Contacts of the helix formed by residues 375 - 389 (chain H) in PDB entry 3AOH
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 SER 375 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114H PHE* 4.0 6.7 + - - -
115H LEU* 2.5 50.3 + - - +
116H GLY* 4.4 0.5 - - - -
373H VAL* 4.2 2.2 + - - +
374H ASN* 1.3 71.5 - - - +
376H ARG* 1.3 65.6 + - - +
377H PRO 3.5 0.6 - - - -
378H LEU 3.6 0.7 + - - -
379H GLU* 3.3 25.2 + - - +
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Residues in contact with ARG 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374H ASN* 3.1 11.1 - - + +
375H SER* 1.3 79.0 - - - +
377H PRO* 1.3 73.5 - - + +
379H GLU* 4.0 3.5 - - - +
380H ALA* 3.0 43.8 + - - +
1280N VAL* 4.3 20.7 - - + +
1282N ARG* 4.1 35.0 - - - +
1295N GLU* 3.4 27.2 + - - +
1297N GLU* 5.8 1.8 + - - -
1316N GLY* 4.3 18.4 - - - +
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Residues in contact with PRO 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347H GLY* 4.5 1.8 - - - +
350H ARG* 4.1 43.7 + - + +
351H LEU* 4.1 6.3 - - - +
374H ASN* 2.9 47.8 - - - +
376H ARG* 1.3 85.6 - - + +
378H LEU* 1.3 56.6 + - - +
379H GLU 3.2 0.3 + - - -
380H ALA* 3.4 4.3 + - + +
381H ALA* 2.9 30.6 + - - +
1282N ARG* 5.6 6.1 - - - +
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Residues in contact with LEU 378 (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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94H LEU* 5.7 2.7 - - + -
115H LEU* 3.1 38.7 - - + +
116H GLY* 5.4 5.1 - - - +
118H ILE* 6.4 0.4 - - + -
344H PHE* 3.3 29.2 - - + +
347H GLY* 3.0 46.1 + - - +
348H LEU* 3.2 24.7 - - + +
351H LEU* 5.3 0.6 - - + +
375H SER 3.6 1.8 + - - -
376H ARG 3.5 0.6 - - - -
377H PRO* 1.3 80.9 - - - +
379H GLU* 1.3 60.8 + - - +
381H ALA* 3.8 1.6 - - - -
382H ILE* 2.6 45.5 + - + +
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Residues in contact with GLU 379 (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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91H GLN* 4.4 1.6 + - - +
116H GLY* 2.7 34.4 - - - -
117H HIS* 2.8 34.5 + - - +
375H SER* 3.3 22.4 + - - +
376H ARG* 4.0 3.6 - - - +
377H PRO 3.2 0.8 + - - -
378H LEU* 1.3 72.7 - - - +
380H ALA* 1.3 59.6 + - - +
381H ALA 3.1 1.3 - - - -
382H ILE* 3.9 2.3 - - - +
383H ARG* 2.7 56.7 + - + +
1297N GLU* 6.0 1.1 - - - +
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Residues in contact with ALA 380 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350H ARG* 6.1 1.1 - - - +
376H ARG* 3.0 38.8 + - - +
377H PRO* 3.8 4.3 - - + +
379H GLU* 1.3 78.3 - - - +
381H ALA* 1.3 66.9 + - - +
383H ARG* 3.7 8.8 - - - +
384H GLU* 2.8 32.6 + - - +
388H ARG* 5.3 3.6 + - - +
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Residues in contact with ALA 381 (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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343H GLN* 4.1 19.4 - - + +
346H VAL* 5.8 0.2 - - + -
347H GLY* 4.0 17.9 - - - +
350H ARG* 4.3 19.4 - - - +
377H PRO 2.9 18.0 + - - +
378H LEU* 3.5 9.4 - - - +
379H GLU 3.1 0.2 - - - -
380H ALA* 1.3 82.5 - - - +
382H ILE* 1.3 72.0 + - + +
384H GLU* 2.9 17.0 + - - +
385H PHE 3.1 4.7 + - - -
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Residues in contact with ILE 382 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H HIS 4.0 21.3 - - - +
118H ILE* 4.4 12.1 - - + -
119H PRO* 4.0 21.5 - - + -
340H MET* 5.7 5.2 - - + +
343H GLN* 4.9 3.1 - - + -
344H PHE* 4.2 27.1 - - + +
378H LEU* 2.6 50.6 + - + +
379H GLU* 3.9 4.0 - - - +
381H ALA* 1.3 77.3 - - + +
383H ARG* 1.3 71.2 + - - +
385H PHE* 2.8 19.8 + - - +
386H PHE* 3.2 21.4 + - + -
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Residues in contact with ARG 383 (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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89H THR* 3.6 17.8 + - - +
91H GLN* 3.5 29.0 - - - +
117H HIS 5.1 1.4 + - - -
129H ILE* 5.1 5.5 - - - +
130H ASN* 4.1 13.7 + - - -
379H GLU* 2.7 40.0 + - - +
380H ALA* 3.7 7.4 - - - +
382H ILE* 1.3 76.1 - - - +
384H GLU* 1.3 61.1 + - - +
386H PHE* 3.5 3.4 + - - +
387H SER* 2.6 35.3 + - - +
388H ARG* 3.7 23.0 - - - +
814H GLU* 5.7 0.4 + - - -
1297N GLU* 3.2 33.7 + - - +
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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
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343H GLN* 5.0 7.2 - - - +
350H ARG* 5.0 6.8 + - - -
380H ALA* 2.8 30.8 + - - +
381H ALA* 3.0 10.3 - - - +
383H ARG* 1.3 73.8 - - - +
385H PHE* 1.3 53.6 + - - +
388H ARG* 2.6 69.9 + - + +
389H SER 3.1 2.1 + - - -
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Residues in contact with PHE 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H ILE* 3.9 28.5 - - + -
339H LEU* 3.6 49.1 - - + -
340H MET* 4.0 6.1 - - - -
343H GLN* 3.9 39.2 + - + -
381H ALA 3.1 1.8 + - - -
382H ILE* 2.8 16.7 + - - +
384H GLU* 1.3 80.3 - - - +
386H PHE* 1.3 84.6 + + + +
389H SER* 2.9 47.6 + - - +
391H LEU* 5.0 5.2 - - + -
392H SER* 4.4 6.5 + - - -
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Residues in contact with PHE 386 (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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26H TYR* 3.7 3.8 - - - -
119H PRO* 3.3 43.5 - - + -
127H PHE* 3.8 17.3 - + - -
129H ILE* 3.2 37.1 - - + +
134H ARG* 3.9 7.8 + - - -
136H ILE* 3.7 25.4 - - + -
340H MET* 3.4 34.1 - - + -
382H ILE* 3.2 24.1 + - + +
383H ARG* 4.2 4.9 - - - +
385H PHE* 1.3 91.9 - + + +
387H SER* 1.3 58.2 + - - +
392H SER* 3.8 22.8 - - - -
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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
----------------------------------------------------------
129H ILE* 4.1 19.7 - - - -
130H ASN* 5.3 2.9 - - - -
134H ARG* 4.2 15.9 + - - +
383H ARG* 2.6 32.6 + - - +
386H PHE* 1.3 78.6 - - - +
388H ARG* 1.3 82.2 + - - +
389H SER 5.3 0.7 - - - -
392H SER 6.0 0.7 - - - -
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Residues in contact with ARG 388 (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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380H ALA* 5.3 3.4 + - - +
383H ARG* 3.7 24.0 - - - +
384H GLU* 2.6 50.4 + - + +
387H SER* 1.3 97.2 + - - +
389H SER* 1.3 65.2 + - - +
390H GLN* 3.3 3.1 + - - -
1297N GLU* 5.0 10.9 + - - +
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Residues in contact with SER 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384H GLU 3.1 3.8 + - - -
385H PHE* 2.9 48.5 + - - +
387H SER 5.3 0.5 - - - -
388H ARG* 1.3 77.7 + - - +
390H GLN* 1.3 61.0 + - - +
391H LEU* 2.6 32.7 + - - +
392H SER* 3.3 19.1 + - - +
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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