Contacts of the helix formed by residues 336 - 347 (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 GLN 336 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A SER 3.9 0.8 + - - -
335A LEU* 1.3 74.1 - - - +
337A LEU* 1.3 66.2 + - - +
338A TRP* 3.9 17.7 - - + +
339A GLN* 2.9 22.0 + - - +
340A PHE* 3.0 20.1 + - - +
375A TRP* 3.8 1.1 - - - -
396A TYR* 3.4 13.9 - - - +
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Residues in contact with LEU 337 (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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336A GLN* 1.3 71.0 - - - +
338A TRP* 1.4 58.3 + - - +
340A PHE* 3.2 5.1 + - + +
341A LEU* 2.9 49.2 + - + +
375A TRP* 3.4 48.9 - - + +
389A LEU* 3.9 24.9 - - + +
392A SER* 3.8 29.4 - - - -
393A LEU* 4.0 21.1 - - + -
396A TYR* 3.0 19.9 + - + +
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Residues in contact with TRP 338 (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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336A GLN* 3.9 11.1 - - + +
337A LEU* 1.4 73.1 - - - +
339A GLN* 1.4 75.1 + - + +
341A LEU* 3.4 4.3 + - - +
342A VAL* 3.1 43.8 + - + +
396A TYR* 3.3 39.2 + + + -
399A LYS* 6.1 0.4 - - - +
401A ILE* 4.3 16.4 - - + +
402A MET* 3.7 28.5 - - + -
414A PHE* 3.8 12.3 - + + -
423A SER 5.7 0.2 + - - -
424A MET* 3.7 57.6 + - + +
421B LEU* 4.6 4.5 - - + -
424B MET* 4.8 4.0 - - + -
425B ALA* 3.6 39.9 - - + -
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Residues in contact with GLN 339 (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 4.4 2.6 - - - +
335A LEU* 3.7 23.6 - - + +
336A GLN* 2.9 36.2 + - - +
338A TRP* 1.4 107.4 - - + +
340A PHE* 1.3 61.2 + - - +
342A VAL* 3.2 5.3 + - - +
343A ALA 2.9 24.4 + - - -
425B ALA* 3.2 25.7 + - + +
426B PHE* 3.3 18.4 - - + -
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Residues in contact with PHE 340 (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* 4.1 12.7 - - + +
336A GLN 3.0 7.0 + - - +
337A LEU* 3.2 15.9 + - + +
339A GLN* 1.3 76.1 - - - +
341A LEU* 1.4 63.8 + - + +
343A ALA* 3.2 4.2 + - - +
344A LEU* 2.9 56.1 + - + +
371A VAL* 4.3 4.3 - - + -
374A ARG* 3.6 26.7 - - + -
375A TRP* 3.5 42.8 - + + -
378A GLN* 3.6 31.9 - - + -
406C ALA* 3.6 14.4 - - + -
407C GLY 3.6 20.6 - - - -
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 2.9 36.8 + - + +
338A TRP* 3.8 4.3 - - - +
340A PHE* 1.4 79.8 - - + +
342A VAL* 1.3 58.3 + - - +
344A LEU* 3.2 6.4 + - + +
345A LEU* 2.8 41.6 + - + +
354A ILE* 3.7 24.2 - - + -
363A PHE* 4.2 14.1 - - + -
365A LEU* 4.8 3.4 - - + -
371A VAL* 3.8 20.9 - - + -
389A LEU* 5.5 2.0 - - + -
393A LEU* 3.8 29.8 - - + -
402A MET* 4.1 15.5 - - + -
414A PHE* 4.7 4.0 - - + -
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Residues in contact with VAL 342 (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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338A TRP* 3.1 24.9 + - + +
339A GLN* 3.2 8.9 + - - +
341A LEU* 1.3 75.9 - - - +
343A ALA* 1.4 57.2 + - - +
345A LEU* 3.3 8.4 + - - +
346A ASP* 3.0 27.9 + - + +
356A TRP* 5.1 4.8 - - + -
414A PHE* 3.5 11.2 - - + -
418B PRO 5.0 1.8 - - - +
421B LEU* 3.4 35.2 - - + +
422B PHE* 3.7 40.6 - - + +
425B ALA* 4.2 6.1 - - + -
426B PHE* 4.3 0.2 - - + -
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Residues in contact with ALA 343 (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* 5.1 1.8 - - + -
339A GLN 2.9 6.8 + - - +
340A PHE* 3.2 9.2 + - - +
342A VAL* 1.4 75.4 - - - +
344A LEU* 1.4 63.1 + - - +
346A ASP* 3.4 10.9 + - - +
347A ASP* 3.7 12.5 + - - +
350A ASN* 4.4 0.6 + - - -
422B PHE* 4.4 8.8 - - + -
426B PHE* 3.6 28.9 - - + -
406C ALA* 3.7 20.2 - - + +
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Residues in contact with LEU 344 (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* 2.9 44.4 + - + +
341A LEU* 3.2 7.4 + - + +
343A ALA* 1.4 75.9 - - - +
345A LEU* 1.3 61.2 + - - +
346A ASP 3.4 0.3 + - - -
347A ASP 3.2 11.4 + - - +
350A ASN* 3.1 39.0 + - - +
353A PHE* 3.9 19.5 - - + -
354A ILE* 3.7 26.7 - - + +
371A VAL* 4.6 7.9 - - + -
374A ARG* 5.1 2.0 - - + -
406C ALA* 3.6 32.3 - - + +
407C GLY* 3.6 11.9 - - - +
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Residues in contact with LEU 345 (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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341A LEU* 2.8 26.1 + - + +
342A VAL* 3.3 4.2 + - - +
344A LEU* 1.3 75.3 - - - +
346A ASP* 1.3 61.4 + - - +
347A ASP 3.3 4.2 + - - +
348A PRO* 5.5 0.3 - - - +
351A SER* 5.4 2.9 + - - -
354A ILE* 3.7 20.4 - - + +
355A ALA* 3.4 38.8 - - - +
356A TRP* 3.4 59.2 + - + +
363A PHE* 3.7 32.1 - - + -
414A PHE* 4.3 6.3 - - + -
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Residues in contact with ASP 346 (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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342A VAL 3.0 10.2 + - - +
343A ALA 3.7 3.6 - - - +
344A LEU 3.3 0.6 - - - -
345A LEU* 1.3 76.1 - - - +
347A ASP* 1.3 56.9 + - + +
348A PRO* 3.5 11.3 - - - +
356A TRP* 4.3 4.9 - - - +
418B PRO* 4.6 7.8 - - - +
419B GLU* 5.3 2.4 - - - -
422B PHE* 3.3 56.5 - - + +
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Residues in contact with ASP 347 (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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343A ALA 3.7 6.7 + - - +
344A LEU 3.2 10.7 + - - +
345A LEU 3.3 2.5 - - - +
346A ASP* 1.3 78.1 - - - +
348A PRO* 1.4 65.1 - - - +
349A SER* 3.1 28.0 + - - -
350A ASN* 3.0 34.5 + - - +
351A SER* 4.1 1.9 + - - -
354A ILE 5.6 0.2 - - - +
359C ARG* 3.6 32.5 + - - -
405C VAL* 5.8 1.4 - - - +
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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