Contacts of the helix formed by residues 401 - 417 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323B GLU* 3.8 26.8 - - + +
326B LEU* 4.6 4.9 - - + -
327B LEU* 4.1 25.1 - - + +
330B PHE* 4.2 16.8 - - + -
397B THR 3.1 22.9 - - - +
398B ILE* 3.2 10.5 - - - +
400B LEU* 1.3 88.3 - - + +
402B VAL* 1.3 64.2 + - - +
403B PRO* 3.4 0.7 - - - -
404B VAL* 3.3 22.5 + - + +
405B ILE* 3.6 11.0 + - + +
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 4.7 14.4 - - + -
398B ILE* 3.0 37.5 - - + +
399B ALA* 4.6 1.8 - - - +
401B PRO* 1.3 77.1 - - - +
403B PRO* 1.3 71.0 - - + +
405B ILE* 2.8 27.3 + - + +
406B VAL* 2.9 28.2 + - + -
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Residues in contact with PRO 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ALA* 2.8 31.4 - - - +
400B LEU 3.7 5.6 - - - +
401B PRO 3.5 2.7 - - - -
402B VAL* 1.3 89.1 - - + +
404B VAL* 1.3 57.6 + - + +
406B VAL* 3.6 10.0 - - + +
407B SER* 2.9 29.5 + - - -
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Residues in contact with VAL 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B GLU* 3.8 31.0 - - + +
400B LEU 4.5 10.1 - - - +
401B PRO* 3.6 13.5 - - + +
402B VAL 3.0 0.6 + - - -
403B PRO* 1.3 77.0 - - + +
405B ILE* 1.3 59.1 + - - +
407B SER* 3.0 9.8 + - - -
408B ASN* 2.9 36.3 + - - +
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Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B THR* 3.8 9.8 - - + +
317B LEU* 5.2 7.4 - - + -
320B SER* 3.8 31.6 - - - +
323B GLU* 4.0 8.5 - - + +
324B LEU* 3.4 39.3 - - + +
327B LEU* 5.2 6.1 - - + -
401B PRO* 3.7 17.5 - - + +
402B VAL* 2.8 19.6 + - + +
404B VAL* 1.3 76.4 - - - +
406B VAL* 1.3 65.4 + - + +
408B ASN* 3.1 4.1 + - - +
409B PHE* 2.9 23.0 + - + +
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B VAL* 2.9 35.6 + - + +
403B PRO* 3.6 11.0 - - + +
405B ILE* 1.3 76.1 - - + +
407B SER* 1.3 59.4 + - - +
409B PHE* 3.4 10.3 + - + +
410B ASN* 2.9 30.1 + - + +
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Residues in contact with SER 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B PRO 2.9 13.7 + - - -
404B VAL* 3.0 14.3 + - - -
406B VAL* 1.3 74.9 - - - +
408B ASN* 1.3 63.8 + - - +
410B ASN* 3.0 8.8 + - - +
411B TYR* 2.9 29.4 + - - +
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Residues in contact with ASN 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B THR* 4.1 5.8 - - + +
319B ALA* 3.7 22.0 + - - +
320B SER* 2.8 28.7 + - - +
323B GLU* 4.7 2.0 + - - -
404B VAL* 2.9 29.0 + - - +
405B ILE* 3.6 6.2 - - - +
407B SER* 1.3 78.0 + - - +
409B PHE* 1.3 63.8 + - - +
411B TYR* 3.2 7.2 + - - +
412B PHE* 3.0 41.1 + - + -
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Residues in contact with PHE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B GLY* 4.9 4.0 - - - -
312B ILE* 3.7 17.9 - - + -
313B LEU* 4.3 20.6 - - + -
316B THR* 3.3 29.5 - - + +
405B ILE* 2.9 13.4 + - + +
406B VAL* 3.6 13.7 - - + +
407B SER 3.2 0.2 - - - -
408B ASN* 1.3 77.1 - - - +
410B ASN* 1.3 58.2 + - + +
411B TYR 3.1 0.2 + - - -
412B PHE* 3.3 0.7 + - - +
413B TYR* 2.7 66.2 + + + +
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Residues in contact with ASN 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B VAL* 2.9 21.4 + - + +
407B SER* 3.0 8.3 + - - +
409B PHE* 1.3 80.7 - - + +
411B TYR* 1.3 61.9 + - - +
413B TYR* 3.7 7.9 - - - +
414B HIS* 3.1 57.3 + - - +
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Residues in contact with TYR 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B GLY* 3.8 20.0 + - - -
407B SER* 2.9 13.8 + - - +
408B ASN* 3.4 10.5 - - - +
409B PHE 3.1 0.2 - - - -
410B ASN* 1.3 75.4 + - - +
412B PHE* 1.3 97.2 + + - +
413B TYR 3.1 0.2 + - - -
414B HIS* 3.9 1.8 - - - +
415B ARG* 2.9 65.3 + - + +
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Residues in contact with PHE 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ILE* 3.8 21.7 - - + +
315B GLN* 3.5 43.2 - - + +
316B THR* 4.0 11.7 - - - +
319B ALA* 3.9 26.7 - - + -
408B ASN* 3.0 33.0 + - + +
409B PHE 4.0 0.4 - - - +
411B TYR* 1.3 102.5 - + - +
413B TYR* 1.3 62.2 + - - +
415B ARG* 3.7 25.9 + - - +
416B GLU* 3.6 19.9 + - - +
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Residues in contact with TYR 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLY* 6.0 2.7 - - - -
312B ILE* 3.6 26.6 - - + +
409B PHE* 2.7 50.2 + + + +
410B ASN* 3.7 7.9 - - - +
412B PHE* 1.3 75.7 - - - +
414B HIS* 1.3 83.5 + + - +
416B GLU* 3.5 3.6 + - - +
417B THR* 3.1 31.4 + - - -
510B PGW 5.5 6.5 - - - -
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Residues in contact with HIS 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B ASN* 3.1 51.4 + - - +
411B TYR* 4.2 2.2 - - - +
413B TYR* 1.3 92.4 - + - +
415B ARG* 1.3 63.2 + - - +
416B GLU 2.9 7.0 + - - -
417B THR* 3.0 29.9 + - - -
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Residues in contact with ARG 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B GLY 4.7 8.7 - - - -
132B TYR* 5.2 13.9 - - + -
315B GLN* 3.9 9.9 + - - +
411B TYR* 2.9 55.8 + - + +
412B PHE* 3.7 29.6 + - - +
414B HIS* 1.3 77.0 - - - +
416B GLU* 1.3 58.5 + - - +
417B THR 5.1 0.5 - - - +
512B PGW 2.7 46.1 + - - -
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B LYS* 4.2 17.7 - - + -
312B ILE* 4.4 11.0 - - + -
315B GLN* 6.1 0.2 - - - +
412B PHE 3.6 10.2 + - - +
413B TYR 3.5 8.2 + - - +
414B HIS 2.9 0.4 - - - -
415B ARG* 1.3 81.4 - - - +
417B THR* 1.3 67.9 + - - +
512B PGW 3.6 27.9 - - - -
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Residues in contact with THR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B TYR* 3.1 27.5 + - - -
414B HIS* 3.0 28.1 + - - -
415B ARG 5.0 0.4 - - - -
416B GLU* 1.3 83.5 - - - +
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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