Contacts of the helix formed by residues 380 - 395 (chain P) in PDB entry 5G04
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 ASN 380 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ALA 2.8 30.5 + - - +
46D GLU* 3.3 7.7 - - - +
47D LYS 3.2 21.2 - - - +
48D ASP 4.3 0.2 - - - +
49D ASN* 2.8 29.5 + - - +
375P TYR* 3.2 20.5 + - + +
378P MET* 3.2 6.1 + - + +
379P LYS* 1.3 72.5 - - - +
381P THR* 1.3 59.4 + - - +
382P SER* 4.0 3.3 + - - -
383P ALA* 3.3 29.2 + - + +
384P ALA 3.3 17.3 + - - -
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Residues in contact with THR 381 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375P TYR 5.1 0.2 - - - -
376P MET* 4.7 6.6 - - - +
379P LYS* 3.1 11.7 + - - +
380P ASN* 1.3 70.8 + - - +
382P SER* 1.3 59.3 + - - +
383P ALA 3.3 1.8 - - - -
384P ALA* 2.9 8.9 + - - +
385P ILE* 2.8 34.9 + - - +
408P THR* 3.0 28.2 + - - -
411P ILE* 5.1 10.3 - - + +
412P LEU* 3.7 26.9 - - + +
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Residues in contact with SER 382 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ASP 4.6 3.1 - - - -
49D ASN* 4.1 13.2 - - - -
51D LEU* 2.8 30.7 + - - +
53D PRO* 3.2 21.9 - - - +
380P ASN* 3.6 3.9 + - - -
381P THR* 1.3 79.1 - - - +
383P ALA* 1.3 65.9 + - - +
385P ILE* 3.3 12.6 + - - +
386P GLN* 3.1 23.7 + - - +
412P LEU* 6.1 0.3 - - - +
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Residues in contact with ALA 383 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ASP* 3.4 30.8 + - - +
375P TYR* 3.6 20.1 - - + -
380P ASN* 3.3 36.2 + - - +
382P SER* 1.3 77.6 - - - +
384P ALA* 1.3 51.4 + - - +
386P GLN* 3.3 4.9 + - - +
387P ALA* 2.7 36.7 + - - +
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Residues in contact with ALA 384 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372P GLY 4.0 5.4 - - - +
375P TYR* 3.8 15.7 - - + -
376P MET* 4.0 14.8 - - - +
380P ASN 3.3 10.1 + - - +
381P THR* 2.9 17.7 + - - +
383P ALA* 1.3 80.2 - - - +
385P ILE* 1.3 51.5 + - - +
387P ALA* 3.1 5.3 + - - +
388P TYR* 2.7 57.1 + - + -
408P THR* 4.4 1.6 - - - +
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Residues in contact with ILE 385 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PRO* 3.6 28.7 - - + -
381P THR 2.8 19.7 + - - +
382P SER* 3.6 14.4 - - - +
383P ALA 3.3 0.2 - - - -
384P ALA* 1.3 73.1 - - - +
386P GLN* 1.3 54.8 + - - +
387P ALA 3.2 0.2 + - - -
388P TYR 3.2 1.6 + - - -
389P ARG* 2.7 67.5 + - - +
405P LEU* 3.6 13.2 - - + +
408P THR* 3.2 22.9 - - + +
409P TYR* 3.8 12.1 - - + +
412P LEU* 3.6 30.1 - - + -
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Residues in contact with GLN 386 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ASP* 3.0 29.9 + - - +
51D LEU* 5.8 1.8 - - + -
510J ARG* 3.7 36.7 + - - +
368P TRP* 5.3 6.6 - - + -
382P SER 3.1 10.5 + - - +
383P ALA 3.5 7.6 - - - +
385P ILE* 1.3 78.5 - - - +
387P ALA* 1.3 67.6 + - - +
389P ARG* 3.0 8.8 + - - +
390P HIS* 2.9 61.4 + - - +
393P GLU* 5.4 0.3 - - - +
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Residues in contact with ALA 387 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368P TRP* 3.4 29.7 - - + +
371P MET 4.3 0.4 - - - -
372P GLY* 3.7 25.8 - - - +
375P TYR* 3.9 15.3 - - + -
383P ALA 2.7 17.3 + - - +
384P ALA 3.2 7.4 - - - +
385P ILE 3.1 0.2 - - - -
386P GLN* 1.3 76.8 - - - +
388P TYR* 1.3 63.0 + - - +
390P HIS* 3.0 20.1 + - - +
391P ALA 3.4 3.6 + - - -
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Residues in contact with TYR 388 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368P TRP 4.7 0.7 - - - -
369P THR* 3.7 12.8 - - - -
372P GLY* 3.5 9.9 + - - -
373P HIS* 2.9 49.7 + + - -
376P MET* 4.0 14.9 - - - +
384P ALA* 2.7 49.7 + - + +
385P ILE 3.8 0.4 - - - +
387P ALA* 1.3 72.4 - - - +
389P ARG* 1.3 64.1 + - - +
391P ALA* 2.9 20.8 + - - +
392P ILE* 3.0 14.9 + - - +
401P ALA* 3.7 20.1 - - - +
404P GLY* 3.6 28.6 - - - -
405P LEU* 3.6 17.7 - - + -
407P GLN* 5.6 1.9 + - - -
408P THR* 3.9 18.2 - - + -
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Residues in contact with ARG 389 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 3.4 27.2 - - + +
503J HIS* 3.2 30.0 + - - +
507J GLY* 5.6 3.4 - - - -
385P ILE* 2.7 34.2 + - - +
386P GLN* 3.3 10.8 - - - +
388P TYR* 1.3 76.6 - - - +
390P HIS* 1.3 56.9 + - - +
392P ILE* 3.0 25.2 - - + +
393P GLU* 2.8 44.6 + - + +
405P LEU* 4.0 14.3 - - - +
409P TYR* 2.7 33.9 + - - -
421P TYR* 2.7 24.8 + - - -
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Residues in contact with HIS 390 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510J ARG* 5.7 0.7 - - - -
368P TRP* 3.3 53.1 - + + -
386P GLN* 2.9 47.4 + - - -
387P ALA 3.0 4.7 + - - +
389P ARG* 1.3 74.6 - - - +
391P ALA* 1.3 65.0 + - - +
393P GLU* 3.1 31.6 + - + +
394P VAL* 2.9 29.6 + - + +
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Residues in contact with ALA 391 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365P LEU 4.6 2.9 - - - +
368P TRP* 3.6 23.4 - - + +
369P THR* 3.8 11.4 - - - +
387P ALA 3.4 2.0 + - - -
388P TYR 2.9 12.1 + - - +
390P HIS* 1.3 76.5 - - - +
392P ILE* 1.3 55.7 + - - +
394P VAL* 3.6 2.2 + - - -
395P ASN* 2.9 38.8 + - - +
398P ASP* 3.9 9.2 - - - +
401P ALA* 3.4 21.8 - - + -
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Residues in contact with ILE 392 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503J HIS* 4.8 17.0 - - + -
388P TYR 3.0 14.7 + - - +
389P ARG* 3.0 36.6 - - + +
391P ALA* 1.3 74.5 - - - +
393P GLU* 1.3 67.1 + - + +
395P ASN 3.0 27.7 - - - +
396P LYS* 3.3 31.4 + - + -
398P ASP 5.8 0.7 - - - +
401P ALA* 4.4 8.7 - - + +
402P TRP* 3.5 39.7 - - + -
405P LEU* 3.8 13.9 - - + -
421P TYR* 5.4 0.4 - - + -
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Residues in contact with GLU 393 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503J HIS 6.1 0.7 - - - +
504J THR* 5.9 6.1 - - - +
507J GLY* 3.7 28.8 - - - +
510J ARG* 6.0 0.3 + - - -
363P ARG* 5.4 1.9 + - - -
386P GLN* 5.4 0.2 - - - +
389P ARG* 2.8 35.0 + - + +
390P HIS* 3.1 38.5 + - + +
392P ILE* 1.3 74.3 - - + +
394P VAL* 1.3 63.0 + - + +
396P LYS* 4.9 8.0 + - - +
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Residues in contact with VAL 394 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362P PRO 4.5 8.7 - - - +
363P ARG* 4.0 59.9 + - + +
365P LEU* 4.9 4.5 - - - +
368P TRP* 4.2 20.2 - - + +
390P HIS* 2.9 18.0 + - + +
391P ALA* 3.8 0.9 - - - +
392P ILE 3.7 0.2 - - - -
393P GLU* 1.3 79.4 - - + +
395P ASN* 1.3 79.7 + - - +
396P LYS 4.3 0.4 + - - -
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Residues in contact with ASN 395 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365P LEU* 3.6 44.3 - - - +
391P ALA* 2.9 26.3 + - - +
392P ILE* 3.0 15.8 - - - +
394P VAL* 1.3 92.0 + - - +
396P LYS* 1.3 61.6 + - - +
397P ARG* 3.0 10.6 + - + +
398P ASP* 3.4 31.1 + - + +
402P TRP* 5.0 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