Contacts of the helix formed by residues 383 - 399 (chain H) in PDB entry 5GJQ
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 383 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H PRO 5.0 0.2 - - - +
219H GLY* 4.2 7.0 - - - -
381H THR* 3.1 13.2 + - - +
382H GLY* 1.3 76.2 - - - +
384H GLU* 1.3 59.6 + - - +
386H ARG* 2.6 36.1 + - - +
387H SER* 3.3 2.1 + - - -
501H ADP 3.3 23.2 - - - +
343I ARG* 3.8 22.2 - - - +
344I PRO* 3.8 18.1 - - + +
345I GLY* 5.7 0.6 - - - -
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Residues in contact with GLU 384 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380H SER* 4.0 28.6 - - - +
381H THR* 3.6 9.5 + - + +
383H ALA* 1.3 74.3 - - - +
385H ILE* 1.3 54.9 + - - +
386H ARG 2.7 6.3 + - - -
387H SER* 2.3 42.1 + - - +
388H VAL* 3.2 7.4 + - - +
416H VAL* 4.3 13.6 - - + +
417H ILE* 4.1 22.3 - - + +
420H TYR* 4.0 19.3 - - - +
424H SER* 4.8 13.6 + - - +
426H THR* 6.2 3.6 - - + -
344I PRO* 3.6 30.6 - - + +
350I LYS* 5.5 1.4 + - - -
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Residues in contact with ILE 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351H ARG* 3.5 42.8 - - + -
354H ILE* 4.1 17.0 - - + +
355H PHE* 2.3 68.3 - - + -
358H HIS* 4.7 1.7 + - - +
377H CYS* 5.1 7.2 - - + -
380H SER* 4.2 9.6 + - - +
381H THR 3.3 19.1 - - - +
382H GLY* 3.9 16.2 - - - +
383H ALA 3.2 0.6 - - - -
384H GLU* 1.3 75.7 - - - +
386H ARG* 1.3 59.7 + - - +
388H VAL* 3.5 7.5 - - - +
389H CYS* 3.3 13.2 + - - +
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Residues in contact with ARG 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358H HIS* 3.3 41.7 - - + +
382H GLY 3.8 1.0 + - - +
383H ALA* 2.6 20.7 + - - +
385H ILE* 1.3 77.3 - - - +
387H SER* 1.3 66.2 - - - +
388H VAL 3.0 4.9 - - - -
389H CYS* 3.3 4.0 + - + +
390H THR* 3.1 49.9 + - + +
501H ADP 5.5 2.2 - - + -
218I PRO 5.0 1.6 + - - -
219I PRO* 5.8 0.2 - - - +
220I LYS* 3.3 37.5 - - - +
344I PRO* 6.0 0.2 - - - -
345I GLY* 3.2 34.4 - - - +
348I ASP* 3.5 20.8 + - - +
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Residues in contact with SER 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383H ALA 3.3 2.0 + - - -
384H GLU* 2.3 35.3 + - - -
386H ARG* 1.3 79.3 - - - +
388H VAL* 1.3 50.8 + - - -
390H THR* 3.5 7.2 + - - -
391H GLU* 2.4 43.8 + - - +
416H VAL* 2.7 32.7 - - - +
344I PRO* 4.3 19.6 - - - +
348I ASP* 5.0 9.0 - - - -
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Residues in contact with VAL 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355H PHE* 4.3 13.9 - - + -
384H GLU 3.4 15.5 - - - +
385H ILE* 3.5 12.6 - - - +
386H ARG 3.0 0.4 - - - -
387H SER* 1.3 82.3 - - - +
389H CYS* 1.3 60.0 + - - +
391H GLU* 2.7 22.3 + - - +
392H ALA* 2.9 15.1 + - - +
409H PHE* 3.9 8.0 - - + +
412H ALA* 3.1 27.8 - - + +
413H VAL* 3.5 26.5 - - + +
416H VAL* 4.1 14.8 - - + -
417H ILE* 4.7 9.4 - - + -
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Residues in contact with CYS 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355H PHE* 4.3 18.6 - - - -
358H HIS* 4.0 17.5 - - + +
359H ALA* 3.5 40.8 - - - -
362H MET* 3.3 29.2 - - - +
370H PHE* 4.7 0.9 - - - -
385H ILE 3.3 6.2 + - - +
386H ARG* 3.3 9.0 + - + +
388H VAL* 1.3 80.1 - - - +
390H THR* 1.3 60.1 + - + +
392H ALA* 4.1 1.6 + - - +
393H GLY 4.1 2.1 + - - -
409H PHE* 4.1 17.9 - - - -
216I ILE* 3.3 7.8 - - - +
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Residues in contact with THR 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386H ARG* 3.1 46.0 + - + +
387H SER* 3.5 4.5 + - - -
389H CYS* 1.3 76.9 - - + +
391H GLU* 1.3 70.7 + - - +
392H ALA 3.3 0.2 - - - -
393H GLY* 2.8 16.6 + - - -
394H MET* 3.6 5.9 + - - +
216I ILE* 3.9 16.5 - - + +
217I LYS* 4.3 27.1 - - + +
218I PRO 5.2 8.0 + - - +
219I PRO* 5.9 1.8 - - - +
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Residues in contact with GLU 391 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387H SER* 2.4 35.8 + - - +
388H VAL* 2.7 10.5 + - - +
390H THR* 1.3 74.8 + - - +
392H ALA* 1.3 53.6 + - - +
394H MET* 2.8 36.7 + - - +
395H PHE* 3.3 33.9 + - + -
398H ARG* 4.2 2.4 + - - -
412H ALA* 3.8 8.3 - - + -
415H LYS* 4.1 12.3 + - + +
416H VAL* 3.8 18.5 - - + +
420H TYR* 5.3 2.0 + - - -
348I ASP* 6.2 0.3 - - - +
349I ARG* 3.4 38.6 + - - -
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Residues in contact with ALA 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362H MET* 5.1 0.2 - - + -
388H VAL 2.9 16.6 + - - +
389H CYS 4.2 3.4 - - - +
391H GLU* 1.3 71.7 - - - +
393H GLY* 1.3 54.4 + - - +
395H PHE* 3.7 11.9 - - - -
396H ALA* 2.4 41.7 + - - +
404H ALA* 4.2 18.6 - - + +
408H ASP* 4.0 17.7 - - + +
409H PHE* 4.2 20.6 - - + -
412H ALA* 4.1 1.6 - - + +
216I ILE* 5.1 1.6 - - + -
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Residues in contact with GLY 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390H THR 2.8 13.2 + - - -
392H ALA* 1.3 78.8 - - - +
394H MET* 1.3 53.0 + - - +
397H ILE* 2.7 43.8 + - - +
211I TYR* 5.3 0.2 - - - -
214I MET* 3.0 9.9 - - - +
216I ILE* 3.2 31.8 - - - +
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Residues in contact with MET 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390H THR 3.6 4.6 + - - +
391H GLU* 2.8 19.7 + - - +
393H GLY* 1.3 68.2 - - - -
395H PHE* 1.3 52.7 + - - +
397H ILE* 2.9 5.6 + - - +
398H ARG* 2.3 50.2 + - - +
199I GLU* 3.3 39.4 - - - +
200I SER* 3.7 12.1 - - - -
203I LEU* 4.9 0.9 - - - -
211I TYR* 3.1 38.6 - - + +
216I ILE* 6.1 0.9 - - + -
217I LYS 5.0 2.2 - - - +
219I PRO* 3.8 15.9 - - + -
349I ARG* 3.1 32.3 - - - +
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Residues in contact with PHE 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391H GLU* 3.3 43.2 + - + -
392H ALA* 3.1 10.7 + - - +
394H MET* 1.3 77.1 - - - +
396H ALA* 1.3 62.8 + - - +
398H ARG* 2.9 38.1 + - + +
399H ALA* 3.2 14.2 + - - +
401H ARG* 5.9 0.3 + - - -
408H ASP* 4.5 21.5 - - + +
411H GLU* 3.5 27.1 - - + -
412H ALA 4.5 4.7 - - - -
415H LYS* 3.6 32.5 - - + -
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Residues in contact with ALA 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392H ALA 2.4 28.9 + - - +
395H PHE* 1.3 74.5 - - - +
397H ILE* 1.3 57.5 + - - +
399H ALA* 4.2 3.1 - - - +
400H ARG 4.2 0.3 - - - -
401H ARG* 3.2 38.1 + - - +
402H LYS 4.6 2.2 - - - +
403H ILE 4.8 1.1 - - - -
404H ALA* 4.1 23.6 - - + +
408H ASP* 5.1 6.0 - - - -
214I MET* 3.1 30.5 - - - -
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Residues in contact with ILE 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393H GLY 2.7 15.1 + - - +
394H MET* 3.5 6.7 - - - +
396H ALA* 1.3 77.5 - - - +
398H ARG* 1.3 57.6 + - - +
399H ALA 2.3 24.8 - - - +
400H ARG* 4.2 3.6 - - - +
401H ARG 4.9 4.9 - - - +
199I GLU* 5.7 2.9 - - - -
203I LEU* 4.6 20.0 - - + -
210I TYR* 3.5 35.2 - - + -
211I TYR* 3.2 35.7 - - + -
214I MET* 3.1 29.6 - - + -
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Residues in contact with ARG 398 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391H GLU* 4.2 3.2 + - - -
394H MET* 2.3 34.9 + - - +
395H PHE* 2.9 43.7 + - + +
397H ILE* 1.3 65.7 - - - +
399H ALA* 1.3 64.8 + - - +
400H ARG* 3.4 16.5 + - - -
415H LYS* 4.2 4.2 - - - +
195I GLN* 3.2 30.2 + - - +
196I GLU* 3.2 25.2 + - - +
199I GLU* 2.6 55.9 + - - +
349I ARG* 3.4 25.4 - - - +
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Residues in contact with ALA 399 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395H PHE 3.2 10.8 + - - +
396H ALA 4.3 1.1 - - - +
397H ILE 2.3 26.5 - - - +
398H ARG* 1.3 78.7 - - - +
400H ARG* 1.3 78.3 + - - +
401H ARG* 3.5 37.0 - - + +
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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
------------------------------------------------------------
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