Contacts of the helix formed by residues 348 - 360 (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 LEU 348 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347H ASP* 1.3 81.0 + - - +
349H GLU* 1.3 65.0 + - + +
351H ARG* 3.0 36.1 + - - +
352H THR* 3.1 26.2 + - + +
374H ALA* 3.8 3.8 - - + +
375H ARG* 3.4 37.5 - - + +
378H PRO* 5.6 2.2 - - + -
32l LYS* 5.2 7.4 - - + +
172l SER 3.6 22.4 - - - +
173l ALA* 4.7 4.9 - - - -
175l GLU* 3.8 34.9 + - + +
176l GLY 5.2 2.7 - - - +
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Residues in contact with GLU 349 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347H ASP* 2.8 22.6 + - - +
348H LEU* 1.3 69.3 - - + +
350H GLY* 1.3 67.7 + - - +
352H THR* 1.9 37.1 + - - +
353H HIS* 3.2 3.7 + - - +
175l GLU* 4.0 12.6 - - - +
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Residues in contact with GLY 350 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H GLY* 4.1 19.5 - - - -
346H PRO* 4.7 4.5 - - - -
347H ASP* 2.9 18.7 + - - -
349H GLU* 1.3 71.5 - - - +
351H ARG* 1.3 54.2 + - - +
353H HIS* 2.7 29.3 + - - +
354H ILE* 2.8 20.2 + - - +
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Residues in contact with ARG 351 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345H LEU 5.8 0.2 - - - -
346H PRO* 3.4 16.6 - - + +
347H ASP* 1.3 63.8 + - - +
348H LEU* 3.0 30.1 + - - +
349H GLU 3.2 0.4 - - - -
350H GLY* 1.3 72.4 - - - +
352H THR* 1.3 54.4 + - - +
354H ILE* 2.8 13.4 + - - +
355H PHE* 2.5 38.5 + - + +
374H ALA* 2.0 42.3 + - + -
377H CYS* 2.2 35.8 + - - +
378H PRO* 2.9 15.3 + - - +
380H SER 4.1 11.7 - - - -
385H ILE* 3.5 26.9 - - + -
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Residues in contact with THR 352 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348H LEU* 3.1 15.9 + - + +
349H GLU* 1.9 40.8 + - - +
351H ARG* 1.3 72.9 - - - +
353H HIS* 1.3 54.3 + - - +
355H PHE* 3.8 4.8 - - - +
356H LYS* 2.8 49.6 + - - +
370H PHE* 5.7 1.6 - - - -
371H GLU* 4.2 33.2 - - + +
374H ALA* 3.8 17.0 - - + +
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Residues in contact with HIS 353 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178H GLY* 4.2 8.7 - - - -
179H GLY 4.1 10.8 - - - +
181H LYS* 4.5 22.6 + - - -
349H GLU 4.2 1.9 + - - +
350H GLY* 2.7 20.5 + - - +
352H THR* 1.3 77.9 + - - +
354H ILE* 1.3 52.8 + - - +
356H LYS* 4.5 13.6 + - + +
357H ILE* 2.4 61.8 + - + +
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Residues in contact with ILE 354 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178H GLY 3.8 7.6 - - - +
179H GLY* 5.2 1.6 - - - +
346H PRO* 3.3 35.2 - - + -
350H GLY* 2.8 12.5 + - - +
351H ARG* 2.8 24.5 + - + +
353H HIS* 1.3 75.3 - - - +
355H PHE* 1.3 55.2 + - - +
357H ILE* 3.7 6.3 - - - +
358H HIS* 2.7 44.9 + - + +
382H GLY* 4.0 27.1 - - - +
385H ILE* 4.1 15.7 - - + -
501H ADP 3.7 30.7 - - + +
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Residues in contact with PHE 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351H ARG* 2.5 25.3 + - + +
352H THR* 3.8 4.3 - - - +
354H ILE* 1.3 69.9 - - - +
356H LYS* 1.3 56.7 - - - +
358H HIS* 3.0 1.5 + - + +
359H ALA* 2.6 40.5 + - - +
370H PHE* 3.5 47.1 - + + -
373H LEU* 3.2 31.6 - - + -
374H ALA* 4.3 6.7 - - + -
377H CYS* 4.9 6.5 - - - -
385H ILE* 2.3 55.4 - - + -
388H VAL* 4.3 22.0 - - + -
389H CYS* 4.3 14.4 - - - -
409H PHE* 5.1 2.5 - + - -
413H VAL* 4.9 2.2 - - + -
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Residues in contact with LYS 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352H THR* 2.8 32.7 + - - +
353H HIS* 4.0 14.3 + - + +
355H PHE* 1.3 73.8 - - - +
357H ILE* 1.3 51.9 + - + +
359H ALA* 5.0 2.0 - - - -
360H ARG* 2.6 42.1 + - - +
370H PHE* 5.1 16.4 - - + -
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Residues in contact with ILE 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175H SER 3.5 19.1 - - - +
176H ASP* 3.8 19.3 - - + +
178H GLY* 3.2 33.4 - - - +
353H HIS* 2.4 51.8 + - + +
354H ILE* 3.7 5.4 - - - +
356H LYS* 1.3 76.6 - - + +
358H HIS* 1.3 75.6 + - + +
360H ARG* 3.2 43.2 + - - +
361H SER* 4.5 1.0 + - - -
501H ADP 5.6 2.2 - - + +
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Residues in contact with HIS 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354H ILE* 2.7 25.1 + - + +
355H PHE* 3.9 4.0 - - + +
357H ILE* 1.3 88.8 - - + +
359H ALA* 1.3 60.0 + - - +
360H ARG 3.5 0.2 + - - -
361H SER* 3.9 9.4 + - - -
362H MET* 4.4 7.1 - - - +
382H GLY 4.1 12.6 + - - -
385H ILE 4.7 0.6 - - - -
386H ARG* 3.3 46.2 + - + +
389H CYS* 4.0 17.8 - - + +
501H ADP 4.6 28.6 + + - -
215I GLY 5.5 1.0 - - - +
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Residues in contact with ALA 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355H PHE 2.6 20.0 + - - +
356H LYS* 4.7 0.4 - - - +
358H HIS* 1.3 68.5 - - - +
360H ARG* 1.3 52.8 + - - +
361H SER 2.7 17.7 + - - -
362H MET* 3.2 29.5 + - - +
364H VAL* 4.0 11.1 - - + +
366H ARG* 4.3 4.5 + - - -
370H PHE* 3.4 36.8 - - + -
389H CYS* 3.5 13.7 - - - -
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Residues in contact with ARG 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175H SER* 4.2 17.5 + - - -
176H ASP* 4.1 12.1 + - - -
356H LYS 2.6 25.4 + - - +
357H ILE* 3.2 48.1 + - - +
358H HIS 3.3 0.8 - - - -
359H ALA* 1.3 76.2 - - - +
361H SER* 1.3 74.8 + - - +
362H MET 3.6 1.5 + - - -
366H ARG* 4.2 17.6 + - - +
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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