Contacts of the helix formed by residues 408 - 420 (chain A) in PDB entry 2CG2
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 VAL 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LEU* 3.4 17.9 - - + +
368A LEU* 3.8 10.4 - - + +
386A HIS* 6.0 0.9 - - - +
389A LEU* 3.4 41.3 - - + +
390A ARG* 5.1 1.3 - - - +
391A LEU* 3.8 38.4 - - + +
401A ASP 5.4 1.3 - - - +
403A GLY* 4.9 4.5 - - - +
407A SER* 1.3 71.5 - - - +
409A SER* 1.3 65.4 + - - +
411A ASN* 3.8 0.6 - - - +
412A ALA* 2.9 25.2 + - + +
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Residues in contact with SER 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A HIS* 3.2 37.7 - - - +
407A SER* 3.1 2.8 + - - -
408A VAL* 1.3 83.7 - - - +
410A HIS* 1.3 62.5 + - - +
412A ALA* 3.4 0.9 + - - +
413A ARG* 2.9 39.2 + - - -
505A TRP* 3.4 24.6 - - - -
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Residues in contact with HIS 410 (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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307A ASN* 2.9 16.2 + - - -
309A TYR* 2.8 40.3 + + + -
311A LEU* 3.3 27.3 - - + +
405A HIS 4.0 4.5 - - - -
406A GLY* 3.7 2.5 - - - -
407A SER* 2.7 44.1 + - - +
409A SER* 1.3 72.8 - - - +
411A ASN* 1.3 69.1 + - - +
413A ARG* 3.6 24.9 + - - +
414A ALA* 3.0 24.9 + - - +
502A ASN* 4.3 1.3 - - - -
505A TRP* 3.1 19.2 + + + +
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Residues in contact with ASN 411 (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 LEU* 3.6 20.2 - - - +
306A HIS 2.9 25.3 + - - -
307A ASN 3.8 0.2 - - - -
308A LEU* 2.9 40.5 + - + +
309A TYR 3.7 0.5 + - - -
368A LEU* 4.1 10.3 - - + +
407A SER 2.9 24.3 + - - +
408A VAL 3.9 1.8 - - - +
410A HIS* 1.3 91.6 + - - +
412A ALA* 1.3 64.3 + - - +
414A ALA* 3.3 5.5 + - - +
415A VAL* 3.0 27.9 + - - +
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Residues in contact with ALA 412 (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 LEU* 4.8 4.2 - - + +
372A THR* 3.1 45.1 - - - +
385A VAL* 4.0 14.8 - - + -
386A HIS* 4.8 4.9 - - - -
389A LEU* 4.2 20.2 - - + -
408A VAL* 2.9 18.5 + - + +
409A SER 3.9 3.6 - - - +
410A HIS 3.4 0.2 - - - -
411A ASN* 1.3 75.1 - - - +
413A ARG* 1.3 63.3 + - - +
415A VAL* 3.3 2.3 + - - -
416A LEU* 3.1 6.9 + - - +
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Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ILE* 3.5 33.6 - - + +
385A VAL* 3.9 10.5 - - + -
386A HIS* 3.4 35.9 + - - +
409A SER* 2.9 33.8 + - - +
410A HIS* 3.6 19.8 - - - +
411A ASN 3.3 0.4 - - - -
412A ALA* 1.3 77.0 - - - +
414A ALA* 1.3 53.8 + - - +
416A LEU* 3.4 3.8 + - - +
417A ASN* 2.8 34.8 + - - +
505A TRP* 3.5 21.0 - - - -
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Residues in contact with ALA 414 (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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308A LEU* 4.3 6.1 - - + -
309A TYR* 3.5 32.1 - - + -
316A VAL* 3.4 18.2 - - + +
410A HIS 3.0 15.5 + - - +
411A ASN* 3.4 12.6 - - - +
412A ALA 3.2 0.2 - - - -
413A ARG* 1.3 74.7 - - - +
415A VAL* 1.3 60.0 + - - +
417A ASN* 3.3 7.0 + - - +
418A ARG* 2.8 30.0 + - - +
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.5 22.9 - - + -
316A VAL* 5.0 1.3 - - + -
317A ARG 6.0 0.9 - - - +
319A ALA* 4.6 4.3 - - + -
368A LEU 4.3 5.4 - - - +
369A HIS* 3.7 41.1 - - + +
372A THR* 3.9 10.3 - - + +
373A LEU* 3.9 12.6 - - + -
411A ASN 3.0 16.5 + - - +
412A ALA 3.3 6.5 + - - +
414A ALA* 1.3 75.2 - - - +
416A LEU* 1.3 64.2 + - - +
418A ARG* 3.0 16.0 + - - +
419A TYR* 3.1 32.6 + - + -
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Residues in contact with LEU 416 (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 THR* 3.8 8.7 - - + -
373A LEU* 4.9 5.4 - - - -
376A ALA* 3.8 20.4 - - + -
380A VAL 3.5 22.9 - - - +
381A THR* 3.7 16.2 - - - +
382A ILE* 3.8 23.1 - - + +
385A VAL* 3.8 17.7 - - + -
412A ALA 3.1 12.6 + - - +
413A ARG* 3.6 10.1 - - - +
415A VAL* 1.3 77.5 - - - +
417A ASN* 1.3 52.0 + - - +
419A TYR* 3.3 1.1 + - - -
420A LEU* 2.7 57.3 + - + +
421A GLY 4.9 2.0 - - - +
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Residues in contact with ASN 417 (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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309A TYR* 6.1 5.1 - - - -
316A VAL* 4.3 14.9 - - + +
382A ILE* 3.9 11.6 - - + +
413A ARG 2.8 21.1 + - - +
414A ALA* 3.6 7.8 - - - +
416A LEU* 1.3 69.7 - - - +
418A ARG* 1.3 65.2 + - - +
421A GLY* 2.8 60.6 + - - +
422A TYR* 3.1 11.5 + - - +
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Residues in contact with ARG 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL* 3.0 40.1 + - + +
317A ARG 3.7 20.6 + - - -
318A ASP* 3.8 29.9 + - - +
319A ALA 5.6 0.4 - - - +
414A ALA 2.8 14.2 + - - +
415A VAL* 3.3 11.7 - - - +
417A ASN* 1.3 79.1 - - - +
419A TYR* 1.3 83.5 + - + +
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Residues in contact with TYR 419 (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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318A ASP* 4.7 3.1 + - - -
320A LEU* 4.5 10.2 - - - +
369A HIS* 2.6 40.8 + + - -
373A LEU* 3.7 33.2 - - + -
415A VAL* 3.1 28.1 + - + +
416A LEU 4.1 2.0 - - - +
418A ARG* 1.3 101.8 + - + +
420A LEU* 1.3 73.4 + - + +
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Residues in contact with LEU 420 (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 LEU* 6.0 1.1 - - + -
376A ALA* 4.0 24.5 - - + +
380A VAL 5.6 0.9 - - - +
416A LEU* 2.7 40.7 + - + +
419A TYR* 1.3 89.0 - - + +
421A GLY* 1.3 59.8 - - - +
423A TYR* 4.5 10.3 + - - +
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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