Contacts of the helix formed by residues 401 - 416 (chain K) 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 ASP 401 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243K TYR 3.8 11.8 - - - +
244K ASN 4.1 1.6 - - - +
245K CYS* 2.8 30.1 - - - +
368K HIS* 3.7 7.0 + - - -
398K ALA* 4.9 11.9 - - + +
399K PRO 3.3 5.3 + - - -
400K GLU* 1.3 77.5 - - - +
402K PRO* 1.3 70.6 - - - +
403K PHE* 3.6 7.8 - - - +
404K VAL* 3.5 30.0 - - + +
405K MET* 3.1 27.6 + - - +
431K LYS* 5.3 0.2 - - - -
3W ARG* 3.4 20.3 + - - -
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Residues in contact with PRO 402 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244K ASN 4.5 4.0 - - - +
245K CYS* 4.3 14.4 - - + -
400K GLU 4.0 5.6 - - - +
401K ASP* 1.3 93.9 - - - +
403K PHE* 1.3 57.0 + - + +
405K MET* 3.5 5.5 + - + +
406K HIS* 2.9 30.7 + - - +
428K ALA* 4.0 19.5 - - + +
431K LYS* 4.3 18.8 - - + +
432K ILE* 4.3 17.9 - - + +
435K ILE* 5.7 4.5 - - + -
436K GLY 6.3 0.7 - - - +
444K TRP* 3.7 26.4 - - + -
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Residues in contact with PHE 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245K CYS* 3.6 27.4 - - - -
247K PHE* 4.1 5.2 - + - -
372K LEU* 4.8 5.2 - - + -
373K TYR* 4.9 4.5 - - - -
401K ASP* 3.1 13.0 - - - +
402K PRO* 1.3 82.4 - - - +
404K VAL* 1.3 62.0 + - + +
406K HIS* 3.6 3.3 + - - +
407K GLU* 2.8 36.8 + - + +
443K LYS* 3.5 34.5 - - + -
444K TRP* 3.6 26.7 - + - -
3W ARG* 3.9 32.5 - - + +
4W ARG 4.0 13.2 - - - -
5W LYS* 4.6 0.9 - - - -
6W PRO* 3.5 33.7 - - + -
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Residues in contact with VAL 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368K HIS* 3.6 25.6 - - + -
372K LEU* 3.7 27.8 - - + -
391K PHE* 5.2 1.3 - - + +
394K ALA* 4.5 17.7 - - + +
395K LEU* 4.9 15.7 - - + +
398K ALA 5.1 6.3 - - - +
399K PRO 5.8 0.9 - - - +
401K ASP* 3.3 31.0 + - + +
403K PHE* 1.3 73.0 - - - +
405K MET* 1.3 62.5 + - + +
407K GLU* 3.2 3.1 + - - +
408K VAL* 3.0 43.5 + - + +
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Residues in contact with MET 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395K LEU* 5.6 6.5 - - + -
399K PRO 3.3 25.6 - - - +
401K ASP 3.1 17.1 + - - +
402K PRO 3.9 3.1 - - - +
404K VAL* 1.3 80.7 - - + +
406K HIS* 1.3 62.0 + - - +
408K VAL* 3.4 6.1 + - - +
409K GLY 3.1 16.8 + - - -
424K TRP* 3.7 37.8 - - + +
427K ASP* 3.5 38.8 - - - +
428K ALA* 4.0 11.0 - - + -
431K LYS* 3.9 33.4 - - - -
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Residues in contact with HIS 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402K PRO 2.9 18.7 + - - +
403K PHE 3.6 3.3 + - - +
405K MET* 1.3 75.2 - - - +
407K GLU* 1.3 70.0 + - - +
409K GLY 3.1 2.1 + - - -
410K VAL* 3.1 28.2 + - + +
425K PHE* 3.4 29.8 - + - -
428K ALA* 4.1 7.0 - - + +
444K TRP* 4.2 10.1 - + + -
446K PRO 4.6 0.2 - - - -
447K LEU* 4.2 22.8 + - + -
450K ASN* 2.9 23.0 + - - -
6W PRO* 3.2 31.0 - - + +
7W THR* 3.0 27.5 + - - -
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Residues in contact with GLU 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372K LEU* 3.4 32.3 - - + +
373K TYR* 5.1 5.7 - - - -
376K LEU* 2.8 44.9 - - - +
391K PHE* 4.4 4.3 - - + -
403K PHE* 2.8 27.2 + - + +
404K VAL 3.2 7.4 + - - +
406K HIS* 1.3 84.0 + - - +
408K VAL* 1.3 66.6 + - - +
410K VAL* 3.1 15.2 + - - +
411K VAL* 3.2 18.7 + - - +
4W ARG* 4.9 5.0 - - - +
6W PRO* 4.2 13.3 - - - +
7W THR* 4.3 7.8 + - - +
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Residues in contact with VAL 408 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391K PHE* 3.8 42.4 - - + -
395K LEU* 4.8 13.0 - - + -
404K VAL* 3.0 24.8 + - + +
405K MET* 3.7 7.2 - - - +
407K GLU* 1.3 74.4 - - - +
409K GLY* 1.3 56.8 + - - +
411K VAL* 3.3 2.9 + - - +
412K ALA* 2.8 30.3 + - + +
424K TRP* 3.3 35.2 - - + +
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Residues in contact with GLY 409 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405K MET 3.1 10.5 + - - -
406K HIS 3.1 5.5 + - - -
408K VAL* 1.3 76.4 - - - +
410K VAL* 1.3 56.9 + - - +
412K ALA* 3.2 7.5 + - - +
413K PHE* 2.8 28.4 + - - +
421K ALA* 3.5 5.5 - - - +
424K TRP* 3.7 22.4 - - - +
425K PHE* 3.5 17.3 - - - -
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Residues in contact with VAL 410 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376K LEU* 5.3 3.6 - - + -
380K LEU* 4.9 9.2 - - + -
406K HIS* 3.1 24.7 + - + +
407K GLU* 3.1 9.6 + - - +
409K GLY* 1.3 74.8 - - - +
411K VAL* 1.3 65.4 + - + +
413K PHE* 3.2 7.5 + - - +
414K GLN* 3.1 31.8 + - + +
425K PHE* 3.9 9.9 - - + -
450K ASN* 3.8 26.2 - - - +
7W THR* 3.8 19.5 - - - +
9W LEU* 3.6 19.5 - - + -
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Residues in contact with VAL 411 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375K GLY 4.1 1.3 - - - +
376K LEU* 4.3 10.5 - - + +
379K GLY* 4.0 22.7 - - - -
380K LEU* 6.0 0.7 - - + -
384K SER* 4.9 3.4 - - - +
387K ALA* 3.9 16.2 - - + -
388K GLU* 5.3 1.1 - - + +
391K PHE* 3.2 45.3 - - + -
407K GLU 3.2 6.7 + - - +
408K VAL 3.7 3.8 - - - +
410K VAL* 1.3 76.3 - - + +
412K ALA* 1.3 65.8 + - - +
414K GLN* 2.9 18.5 + - + +
415K ASN* 3.1 25.9 + - - +
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Residues in contact with ALA 412 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408K VAL* 2.8 14.6 + - + +
409K GLY* 3.4 11.0 - - - +
411K VAL* 1.3 75.2 - - - +
413K PHE* 1.3 62.7 + - - +
415K ASN* 3.0 22.1 + - - +
416K GLY 3.1 8.7 + - - -
417K GLU* 3.1 14.0 + - + +
420K THR* 3.8 24.2 - - - +
421K ALA* 3.9 13.5 - - + +
424K TRP* 4.6 4.9 - - + +
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Residues in contact with PHE 413 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409K GLY 2.8 14.7 + - - +
410K VAL 3.3 10.5 - - - +
412K ALA* 1.3 77.4 - - - +
414K GLN* 1.3 64.5 + - - +
416K GLY* 3.1 17.8 + - - +
417K GLU 5.0 0.9 - - - +
418K TRP* 4.8 7.0 + + - -
421K ALA* 3.9 6.5 - - + +
425K PHE* 4.9 0.7 - + + -
453K HIS* 4.2 17.5 - + + -
454K VAL* 3.5 45.5 - - + -
457K LYS* 4.0 38.1 - - + -
9W LEU* 3.6 41.5 - - + -
10W GLU 5.9 1.8 - - - -
15W ASP* 5.9 1.3 - - - -
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Residues in contact with GLN 414 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379K GLY* 4.1 25.8 - - - +
380K LEU* 4.0 17.8 - - + +
382K ASN* 4.7 10.9 + - - +
410K VAL* 3.1 22.3 + - + +
411K VAL* 2.9 12.5 + - - +
413K PHE* 1.3 83.9 - - - +
415K ASN* 1.3 61.7 + - - +
416K GLY 3.1 1.2 + - - -
9W LEU* 3.5 26.8 - - - +
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Residues in contact with ASN 415 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379K GLY* 5.7 0.9 - - - +
382K ASN* 4.9 6.5 + - - +
384K SER* 2.9 40.1 + - - -
388K GLU* 6.1 1.2 - - - +
411K VAL* 3.6 19.2 + - - +
412K ALA* 3.0 13.3 + - - +
414K GLN* 1.3 78.9 - - - +
416K GLY* 1.3 61.0 + - - +
417K GLU* 3.4 29.9 + - + +
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Residues in contact with GLY 416 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412K ALA 3.1 2.8 + - - -
413K PHE 3.1 14.0 + - - -
414K GLN 3.1 1.6 + - - -
415K ASN* 1.3 80.3 - - - +
417K GLU* 1.3 60.6 + - - +
418K TRP* 2.8 51.4 + - - -
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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
------------------------------------------------------------
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