Contacts of the helix formed by residues 336 - 347 (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 GLN 336 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334C SER 5.3 2.0 - - - +
335C LEU* 1.3 78.6 - - - +
337C LEU* 1.3 67.0 + - - +
338C TRP* 3.2 26.8 + - + -
339C GLN* 2.9 22.0 + - - +
340C PHE* 3.1 19.4 + - - +
375C TRP* 3.8 1.3 - - - -
395C TYR* 5.3 8.1 - - - -
396C TYR* 3.6 19.0 + - - +
401C ILE* 5.8 0.3 - - - +
423C SER 5.3 3.3 - - - +
424C MET 5.7 0.7 - - - +
426C PHE 6.1 0.7 - - - -
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Residues in contact with LEU 337 (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* 1.3 70.3 - - - +
338C TRP* 1.4 56.6 + - - +
340C PHE* 3.2 5.1 + - + +
341C LEU* 2.9 49.4 + - + +
375C TRP* 3.4 41.5 - - + +
389C LEU* 3.6 36.3 - - + +
392C SER* 3.5 33.4 - - - -
393C LEU* 4.2 11.4 - - + -
396C TYR* 3.0 23.1 + - + +
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Residues in contact with TRP 338 (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* 3.2 26.4 + - + -
337C LEU* 1.4 74.3 - - - +
339C GLN* 1.4 73.2 + - + +
341C LEU* 3.4 3.9 + - - +
342C VAL* 3.0 43.5 + - + +
396C TYR* 3.0 45.9 + + + -
401C ILE* 4.3 13.8 - - + +
402C MET* 4.0 20.0 - - + -
414C PHE* 3.9 14.6 - + + -
423C SER 5.4 0.4 + - - -
424C MET* 3.8 55.3 - - + +
338D TRP* 6.5 0.2 - + - -
421D LEU* 4.2 9.4 - - + -
424D MET* 4.6 4.9 - - + -
425D ALA* 3.7 37.2 - - + -
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Residues in contact with GLN 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C SER 4.5 2.3 - - - +
335C LEU* 3.7 23.2 - - + +
336C GLN* 2.9 38.6 + - + +
338C TRP* 1.4 104.6 - - + +
340C PHE* 1.3 61.9 + - - +
342C VAL* 3.3 3.0 + - - +
343C ALA 2.9 24.3 + - - -
424D MET 5.3 0.2 + - - -
425D ALA* 2.9 35.8 + - + +
426D PHE* 3.3 16.4 - - + -
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Residues in contact with PHE 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU* 4.1 14.7 - - + +
336C GLN 3.1 6.2 + - - +
337C LEU* 3.2 15.7 + - + +
339C GLN* 1.3 76.9 - - - +
341C LEU* 1.4 61.9 + - + +
343C ALA* 3.2 6.9 + - + +
344C LEU* 2.9 65.0 + - + +
371C VAL* 4.3 3.6 - - + -
374C ARG* 3.5 27.1 - - + -
375C TRP* 3.5 45.5 - + + -
378C GLN* 3.7 39.5 - - + -
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Residues in contact with LEU 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C LEU* 2.9 36.4 + - + +
338C TRP* 3.8 4.7 - - - +
339C GLN 3.3 0.2 - - - -
340C PHE* 1.4 79.6 - - + +
342C VAL* 1.3 57.8 + - - +
344C LEU* 3.2 6.4 + - + +
345C LEU* 2.8 42.0 + - + +
354C ILE* 3.8 15.9 - - + -
363C PHE* 4.2 11.4 - - + -
365C LEU* 4.8 2.7 - - + -
371C VAL* 3.8 29.6 - - + -
389C LEU* 5.5 1.1 - - + -
393C LEU* 3.7 29.8 - - + -
402C MET* 3.9 16.8 - - + -
414C PHE* 4.8 4.3 - - + -
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Residues in contact with VAL 342 (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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338C TRP* 3.0 24.4 + - + +
339C GLN* 3.3 8.7 + - - +
341C LEU* 1.3 74.9 - - - +
343C ALA* 1.3 62.6 + - - +
345C LEU* 3.3 8.4 + - - +
346C ASP* 3.0 23.1 + - + +
356C TRP* 5.1 5.7 - - + -
414C PHE* 3.5 12.3 - - + -
418D PRO 4.7 2.5 - - - +
421D LEU* 3.4 34.5 - - + +
422D PHE* 3.6 42.2 - - + +
425D ALA* 4.6 4.0 - - + -
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Residues in contact with ALA 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU* 5.3 3.4 - - + -
339C GLN 2.9 13.7 + - - +
340C PHE* 3.2 12.8 + - + +
342C VAL* 1.3 77.6 - - - +
344C LEU* 1.4 64.2 + - + +
346C ASP* 3.3 12.3 + - - +
347C ASP* 3.7 8.1 + - - +
350C ASN* 4.6 0.2 + - - -
422D PHE* 4.1 14.9 - - + -
426D PHE* 3.7 18.1 - - + -
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Residues in contact with LEU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C PHE* 2.9 57.6 + - + +
341C LEU* 3.6 6.7 - - + +
343C ALA* 1.4 76.8 - - + +
345C LEU* 1.4 61.6 + - - +
347C ASP 3.3 10.9 + - - +
350C ASN* 2.9 39.2 + - - +
353C PHE* 4.0 24.5 - - + -
354C ILE* 3.7 21.6 - - + +
371C VAL* 4.6 13.2 - - + -
374C ARG* 4.8 10.8 - - + +
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Residues in contact with LEU 345 (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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341C LEU* 2.8 31.0 + - + +
342C VAL* 3.3 4.5 + - - +
344C LEU* 1.4 71.4 - - - +
346C ASP* 1.3 60.8 + - - +
347C ASP 3.3 4.8 + - - +
348C PRO* 4.9 1.2 - - - +
354C ILE* 3.7 19.2 - - + +
355C ALA* 3.4 39.1 - - - -
356C TRP* 3.3 57.1 + - + +
363C PHE* 3.7 32.8 - - + -
414C PHE* 4.3 6.1 - - + -
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Residues in contact with ASP 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C VAL* 3.0 16.5 + - + +
343C ALA 3.6 5.8 - - - +
344C LEU 3.3 0.6 - - - -
345C LEU* 1.3 75.8 - - - +
347C ASP* 1.3 58.5 + - + +
348C PRO* 3.4 11.4 - - - +
356C TRP* 4.6 4.5 - - - +
418D PRO* 4.8 8.1 - - - +
419D GLU* 5.4 2.4 - - - -
422D PHE* 3.6 44.7 - - + +
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Residues in contact with ASP 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C ALA 3.7 5.3 + - - +
344C LEU 3.3 11.2 + - - +
345C LEU 3.3 3.3 - - - +
346C ASP* 1.3 77.9 - - - +
348C PRO* 1.4 63.6 - - - +
349C SER* 3.0 28.8 + - - -
350C ASN* 3.0 37.6 + - - +
351C SER 4.2 1.0 + - - -
354C ILE 5.4 0.3 - - - +
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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