Contacts of the helix formed by residues 414 - 425 (chain B) in PDB entry 2J25
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 GLN 414 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B VAL* 3.5 4.2 - - - +
352B VAL* 3.8 9.5 - - - +
353B ARG 3.3 12.0 + - - -
354B LEU* 3.5 11.9 - - + -
355B GLY* 2.9 28.6 + - - -
356B SER* 5.1 0.9 - - - -
359B ARG* 5.7 0.4 - - - +
399B ASP* 2.8 36.6 + - - -
400B SER 3.2 19.3 - - - +
401B PRO 2.8 15.0 + - - +
403B ILE* 4.2 7.0 - - + -
412B TYR 4.7 0.7 - - - +
413B LYS* 1.3 75.3 - - - +
415B PRO* 1.3 73.4 - - + +
416B MET* 3.6 19.8 - - + +
417B PHE* 2.8 17.2 + - - +
418B TYR* 3.4 4.8 - - - -
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Residues in contact with PRO 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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14B VAL 3.7 20.9 - - - +
48B ARG* 4.2 11.2 - - - +
355B GLY* 3.6 26.5 - - - +
356B SER 3.3 27.1 - - - +
357B TRP* 3.9 22.7 - - + +
360B GLY* 4.1 5.4 - - - -
413B LYS 4.2 0.2 - - - +
414B GLN* 1.3 84.9 - - + +
416B MET* 1.3 64.1 + - - +
418B TYR* 2.9 21.2 + - + +
419B HIS* 2.9 18.8 + - + -
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Residues in contact with MET 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B VAL* 4.0 15.5 - - - -
356B SER 5.5 0.7 - - - +
359B ARG* 3.8 6.1 - - + -
360B GLY* 3.6 27.1 - - - +
363B TYR* 3.4 42.1 - - + -
399B ASP* 3.6 17.9 - - - +
400B SER 3.0 39.5 - - - +
401B PRO* 3.3 9.2 - - + -
414B GLN* 3.6 13.4 - - + +
415B PRO* 1.3 78.3 - - + +
417B PHE* 1.3 64.6 + - - +
418B TYR 3.1 0.2 + - - -
419B HIS* 3.1 3.7 + - - +
420B LEU* 2.9 28.5 + - - +
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Residues in contact with PHE 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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26B PHE* 5.6 2.2 - + - -
107B SER* 3.4 32.1 - - - -
108B TYR* 3.7 26.2 - + - -
113B GLY* 5.4 0.7 - - - -
114B ILE* 3.4 37.8 - - + +
401B PRO* 3.6 23.3 - - + +
402B ILE* 4.0 13.5 - - + -
413B LYS* 3.4 28.7 - - + -
414B GLN 2.8 18.3 + - - +
416B MET* 1.3 75.5 - - - +
418B TYR* 1.3 91.1 + + + +
420B LEU* 3.5 4.5 + - - +
421B GLY* 2.9 20.6 + - - -
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Residues in contact with TYR 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B CYS* 3.0 29.5 - - - +
24B ASP* 2.3 33.3 + - - -
26B PHE* 5.4 4.9 - + - -
42B SER* 4.1 16.6 - - - +
48B ARG* 3.6 31.6 - - + -
49B MET* 3.3 25.8 - - + +
357B TRP* 6.2 0.2 - - + -
413B LYS* 3.5 31.1 - - + -
414B GLN 3.4 11.2 - - - -
415B PRO* 2.9 8.2 + - + +
417B PHE* 1.3 99.2 - + - +
419B HIS* 1.3 66.6 + - + +
420B LEU 3.2 0.2 - - - -
421B GLY 3.0 0.7 + - - -
422B HIS* 2.9 31.7 + - - -
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Residues in contact with HIS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B TRP* 3.4 43.6 - + - -
360B GLY* 3.0 38.0 + - - +
361B MET* 3.5 12.3 - - + -
363B TYR* 4.3 4.3 - - + -
364B SER* 2.8 29.5 + - - -
367B ILE* 5.2 0.7 - - - -
415B PRO* 2.9 30.1 + - + -
416B MET* 3.6 6.1 - - - +
418B TYR* 1.3 78.0 - - + +
420B LEU* 1.3 58.8 + - - +
422B HIS* 3.6 8.2 + - - +
423B PHE* 2.9 30.9 - - - -
461B LEU* 4.3 2.7 - - + -
489B ILE* 4.0 17.5 - - + +
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Residues in contact with LEU 420 (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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81B PHE* 5.1 8.4 - - + -
82B GLY 4.9 2.2 - - - +
114B ILE* 4.4 2.7 - - + -
116B TYR* 3.3 32.1 - - + +
363B TYR* 3.6 28.9 - - + +
367B ILE* 3.8 7.6 - - + -
378B TRP* 3.4 34.3 - - + +
380B ASP* 4.0 6.1 - - + +
401B PRO* 3.8 19.3 - - + -
416B MET 2.9 18.5 + - - +
417B PHE* 3.6 7.2 - - - +
419B HIS* 1.3 73.2 - - - +
421B GLY* 1.3 62.0 + - - +
423B PHE* 2.9 10.9 + - - +
424B SER* 2.8 26.7 + - - -
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Residues in contact with GLY 421 (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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49B MET* 3.2 25.1 - - - -
114B ILE* 3.7 10.9 - - - +
417B PHE 2.9 12.1 + - - -
418B TYR 3.0 0.8 + - - -
420B LEU* 1.3 71.7 - - - +
422B HIS* 1.3 54.1 + - - +
423B PHE 2.7 16.5 + - - -
424B SER* 3.5 12.3 - - - -
425B LYS* 2.9 26.2 + - - +
426B PHE* 4.0 1.6 - - - -
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Residues in contact with HIS 422 (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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40B TYR* 3.0 36.5 - - + +
42B SER* 2.9 30.9 + - - -
49B MET* 3.8 9.8 - - + +
418B TYR 2.9 26.9 + - - -
419B HIS 3.7 10.3 - - - +
420B LEU 3.2 0.6 - - - -
421B GLY* 1.3 74.0 - - - +
423B PHE* 1.3 59.2 + - + +
426B PHE* 3.6 8.4 - - - -
427B ILE* 4.7 1.2 - - - +
459B VAL* 3.8 8.7 - - + +
489B ILE* 3.2 43.9 - - + +
490B HIS 3.7 2.0 - - - -
491B THR* 2.7 50.4 + - - +
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Residues in contact with PHE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 3.9 16.4 - - + -
364B SER* 3.6 22.0 - - - -
367B ILE* 3.3 31.4 - - + -
368B ILE* 3.6 36.3 - - + -
371B LEU* 4.3 6.5 - - + -
419B HIS 2.9 29.8 - - - -
420B LEU 2.9 4.0 + - - +
421B GLY 2.7 1.4 + - - -
422B HIS* 1.3 78.0 - - - +
424B SER* 1.3 67.7 + - - +
425B LYS 3.0 1.3 - - - -
426B PHE 2.9 14.0 + - - -
427B ILE* 3.0 37.4 + - + +
447B VAL* 4.4 0.4 - - + -
459B VAL* 3.6 32.1 - - + -
489B ILE* 4.0 5.4 - - + -
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Residues in contact with SER 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 3.5 37.0 - - - +
114B ILE* 2.6 43.7 + - - +
115B GLY 3.4 12.8 - - - +
116B TYR* 3.7 14.1 - - - -
170B ARG* 3.5 8.8 + - - -
420B LEU* 2.8 20.3 + - - -
421B GLY* 3.5 1.2 - - - -
423B PHE* 1.3 73.5 - - - +
425B LYS* 1.3 61.4 + - - +
426B PHE 3.7 0.2 + - - -
427B ILE 4.4 4.2 + - - +
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Residues in contact with LYS 425 (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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26B PHE* 3.6 41.8 - - + +
27B ASP 4.7 3.5 + - - -
29B PRO* 5.2 10.6 - - - +
40B TYR* 4.9 5.2 - - - -
49B MET* 4.8 1.1 - - - -
111B GLU* 2.7 30.7 + - - +
113B GLY 2.9 18.5 + - - +
114B ILE* 3.4 18.4 - - + +
115B GLY 5.2 0.2 - - - +
170B ARG* 2.7 21.3 + - - +
421B GLY 2.9 17.1 + - - +
423B PHE 2.9 0.2 + - - -
424B SER* 1.3 81.4 + - - +
426B PHE* 1.3 88.6 + - + +
1515B SO4 4.8 2.1 + - - -
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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