Contacts of the helix formed by residues 361 - 376 (chain A) in PDB entry 3V4O
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 ALA 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A LYS* 1.3 75.6 - - - +
362A PRO* 1.4 67.3 - - - +
363A LEU 3.0 3.6 + - - -
364A VAL* 3.2 6.3 + - - +
365A ASP* 2.9 22.3 + - - +
500A GLU* 3.1 23.1 + - + +
504A SER* 3.8 17.0 + - - +
505A GLY 5.8 0.7 - - - -
507A ALA 3.8 5.4 - - - +
509A GLY 3.7 14.1 - - - +
5B ARG* 3.2 19.7 - - - +
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Residues in contact with PRO 362 (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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349A GLY* 3.8 24.2 - - - -
350A ASN 3.5 17.9 - - - +
351A MET* 3.6 15.7 - - + -
359A LEU* 3.8 7.2 - - + -
360A LYS 3.3 9.6 - - - +
361A ALA* 1.4 87.7 - - - +
363A LEU* 1.3 62.8 + - - +
365A ASP* 3.7 1.5 - - + +
366A VAL* 2.9 29.0 + - - +
413A ALA* 3.8 19.3 - - + +
500A GLU* 3.3 12.3 - - - +
5B ARG* 3.6 13.0 - - - +
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Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A MET* 3.5 24.2 - - + -
360A LYS 4.0 5.4 - - - +
361A ALA 3.0 0.8 + - - -
362A PRO* 1.3 81.1 - - - +
364A VAL* 1.3 63.6 + - + +
366A VAL* 3.3 1.7 + - - +
367A TYR* 2.8 35.1 + - + +
384A LEU* 3.9 31.9 - - + -
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Residues in contact with VAL 364 (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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360A LYS 4.7 0.4 + - - +
361A ALA* 3.2 7.6 + - - +
363A LEU* 1.3 86.8 - - + +
365A ASP* 1.3 57.1 + - - +
367A TYR* 3.7 10.3 - - + +
368A GLU* 2.9 31.5 + - - +
505A GLY 4.5 10.3 - - - +
506A LEU* 3.7 35.0 - - + +
507A ALA 3.8 13.2 - - - +
508A ASN* 3.2 24.2 - - - +
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Residues in contact with ASP 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ALA 2.9 16.9 + - - +
362A PRO* 3.7 6.3 - - + +
364A VAL* 1.3 75.7 - - - +
366A VAL* 1.3 64.0 + - - +
368A GLU* 3.4 2.9 + - - +
369A LEU* 3.1 24.6 + - - +
411A TYR* 3.3 19.6 + - + +
462A ASP* 3.8 1.7 - - - +
508A ASN* 3.0 26.4 + - - +
509A GLY* 3.0 21.1 + - - -
512A MET* 3.4 18.3 - - + +
5B ARG* 2.7 34.1 + - - -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.8 11.4 - - + +
348A ILE 3.8 7.9 - - - +
349A GLY* 3.6 29.8 - - - +
362A PRO 2.9 20.6 + - - +
363A LEU* 3.8 2.9 - - + +
365A ASP* 1.3 73.9 - - - +
367A TYR* 1.3 63.1 + - - +
370A THR* 2.6 42.9 + - - +
382A SER* 3.9 18.8 - - - -
383A LEU 4.6 3.6 - - - +
384A LEU* 4.2 14.4 - - + -
411A TYR* 4.0 18.6 - - + -
413A ALA* 4.9 0.4 - - + -
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Residues in contact with TYR 367 (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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363A LEU* 2.8 25.7 + - + +
364A VAL* 3.7 11.0 - - + +
366A VAL* 1.3 79.9 - - - +
368A GLU* 1.3 70.8 + - + +
370A THR* 3.4 6.9 + - - -
371A ASN* 3.2 41.1 + - - +
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Residues in contact with GLU 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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364A VAL 2.9 17.9 + - - +
365A ASP 3.7 3.8 - - - +
366A VAL 3.2 0.2 - - - -
367A TYR* 1.3 86.1 - - + +
369A LEU* 1.3 61.4 + - - +
371A ASN* 3.2 9.6 + - - +
372A LEU* 3.0 51.7 + - + +
508A ASN* 4.1 8.2 - - - +
512A MET* 4.3 6.7 - - + -
516A LYS* 3.7 42.4 + - + +
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Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.8 15.5 - - + -
365A ASP 3.1 16.8 + - - +
366A VAL* 4.8 0.7 - - - -
368A GLU* 1.3 73.8 - - - +
370A THR* 1.3 67.4 + - - +
372A LEU* 4.4 4.9 - - + -
373A LEU* 2.9 44.2 + - + +
409A LEU* 4.7 0.2 - - + -
411A TYR* 3.4 45.5 - - + -
460A LEU* 4.5 10.5 - - + -
512A MET* 3.5 16.8 - - + -
515A LEU* 4.6 5.8 - - + -
519A LEU* 3.1 35.2 - - + -
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Residues in contact with THR 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.2 11.0 - - - +
366A VAL* 2.6 23.2 + - - +
367A TYR* 3.5 7.4 - - - -
369A LEU* 1.3 78.1 - - - +
371A ASN* 1.3 57.6 - - - +
373A LEU* 3.8 0.9 - - - +
374A ARG* 2.9 67.1 + - - +
380A VAL* 3.9 7.5 - - + +
382A SER* 2.8 34.7 + - - +
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Residues in contact with ASN 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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367A TYR* 3.2 33.9 + - + +
368A GLU* 3.2 15.4 + - - +
370A THR* 1.3 80.5 - - - +
372A LEU* 1.3 64.6 + - + +
374A ARG* 3.3 8.3 + - - +
375A GLN* 3.0 41.8 + - - +
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLU* 3.0 43.0 + - + +
369A LEU* 3.8 6.7 - - + +
371A ASN* 1.3 81.6 - - + +
373A LEU* 1.3 61.9 + - - +
375A GLN* 3.1 33.1 + - - +
376A LEU* 3.2 16.6 + - - +
512A MET* 5.1 1.8 - - - -
516A LYS* 3.7 35.4 - - + +
519A LEU* 4.0 25.6 - - + -
520A LEU* 3.8 23.5 - - + +
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Residues in contact with LEU 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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345A ALA* 3.9 15.0 - - + -
347A LEU* 3.9 27.4 - - + -
369A LEU* 2.9 40.3 + - + +
372A LEU* 1.3 74.2 - - - +
374A ARG* 1.3 64.1 + - - +
376A LEU* 3.1 17.1 + - + +
378A PHE* 3.0 48.6 + - + +
380A VAL* 3.8 13.5 - - + -
409A LEU* 4.1 21.3 - - + -
519A LEU* 4.1 16.2 - - + -
560A LEU* 4.6 3.6 - - + -
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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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370A THR* 2.9 45.8 + - - +
371A ASN* 3.7 7.0 - - - +
373A LEU* 1.3 75.7 - - - +
375A GLN* 1.3 62.7 + - - +
377A ASP* 2.9 17.7 + - - +
378A PHE 4.1 10.1 - - - +
380A VAL* 3.3 36.9 + - + +
382A SER* 4.8 3.4 + - - +
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Residues in contact with GLN 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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371A ASN* 3.0 37.4 + - - +
372A LEU* 3.1 28.1 + - - +
374A ARG* 1.3 76.9 - - - +
376A LEU* 1.3 58.5 - - - +
377A ASP* 3.2 10.4 + - - +
520A LEU* 3.8 24.7 - - + +
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Residues in contact with LEU 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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343A LYS* 2.8 28.6 + - - -
372A LEU 3.6 13.0 - - - +
373A LEU* 3.1 20.6 + - + +
375A GLN* 1.3 76.9 - - - +
377A ASP* 1.3 65.3 + - - +
378A PHE* 3.3 7.2 + - + -
519A LEU* 3.7 24.9 - - + +
520A LEU* 3.9 21.8 - - + +
560A LEU* 4.0 26.2 - - + +
561A THR* 3.4 32.5 - - + +
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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