Contacts of the helix formed by residues 421 - 431 (chain A) in PDB entry 2J2M
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 PHE 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A PRO* 3.7 24.2 - - + -
174A THR* 3.7 23.1 - - + -
419A ASN* 4.4 0.2 - - - +
420A ASN* 1.3 90.7 - - + +
422A GLY* 1.3 62.4 + - - +
423A GLN 3.5 1.8 - - - -
424A ALA* 4.0 6.7 - - - -
425A GLY 3.0 23.2 + - - -
462A ASN* 3.4 43.1 - - - -
465A ARG* 3.6 59.5 - - + +
466A ALA* 3.2 12.4 - - - +
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Residues in contact with GLY 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ASN* 3.0 19.6 + - - -
421A PHE* 1.3 78.3 - - - +
423A GLN* 1.3 62.6 + - - +
425A GLY* 3.3 3.7 + - - -
426A GLU* 3.2 28.7 + - - +
429A ARG* 4.4 3.1 + - - -
465A ARG 5.7 0.4 - - - -
466A ALA 5.1 0.4 - - - +
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Residues in contact with GLN 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ASN* 3.3 17.9 + - - +
274A ASP* 5.6 0.4 - - - +
275A PHE* 3.8 28.2 - - + -
282A LYS* 3.4 22.3 - - + -
283A ASP* 2.5 49.8 + - - +
285A PHE* 3.7 29.6 - - + -
419A ASN* 3.7 11.9 + - - +
422A GLY* 1.3 72.8 - - - +
424A ALA* 1.3 56.3 + - - +
426A GLU* 3.1 14.6 + - - +
427A VAL* 2.8 33.5 + - + +
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Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A THR* 3.9 18.6 - - + -
175A ASN* 3.3 44.9 + - + +
178A MET* 3.8 9.9 - - + +
420A ASN 4.3 3.3 + - - +
421A PHE 3.6 11.8 - - - +
423A GLN* 1.3 77.4 - - - +
425A GLY* 1.3 56.0 + - - +
427A VAL* 3.3 3.5 + - - +
428A TYR* 2.9 27.4 + - - +
466A ALA* 4.0 4.7 - - + -
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Residues in contact with GLY 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A PHE 3.0 11.7 + - - -
422A GLY 3.3 3.8 + - - -
423A GLN 3.2 0.4 - - - -
424A ALA* 1.3 74.6 - - - +
426A GLU* 1.3 61.6 + - - +
428A TYR* 3.0 8.6 + - - +
429A ARG* 3.0 33.4 + - - -
466A ALA* 3.1 33.1 - - - +
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Residues in contact with GLU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ASP* 4.0 21.1 - - - +
285A PHE* 4.0 22.6 - - + -
422A GLY 3.2 11.3 + - - +
423A GLN* 3.1 28.6 + - - +
425A GLY* 1.3 73.1 - - - +
427A VAL* 1.3 57.7 + - - +
429A ARG* 3.2 18.5 + - - +
430A ARG* 2.9 43.5 + - - +
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Residues in contact with VAL 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ASN* 3.3 24.7 - - - +
178A MET* 4.2 6.5 - - + -
179A HIS* 3.7 33.2 - - + +
283A ASP* 5.5 0.7 - - + -
285A PHE* 3.9 24.2 - - + -
423A GLN* 2.8 17.3 + - + +
424A ALA 3.5 8.3 - - - +
426A GLU* 1.3 71.0 - - - +
428A TYR* 1.3 65.1 + - - +
430A ARG* 3.3 16.7 + - - +
431A MET* 3.5 29.5 + - + +
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Residues in contact with TYR 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A MET* 4.0 11.4 - - + -
424A ALA 2.9 14.0 + - - +
425A GLY* 3.0 9.6 + - - +
427A VAL* 1.3 76.1 - - - +
429A ARG* 1.3 61.4 + - + +
431A MET* 3.1 27.6 + - - +
436A GLN* 3.0 65.1 + - + +
439A LEU* 3.6 30.1 - - + -
467A ASP* 3.3 37.5 - - + -
469A SER* 4.3 5.6 + - - -
470A LEU* 3.8 31.1 + - + +
473A LYS* 4.2 17.3 + - - +
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A GLY 4.4 2.6 + - - -
425A GLY* 3.0 31.5 + - - +
426A GLU* 3.2 18.6 + - - +
428A TYR* 1.3 79.9 - - + +
430A ARG* 1.3 59.5 + - - +
431A MET 3.2 7.0 + - - +
436A GLN* 4.0 6.8 + - - +
466A ALA 3.2 20.2 + - - -
467A ASP* 2.8 44.5 + - - +
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Residues in contact with ARG 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A PHE* 3.6 59.0 - - - +
287A ASP* 3.0 37.0 + - - +
288A VAL* 4.5 5.1 - - - +
426A GLU* 2.9 29.0 + - - +
427A VAL* 3.7 7.6 - - - +
428A TYR 3.2 0.2 - - - -
429A ARG* 1.3 77.0 - - - +
431A MET* 1.3 59.2 + - - +
432A THR* 4.0 1.7 + - - +
435A GLU* 4.7 0.5 - - - +
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Residues in contact with MET 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A MET* 3.4 28.3 - - + +
179A HIS* 5.3 0.7 - - + -
182A THR* 3.8 19.3 - - + -
427A VAL* 3.5 33.7 - - + +
428A TYR* 3.1 23.9 + - - +
429A ARG 3.9 6.8 - - - +
430A ARG* 1.3 80.2 - - - +
432A THR* 1.3 69.8 + - - +
435A GLU* 3.2 28.9 - - + +
436A GLN* 3.7 12.4 + - + -
439A LEU* 4.2 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