Contacts of the helix formed by residues 367 - 379 (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 GLU 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A HIS* 3.3 35.8 - - - +
353A PHE* 3.1 23.8 + - + +
366A ILE* 1.3 82.0 - - + +
368A PRO* 1.4 65.6 - - - +
369A GLU 3.2 3.4 - - - -
370A GLU* 3.0 27.8 + - + +
371A VAL* 3.1 14.4 + - - +
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Residues in contact with PRO 368 (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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365A LEU* 3.4 27.6 - - + +
366A ILE 3.5 5.2 - - - +
367A GLU* 1.4 82.6 - - - +
369A GLU* 1.4 69.0 + - + +
371A VAL* 3.4 6.0 + - + +
372A ALA* 3.1 22.3 + - - +
386A TYR* 3.6 31.2 - - + -
389A LEU* 5.2 0.3 - - - +
410A TYR* 3.7 40.4 - - + +
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Residues in contact with GLU 369 (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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367A GLU 3.2 0.8 - - - -
368A PRO* 1.4 82.7 - - + +
370A GLU* 1.4 58.6 + - - +
372A ALA* 3.4 5.1 + - - +
373A ARG* 2.9 28.6 + - - +
385A ASN* 4.5 5.9 - - - +
386A TYR* 3.4 39.5 + - - +
410A TYR* 5.3 2.6 + - - -
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Residues in contact with GLU 370 (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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352A HIS* 5.7 0.7 - - - +
353A PHE* 3.8 24.2 - - + -
367A GLU* 3.0 31.9 + - + +
369A GLU* 1.4 76.2 - - - +
371A VAL* 1.4 64.5 + - - +
373A ARG* 2.7 48.5 + - - +
374A ARG* 2.8 50.8 + - - +
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Residues in contact with VAL 371 (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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340A PHE* 4.3 2.5 - - + -
341A LEU* 3.8 28.7 - - + -
344A LEU* 4.6 6.3 - - + -
353A PHE* 3.5 40.8 - - + +
354A ILE* 3.9 12.3 - - + -
365A LEU* 4.2 16.6 - - + -
367A GLU 3.1 9.6 + - - +
368A PRO* 3.4 8.0 + - + +
370A GLU* 1.4 74.3 - - - +
372A ALA* 1.3 58.6 + - - +
374A ARG* 3.3 4.4 + - - +
375A TRP* 2.9 27.4 + - - +
389A LEU* 4.3 18.2 - - + -
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Residues in contact with ALA 372 (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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368A PRO 3.1 12.3 + - - +
369A GLU* 3.4 9.9 - - - +
370A GLU 3.2 0.2 - - - -
371A VAL* 1.3 77.1 - - - +
373A ARG* 1.3 60.7 + - - +
375A TRP 3.3 1.0 + - - -
376A GLY 3.0 18.2 + - - -
384A MET* 3.1 15.7 - - - +
385A ASN* 3.4 37.2 - - - +
386A TYR* 3.4 9.0 - - - +
389A LEU* 4.1 15.2 - - + +
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Residues in contact with ARG 373 (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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369A GLU 2.9 17.5 + - - +
370A GLU* 2.7 45.4 + - - +
372A ALA* 1.3 74.6 - - - +
374A ARG* 1.3 74.4 + - - +
376A GLY* 3.2 4.1 + - - -
377A ILE* 3.0 54.8 + - + +
384A MET* 4.8 6.3 + - - -
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Residues in contact with ARG 374 (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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340A PHE* 3.6 19.5 - - + -
344A LEU* 5.1 0.2 - - + -
350A ASN* 3.9 6.7 + - - -
352A HIS* 4.4 9.7 + - - -
353A PHE* 3.4 42.6 - - + -
370A GLU* 2.8 41.4 + - - +
371A VAL* 3.8 5.2 - - - +
373A ARG* 1.3 87.9 - - - +
375A TRP* 1.4 59.2 + - - +
377A ILE* 3.3 12.0 + - + +
378A GLN* 3.0 23.0 + - - +
407C GLY* 2.6 46.2 + - - +
408C GLU* 5.5 2.6 + - - -
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Residues in contact with TRP 375 (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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335A LEU 3.7 10.1 - - - -
336A GLN* 4.5 0.2 - - - -
337A LEU* 3.4 44.1 - - + +
340A PHE* 3.5 49.9 - + + -
371A VAL 2.9 17.0 + - - +
372A ALA 3.6 4.5 - - - +
374A ARG* 1.4 73.1 - - - +
376A GLY* 1.3 56.6 + - - +
378A GLN* 3.2 10.8 + - + +
379A LYS* 3.0 60.9 + - + +
384A MET* 3.6 33.6 - - + +
389A LEU* 3.6 27.7 - - + +
392A SER* 5.4 4.9 + - - -
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Residues in contact with GLY 376 (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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372A ALA 3.0 9.9 + - - -
373A ARG 3.2 6.2 + - - -
374A ARG 3.2 0.2 - - - -
375A TRP* 1.3 73.7 - - - +
377A ILE* 1.3 57.6 - - - +
379A LYS 3.4 0.3 + - - -
380A ASN* 2.9 10.9 + - - -
381A ARG* 2.8 51.2 + - - -
382A PRO* 4.9 2.6 - - - +
384A MET* 3.6 12.7 - - - +
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Residues in contact with ILE 377 (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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373A ARG* 3.0 54.9 + - + +
374A ARG* 3.3 14.3 + - + +
376A GLY* 1.3 73.1 - - - +
378A GLN* 1.3 64.3 + - - +
380A ASN* 3.4 11.5 + - - +
404C LYS* 3.0 32.0 + - - +
407C GLY 5.5 3.6 - - - +
408C GLU 3.9 20.0 - - - +
409C ARG* 4.0 19.3 - - + +
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Residues in contact with GLN 378 (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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335A LEU* 3.9 22.3 - - + +
340A PHE* 3.6 26.0 - - + -
374A ARG 3.0 13.2 + - - +
375A TRP* 3.3 22.4 - - + +
377A ILE* 1.3 79.0 - - - +
379A LYS* 1.3 62.7 - - + +
380A ASN 3.8 0.2 + - - -
397C TYR* 5.7 3.7 - - - -
404C LYS* 3.4 45.7 + - - +
405C VAL 3.8 4.9 - - - +
406C ALA* 3.3 25.9 + - - -
407C GLY 4.0 1.7 + - - -
408C GLU 5.3 0.9 - - - +
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Residues in contact with LYS 379 (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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334A SER* 5.3 6.1 - - - +
335A LEU 4.1 12.1 - - - +
375A TRP* 3.0 62.1 + - + +
376A GLY 4.5 0.7 - - - +
378A GLN* 1.3 83.0 - - + +
380A ASN* 1.3 71.5 + - - +
381A ARG* 3.2 12.4 + - + +
384A MET* 5.8 2.5 - - + -
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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