Contacts of the helix formed by residues 357 - 374 (chain A) in PDB entry 3V6C
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 ASP 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A PHE* 4.5 0.7 - - - -
356A GLN* 1.3 78.1 + - - +
358A ALA* 1.3 59.4 + - - +
359A GLN* 2.9 10.6 + - - +
360A GLU* 2.9 37.9 + - + +
361A PHE* 3.0 27.7 + - - +
558A TYR* 4.1 0.2 - - - -
592A TYR* 2.6 27.2 + - - -
42B ARG* 3.3 15.5 + - - -
72B ARG* 3.3 25.5 - - + -
73B LEU 2.8 26.9 + - - +
74B ARG* 3.8 2.4 - - - +
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Residues in contact with ALA 358 (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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277A PHE* 4.3 11.4 - - - +
281A ILE* 3.6 30.1 - - + +
356A GLN 3.7 0.6 + - - -
357A ASP* 1.3 68.9 + - - +
359A GLN* 1.3 60.2 + - - +
361A PHE* 3.4 3.3 + - - +
362A LEU* 2.8 28.2 + - - +
547A SER* 3.9 10.3 - - - +
558A TYR* 3.1 38.4 + - + +
593A LEU* 4.3 5.6 - - + -
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Residues in contact with GLN 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASP* 2.9 11.9 + - - +
358A ALA* 1.3 72.0 - - - +
360A GLU* 1.4 61.1 + - - +
362A LEU* 3.3 3.1 + - + +
363A ARG* 2.9 48.9 + - + +
440A ASP* 2.8 32.8 + - - +
442A SER* 3.9 5.3 + - - -
501A HIS* 3.5 45.5 + - + +
592A TYR* 4.5 0.4 - - - +
593A LEU* 4.0 21.8 - - + +
42B ARG* 2.8 33.4 + - - -
44B ILE* 4.1 9.3 - - - +
70B VAL* 4.0 1.6 - - - +
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Residues in contact with GLU 360 (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 ARG* 2.9 35.7 + - - -
350A PHE* 4.3 6.5 - - + -
356A GLN* 4.6 6.7 - - - +
357A ASP* 2.9 21.9 + - + +
359A GLN* 1.4 76.0 - - - +
361A PHE* 1.4 61.8 + - - +
363A ARG* 3.2 3.8 + - - +
364A PHE* 3.0 38.9 + - + -
42B ARG* 3.5 27.6 - - - +
49B GLN* 3.0 18.8 + - - +
72B ARG* 2.8 33.1 + - - +
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Residues in contact with PHE 361 (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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277A PHE* 3.7 25.1 - + + -
278A MET* 3.5 37.7 - - + -
281A ILE* 3.7 37.7 - - + -
282A LEU* 4.6 2.0 - - + -
339A PHE* 3.7 19.5 - + - -
343A ILE* 3.7 35.2 - - + -
350A PHE* 3.6 21.7 - + + -
357A ASP 3.0 14.8 + - - +
358A ALA 3.6 5.4 - - - +
360A GLU* 1.4 76.6 - - - +
362A LEU* 1.3 51.5 + - - +
364A PHE 3.3 1.2 + - - -
365A LEU* 2.8 49.9 + - + +
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Residues in contact with LEU 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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281A ILE* 3.7 28.5 - - + -
285A LEU* 4.2 15.5 - - + -
358A ALA 2.8 20.5 + - - +
359A GLN* 3.5 6.1 - - + +
361A PHE* 1.3 72.7 - - - +
363A ARG* 1.4 77.0 + - - +
365A LEU* 3.9 1.7 - - - -
366A LEU* 2.9 59.5 + - + +
440A ASP* 4.5 2.0 - - - +
499A VAL* 4.0 18.8 - - + -
593A LEU* 3.7 23.6 - - + -
595A PHE* 4.3 11.0 - - + -
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Residues in contact with ARG 363 (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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359A GLN* 2.9 37.3 + - - +
360A GLU* 3.2 5.8 + - - +
362A LEU* 1.4 95.6 - - - +
364A PHE* 1.3 57.6 + - - +
366A LEU* 3.7 26.7 - - - +
367A ASP* 3.0 29.5 + - - +
439A TRP* 3.4 24.5 + - - +
440A ASP* 2.9 39.5 + - - +
499A VAL* 5.9 0.4 - - - +
702A GOL 2.9 25.0 + - - -
44B ILE* 3.9 23.1 - - + -
47B GLY* 2.8 29.8 + - - +
49B GLN* 4.8 10.5 - - + +
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Residues in contact with PHE 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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343A ILE* 4.4 2.5 - - + -
346A TYR* 3.5 17.9 - + - -
347A ALA* 3.8 21.8 - - + -
349A ARG* 3.4 37.7 - - - -
350A PHE* 3.8 25.1 - + + -
360A GLU* 3.0 31.2 + - + +
361A PHE 4.0 0.7 - - - +
363A ARG* 1.3 75.1 - - - +
365A LEU* 1.3 60.3 + - - +
367A ASP* 3.3 6.8 + - + +
368A GLY* 2.9 25.1 + - - -
49B GLN* 3.6 41.5 - - + -
51B GLU* 3.7 26.5 - - + -
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Residues in contact with LEU 365 (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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281A ILE* 4.7 1.1 - - + -
282A LEU* 4.5 2.2 - - + -
285A LEU* 3.6 30.3 - - + -
314A LEU* 4.1 12.5 - - + +
318A PHE* 4.4 9.0 - - + -
339A PHE* 3.7 30.5 - - + -
343A ILE* 3.8 12.5 - - + +
361A PHE* 2.8 46.7 + - + +
362A LEU 3.9 2.5 - - - +
364A PHE* 1.3 72.9 - - - +
366A LEU* 1.3 58.7 + - - +
368A GLY* 3.1 2.8 + - - -
369A LEU* 2.9 54.0 + - + +
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Residues in contact with LEU 366 (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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285A LEU* 4.4 13.2 - - + -
291A LEU* 4.9 2.9 - - + -
362A LEU* 2.9 45.1 + - + +
363A ARG* 3.7 26.7 - - - +
365A LEU* 1.3 72.9 - - + +
367A ASP* 1.4 57.4 + - - +
369A LEU* 3.8 17.1 - - + +
370A HIS* 2.8 33.6 + - - +
411A ILE* 3.8 21.7 - - + +
415A PHE* 4.0 39.9 - - + -
439A TRP* 4.6 4.5 - - + -
702A GOL 4.1 5.8 - - - +
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Residues in contact with ASP 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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346A TYR* 2.5 26.4 + - - -
363A ARG 3.0 19.7 + - - +
364A PHE* 3.5 10.7 - - + +
365A LEU 3.2 0.2 - - - -
366A LEU* 1.4 76.7 - - - +
368A GLY* 1.4 57.0 + - - +
370A HIS* 3.7 1.4 - - - +
371A ASN* 2.9 39.7 + - - -
702A GOL 3.0 34.2 + - - +
47B GLY 5.3 0.7 - - - +
48B LYS* 2.8 36.2 + - - -
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Residues in contact with GLY 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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314A LEU* 3.6 17.7 - - - -
346A TYR* 3.3 29.8 - - - -
364A PHE 2.9 12.5 + - - -
365A LEU 3.1 0.2 + - - -
367A ASP* 1.4 75.6 - - - +
369A LEU* 1.3 60.6 + - - +
371A ASN* 3.4 1.0 + - - +
372A GLU* 3.0 33.3 + - - +
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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
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291A LEU* 5.4 1.1 - - + -
314A LEU* 3.8 12.5 - - + +
315A VAL* 3.7 38.8 - - + +
318A PHE* 3.8 42.2 - - + -
365A LEU* 2.9 38.7 + - + +
366A LEU* 3.8 19.7 - - + +
368A GLY* 1.3 73.9 - - - +
370A HIS* 1.3 63.1 + - - +
372A GLU* 3.1 5.2 + - - +
373A VAL* 3.1 23.6 + - - +
411A ILE* 4.1 20.4 - - + -
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Residues in contact with HIS 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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366A LEU 2.8 21.3 + - - +
367A ASP 3.7 1.6 - - - +
369A LEU* 1.3 72.0 - - - +
371A ASN* 1.3 80.6 + - - +
372A GLU 3.2 0.2 + - - -
373A VAL* 3.2 1.7 + - - -
374A ASN* 2.9 29.7 + - - -
379A ARG* 4.6 0.4 - - - -
407A GLU* 2.8 31.3 + - + +
408A ASP 3.7 23.6 - - - -
409A SER* 2.7 31.1 + - - +
411A ILE* 3.9 11.3 - - + +
412A GLY* 5.0 1.3 - - - -
439A TRP* 3.5 27.8 - + + -
702A GOL 3.4 20.5 - - - -
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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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305A HIS* 6.0 0.7 - - - -
346A TYR* 2.8 31.1 + - + +
367A ASP* 2.9 31.5 + - - +
368A GLY* 4.0 4.0 - - - +
369A LEU 3.4 0.2 - - - -
370A HIS* 1.3 85.0 - - - +
372A GLU* 1.3 64.7 + - + +
373A VAL 3.5 0.2 + - - -
374A ASN* 3.6 14.9 + - - +
379A ARG* 3.0 29.5 + - - +
407A GLU* 4.3 0.2 - - - +
48B LYS* 4.3 7.8 + - - +
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Residues in contact with GLU 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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303A ASP 4.0 5.4 - - - +
304A LEU* 3.6 21.2 - - + +
305A HIS* 4.6 8.1 + - - -
312A THR* 3.0 31.0 - - - +
314A LEU* 3.6 19.4 - - - +
315A VAL* 3.2 37.7 + - + +
316A GLU* 3.7 3.6 - - - +
346A TYR* 5.2 9.1 - - + -
368A GLY 3.0 18.0 + - - +
370A HIS 3.1 0.4 - - - -
371A ASN* 1.3 81.2 - - + +
373A VAL* 1.3 59.1 + - - +
374A ASN 3.9 0.3 + - - -
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Residues in contact with VAL 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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294A TYR* 3.5 28.3 - - + +
300A TYR* 4.3 7.6 - - + -
303A ASP* 3.7 26.5 - - + +
304A LEU* 3.9 21.1 - - + -
315A VAL* 4.1 12.1 - - + -
369A LEU 3.1 13.7 + - - +
370A HIS 3.6 0.7 - - - +
372A GLU* 1.3 80.0 - - - +
374A ASN* 1.3 64.7 + - - +
375A ARG* 3.3 6.4 + - - +
409A SER* 3.7 15.8 - - - -
410A ARG 4.8 1.3 - - - +
411A ILE* 3.8 25.4 - - + -
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Residues in contact with ASN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A HIS* 2.6 33.8 + - - -
370A HIS* 2.9 19.1 + - - +
371A ASN* 3.6 11.9 - - - +
372A GLU 3.5 2.4 - - - -
373A VAL* 1.3 74.2 - - - +
375A ARG* 1.3 60.7 + - - +
376A VAL* 3.3 23.5 + - - +
379A ARG* 3.2 25.3 - - - +
406A ARG 3.1 23.2 + - - -
407A GLU* 3.5 3.6 + - - -
408A ASP 2.9 29.8 + - - +
409A SER* 3.9 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