352B HIS* 4.6 7.9 + - - -
353B PHE* 3.3 45.8 - - - -
370B GLU* 2.8 41.0 + - - +
371B VAL* 3.8 4.7 - - - +
373B ARG* 1.3 87.2 - - - +
375B TRP* 1.4 65.8 + - - +
377B ILE* 3.3 12.7 + - + +
378B GLN* 3.0 19.1 + - - +
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Residues in contact with TRP 375 (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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335B LEU* 3.6 11.0 - - + -
336B GLN 4.2 0.9 - - - -
337B LEU* 3.4 43.2 - - + +
340B PHE* 3.5 46.8 - + + -
371B VAL 2.9 16.9 + - - +
372B ALA 3.2 3.8 + - - +
374B ARG* 1.4 73.7 - - - +
376B GLY* 1.3 62.2 + - - +
378B GLN* 3.2 10.2 + - + +
379B LYS* 3.0 58.7 + - + +
381B ARG* 5.7 0.6 - - - +
384B MET* 3.6 35.9 - - + +
389B LEU* 3.6 26.0 - - + +
392B SER* 5.1 5.9 + - - -
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Residues in contact with GLY 376 (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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372B ALA 2.8 10.1 + - - -
373B ARG* 3.1 5.8 + - - -
375B TRP* 1.3 76.3 - - - +
377B ILE* 1.3 55.3 - - - +
379B LYS* 3.4 0.6 + - - -
380B ASN* 3.0 9.9 + - - -
381B ARG* 2.8 50.4 + - - -
382B PRO* 4.9 2.7 - - - -
384B MET* 3.6 13.0 - - - +
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Residues in contact with ILE 377 (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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373B ARG* 3.0 54.4 + - + +
374B ARG* 3.3 13.0 + - + +
376B GLY* 1.3 73.5 - - - +
378B GLN* 1.3 64.3 + - - +
379B LYS 3.3 0.5 + - - -
380B ASN* 3.3 17.4 + - - +
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Residues in contact with GLN 378 (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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335B LEU* 3.8 27.0 - - + +
340B PHE* 3.7 34.6 - - + -
374B ARG 3.0 12.4 + - - +
375B TRP* 3.3 22.4 - - + +
377B ILE* 1.3 80.1 - - - +
379B LYS* 1.3 63.9 + - + +
380B ASN* 3.4 7.3 - - - +
348D PRO* 6.0 0.2 - - - +
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Residues in contact with LYS 379 (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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334B SER* 2.8 31.5 + - - +
335B LEU 3.1 23.7 + - - +
375B TRP* 3.0 58.1 + - + +
376B GLY 4.4 0.9 - - - +
378B GLN* 1.3 83.0 - - + +
380B ASN* 1.3 71.3 + - - +
381B ARG* 3.2 19.0 + - + +
384B MET* 5.7 1.6 - - + -
348D PRO* 4.5 4.3 - - - +
351D SER* 3.3 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