Contacts of the helix formed by residues 401 - 417 (chain H) in PDB entry 2R9R
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 PRO 401 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323H GLU* 3.7 27.1 - - + +
326H LEU* 4.5 4.5 - - + -
327H LEU* 4.1 21.3 - - + +
330H PHE* 4.1 23.8 - - + -
397H THR 3.1 22.4 - - - +
398H ILE 3.3 7.0 - - - +
400H LEU* 1.3 90.2 - - + +
402H VAL* 1.3 65.0 + - - +
403H PRO 3.4 0.2 - - - -
404H VAL* 3.3 23.5 + - + +
405H ILE* 3.6 10.4 + - + +
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Residues in contact with VAL 402 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327H LEU* 4.7 14.1 - - + -
398H ILE* 3.0 42.0 - - + +
399H ALA* 4.8 1.8 - - - +
401H PRO* 1.3 75.8 - - - +
403H PRO* 1.4 66.1 - - + +
405H ILE* 2.8 32.1 + - + +
406H VAL* 2.9 27.2 + - + -
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Residues in contact with PRO 403 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399H ALA* 2.9 29.2 - - - +
400H LEU 3.6 5.6 - - - +
401H PRO 3.5 3.6 - - - -
402H VAL* 1.4 90.0 - - + +
404H VAL* 1.3 56.9 + - + +
406H VAL* 3.2 11.1 + - + +
407H SER* 2.8 29.3 + - - -
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Residues in contact with VAL 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H GLU* 3.7 31.6 - - + +
400H LEU 4.5 7.6 - - - +
401H PRO* 3.5 15.7 - - + +
402H VAL 3.2 0.4 - - - -
403H PRO* 1.3 76.6 - - + +
405H ILE* 1.3 57.0 + - - +
407H SER* 3.1 10.2 + - - -
408H ASN* 2.9 41.5 + - - +
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Residues in contact with ILE 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H THR* 3.7 10.1 - - + +
317H LEU* 5.2 7.9 - - + -
320H SER* 3.9 30.7 - - - +
323H GLU* 4.0 9.2 - - + +
324H LEU* 3.4 39.5 - - + +
327H LEU* 5.2 7.2 - - + -
401H PRO* 3.7 16.8 - - + +
402H VAL* 2.8 16.5 + - + +
404H VAL* 1.3 72.1 - - - +
406H VAL* 1.3 67.5 + - + +
408H ASN* 3.4 3.1 + - - +
409H PHE* 3.0 22.6 + - + +
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Residues in contact with VAL 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402H VAL* 2.9 37.0 + - + +
403H PRO* 3.5 10.1 - - + +
405H ILE* 1.3 74.3 - - + +
407H SER* 1.3 67.1 + - - +
409H PHE* 3.4 10.5 + - + +
410H ASN* 2.9 24.7 + - + +
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Residues in contact with SER 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403H PRO 2.8 14.5 + - - -
404H VAL* 3.1 13.9 - - - -
406H VAL* 1.3 76.5 - - - +
408H ASN* 1.3 67.2 + - - +
410H ASN* 2.9 10.0 + - - +
411H TYR* 2.9 22.8 + - - +
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Residues in contact with ASN 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H THR* 4.1 5.8 - - + +
319H ALA* 3.6 21.1 + - - +
320H SER* 2.8 28.2 + - - +
323H GLU* 4.8 2.2 + - - -
404H VAL* 2.9 25.5 + - - +
405H ILE* 3.6 6.6 - - - +
407H SER* 1.3 76.9 + - - +
409H PHE* 1.3 63.2 + - - +
411H TYR* 3.2 8.6 + - - +
412H PHE* 3.0 41.3 + - + -
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Residues in contact with PHE 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H GLY* 4.8 4.0 - - - -
312H ILE* 3.7 17.0 - - + -
313H LEU* 4.4 21.8 - - + -
316H THR* 3.3 31.1 - - + +
405H ILE* 3.0 14.9 + - + +
406H VAL* 3.6 13.9 - - + +
408H ASN* 1.3 76.5 - - - +
410H ASN* 1.3 59.2 + - + +
412H PHE* 3.4 0.7 + - - +
413H TYR* 2.7 67.5 + + + +
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Residues in contact with ASN 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406H VAL* 2.9 16.1 + - + +
407H SER* 2.9 13.1 + - - +
409H PHE* 1.3 82.3 - - + +
411H TYR* 1.3 64.2 + - - +
413H TYR* 3.6 8.3 - - - +
414H HIS* 3.1 60.5 + - - -
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Residues in contact with TYR 411 (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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130H GLU 5.3 2.9 - - - -
131H GLY* 3.1 33.0 - - - -
407H SER* 2.9 12.3 + - - +
408H ASN* 3.3 10.5 - - - +
410H ASN* 1.3 78.4 + - - +
412H PHE* 1.3 100.6 + + - +
413H TYR 3.0 0.7 + - - -
414H HIS* 3.8 2.3 - - - +
415H ARG* 2.9 56.3 + - + +
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Residues in contact with PHE 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ILE* 3.9 21.6 - - + +
315H GLN* 3.5 41.8 - - + +
316H THR* 4.1 12.8 - - - +
319H ALA* 3.8 30.3 - - + -
408H ASN* 3.0 32.1 + - + +
409H PHE 4.0 0.2 - - - +
411H TYR* 1.3 103.3 - + - +
413H TYR* 1.3 62.4 + - - +
415H ARG* 3.7 26.3 + - - +
416H GLU* 3.6 20.3 + - - +
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Residues in contact with TYR 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H GLY* 6.0 2.7 - - - -
312H ILE* 3.6 27.2 - - + +
409H PHE* 2.7 50.2 + + + +
410H ASN* 3.6 8.3 - - - +
411H TYR 3.0 0.2 + - - -
412H PHE* 1.3 76.0 - - - +
414H HIS* 1.3 82.7 + + - +
416H GLU* 3.6 3.5 + - - +
417H THR* 3.1 32.4 + - - -
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Residues in contact with HIS 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410H ASN* 3.1 53.3 + - - +
411H TYR* 4.0 1.8 - - - +
413H TYR* 1.3 93.5 - + - +
415H ARG* 1.3 65.6 + - - +
416H GLU 3.0 3.7 + - - -
417H THR* 3.1 28.6 + - - -
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Residues in contact with ARG 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H GLY* 4.6 11.4 + - - -
315H GLN* 3.8 19.0 + - - +
411H TYR* 2.9 55.5 + - + +
412H PHE* 3.7 29.0 + - - +
413H TYR 3.4 0.2 - - - -
414H HIS* 1.3 76.7 - - - +
416H GLU* 1.3 61.2 + - - +
417H THR 5.0 0.2 - - - +
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Residues in contact with GLU 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H LYS* 4.2 27.6 - - + -
312H ILE* 4.4 10.8 - - + -
315H GLN* 6.2 0.2 - - - +
412H PHE 3.6 15.4 + - - +
413H TYR 3.9 4.0 - - - +
414H HIS 3.0 0.2 - - - -
415H ARG* 1.3 83.7 - - - +
417H THR* 1.3 68.4 + - - +
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Residues in contact with THR 417 (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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413H TYR* 3.1 24.9 + - - -
414H HIS* 3.1 27.0 + - - -
415H ARG 4.9 0.2 - - - -
416H GLU* 1.3 85.8 - - - +
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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