Contacts of the helix formed by residues 367 - 379 (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 GLU 367 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352C HIS* 3.3 34.5 - - - +
353C PHE* 3.1 24.6 + - + +
366C ILE* 1.3 81.3 - - + +
368C PRO* 1.4 65.7 - - - +
369C GLU 3.3 2.7 - - - -
370C GLU* 3.0 27.8 + - + +
371C VAL* 3.1 14.2 + - - +
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Residues in contact with PRO 368 (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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365C LEU* 3.4 28.2 - - + +
366C ILE 3.5 4.5 - - - +
367C GLU* 1.4 82.7 - - - +
369C GLU* 1.4 62.7 + - + +
371C VAL* 3.4 5.1 + - + +
372C ALA* 3.0 27.0 + - - +
386C TYR* 3.6 32.5 - - + -
389C LEU* 4.5 0.5 - - - +
410C TYR* 3.7 39.9 - - + +
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Residues in contact with GLU 369 (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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367C GLU 3.3 1.0 - - - -
368C PRO* 1.4 82.6 - - + +
370C GLU* 1.3 58.0 + - - +
372C ALA* 3.4 4.8 + - - +
373C ARG* 2.9 28.5 + - - +
385C ASN* 4.4 6.1 - - - +
386C TYR* 3.4 38.7 + - - +
410C TYR* 5.4 2.8 + - - -
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Residues in contact with GLU 370 (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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352C HIS* 5.7 0.4 - - + +
353C PHE* 3.9 25.6 - - + -
367C GLU* 3.0 31.3 + - + +
369C GLU* 1.3 74.3 - - - +
371C VAL* 1.3 65.9 + - - +
373C ARG* 2.8 49.1 + - - +
374C ARG* 2.8 48.8 + - - +
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Residues in contact with VAL 371 (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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340C PHE* 4.3 2.3 - - + -
341C LEU* 3.8 29.8 - - + -
344C LEU* 4.6 5.4 - - + -
353C PHE* 3.6 40.8 - - + +
354C ILE* 4.0 14.8 - - + -
365C LEU* 4.3 13.7 - - + -
367C GLU 3.1 9.3 + - - +
368C PRO* 3.7 7.9 - - + +
370C GLU* 1.3 76.5 - - - +
372C ALA* 1.4 55.3 + - - +
374C ARG* 3.3 4.6 + - - +
375C TRP* 3.0 27.0 + - - +
389C LEU* 4.0 17.0 - - + -
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Residues in contact with ALA 372 (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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368C PRO 3.0 12.7 + - - +
369C GLU* 3.5 9.6 - - - +
370C GLU 3.3 0.2 - - - -
371C VAL* 1.4 73.0 - - - +
373C ARG* 1.4 57.6 + - - +
375C TRP* 3.1 2.6 + - - +
376C GLY 2.9 25.1 + - - -
384C MET* 3.2 12.9 - - - +
385C ASN* 3.4 38.4 - - - +
386C TYR* 3.4 8.5 - - - +
389C LEU* 4.2 16.7 - - + +
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Residues in contact with ARG 373 (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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369C GLU 2.9 19.9 + - - +
370C GLU* 2.8 45.7 + - - +
372C ALA* 1.4 71.7 - - - +
374C ARG* 1.4 75.2 + - - +
376C GLY* 3.2 4.1 + - - -
377C ILE* 3.0 59.3 + - + +
384C MET* 4.9 6.9 + - - -
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Residues in contact with ARG 374 (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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340C PHE* 3.5 21.6 - - + -
344C LEU* 4.8 9.3 - - + +
350C ASN* 4.2 7.1 + - - -
352C HIS* 4.6 7.1 + - - -
353C PHE* 3.4 46.9 - - - -
370C GLU* 2.8 39.7 + - - +
371C VAL* 3.7 4.9 - - - +
373C ARG* 1.4 85.9 - - - +
375C TRP* 1.3 60.7 + - - +
377C ILE* 3.3 12.3 + - + +
378C GLN* 3.0 23.6 + - - +
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Residues in contact with TRP 375 (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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335C LEU 3.6 10.5 - - - -
336C GLN* 4.2 1.1 - - - -
337C LEU* 3.4 42.4 - - + +
340C PHE* 3.5 46.4 - + + -
371C VAL 3.0 14.2 + - - +
372C ALA 3.1 7.2 + - - +
374C ARG* 1.3 75.6 - - - +
376C GLY* 1.3 59.9 + - - +
378C GLN* 3.2 10.6 + - + +
379C LYS* 3.0 57.4 + - + +
381C ARG* 5.5 1.2 - - - +
384C MET* 3.6 35.4 - - + +
389C LEU* 3.5 27.7 - - + +
392C SER* 5.0 6.6 + - - -
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Residues in contact with GLY 376 (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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372C ALA 2.9 10.7 + - - -
373C ARG* 3.2 4.9 + - - -
375C TRP* 1.3 75.9 - - - +
377C ILE* 1.4 55.4 + - - +
379C LYS 3.3 0.9 + - - -
380C ASN* 2.9 10.6 + - - -
381C ARG* 2.8 51.2 + - - -
382C PRO* 5.2 1.8 - - - -
384C MET* 3.5 14.9 - - - +
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Residues in contact with ILE 377 (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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373C ARG* 3.0 55.8 + - + +
374C ARG* 3.3 11.6 + - + +
376C GLY* 1.4 73.5 - - - +
378C GLN* 1.3 65.3 + - - +
379C LYS 3.3 0.5 + - - -
380C ASN* 3.3 11.9 + - - +
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Residues in contact with GLN 378 (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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335C LEU* 3.9 28.0 - - + +
340C PHE* 3.7 33.6 - - + -
374C ARG 3.0 13.4 + - - +
375C TRP* 3.2 23.1 + - + +
377C ILE* 1.3 79.5 - - - +
379C LYS* 1.3 65.3 + - + +
380C ASN 3.8 0.3 + - - -
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Residues in contact with LYS 379 (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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334C SER* 2.8 31.1 + - - +
335C LEU 3.1 24.7 + - - +
375C TRP* 3.0 57.4 + - + +
376C GLY 4.3 1.1 - - - +
378C GLN* 1.3 82.8 - - + +
380C ASN* 1.3 69.6 + - - +
381C ARG* 3.2 24.3 + - + +
384C MET* 5.7 0.9 - - + -
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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