Contacts of the strand formed by residues 420 - 428 (chain B) in PDB entry 4JWE
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 THR 420 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B ILE* 3.9 27.7 - - + +
416B THR* 3.5 26.1 - - + +
417B THR 3.4 12.8 - - - +
418B ILE* 4.6 3.6 - - + -
419B PRO* 1.3 75.6 - - - +
421B LYS* 1.3 71.4 + - - +
422B HIS* 5.9 0.2 - - - +
476B PHE 4.2 0.2 - - - +
477B ASP* 3.6 2.0 - - - +
478B ILE* 2.9 47.0 + - + +
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Residues in contact with LYS 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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412B ILE* 5.4 1.1 - - - -
420B THR* 1.3 83.1 + - - +
422B HIS* 1.3 67.7 + - - +
423B SER* 5.3 2.5 - - - +
475B THR* 3.9 20.9 - - + -
476B PHE 3.2 13.2 - - - +
477B ASP* 3.4 25.6 - - - +
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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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410B THR 5.5 0.2 - - - -
411B LEU* 3.2 44.2 - - + +
412B ILE* 4.5 7.4 - - + +
420B THR* 5.9 0.4 - - - +
421B LYS* 1.3 78.0 + - - +
423B SER* 1.3 87.5 + - - +
424B GLN* 4.8 7.6 + - + +
475B THR* 3.5 2.8 - - - +
476B PHE* 2.9 33.0 + - - +
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Residues in contact with SER 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU* 4.4 0.4 - - - -
421B LYS* 5.3 3.1 - - - +
422B HIS* 1.3 95.4 + - - +
424B GLN* 1.3 60.4 + - - +
473B GLU* 4.2 19.8 - - - -
474B VAL 3.2 6.3 - - - -
475B THR* 2.8 32.7 + - - +
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Residues in contact with GLN 424 (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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409B THR* 3.8 16.0 - - - +
410B THR 3.9 12.8 - - - +
411B LEU* 4.1 9.8 - - + +
422B HIS* 4.8 7.6 + - - +
423B SER* 1.3 76.6 - - - +
425B VAL* 1.3 68.3 + - - +
426B PHE* 3.4 25.7 - - + -
473B GLU* 4.6 1.6 - - - -
474B VAL 2.8 33.6 + - - +
8C PRO* 3.5 33.1 - - - +
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Residues in contact with VAL 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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424B GLN* 1.3 83.5 + - - +
426B PHE* 1.3 74.7 + - - +
471B GLN* 3.8 30.7 - - + +
472B ILE 3.5 7.2 - - - +
473B GLU* 4.1 12.3 - - + +
491B LYS* 3.6 24.0 - - - +
7C ARG* 3.5 42.6 + - - +
8C PRO* 4.0 6.1 - - - +
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Residues in contact with PHE 426 (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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401B ILE* 3.6 23.6 - - + -
403B THR* 3.7 26.9 - - + -
409B THR* 3.8 8.3 - - + -
411B LEU* 3.9 13.5 - - + -
424B GLN* 3.4 47.6 - - + -
425B VAL* 1.3 77.9 - - - +
427B SER* 1.3 63.8 + - - +
470B PRO 3.5 2.9 - - - +
472B ILE* 2.8 33.7 + - - +
474B VAL* 3.7 20.9 - - + -
7C ARG* 3.9 3.5 - - - -
8C PRO* 3.4 34.3 - - + +
10C LEU* 3.6 21.5 - - + -
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Residues in contact with SER 427 (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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426B PHE* 1.3 72.5 - - - +
428B THR* 1.3 64.5 + - - +
468B GLY* 3.0 35.4 - - - -
469B MET 3.4 1.6 + - - -
470B PRO* 2.7 26.9 + - - +
472B ILE* 4.7 5.6 - - - -
7C ARG* 4.1 13.0 - - - -
8C PRO 3.1 8.1 + - - -
9C ARG* 4.1 5.8 - - - -
10C LEU* 2.8 36.1 + - - +
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Residues in contact with THR 428 (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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427B SER* 1.3 79.1 + - - +
429B ALA* 1.3 61.4 + - - +
430B GLU 3.6 7.1 + - - -
433B GLN* 3.6 36.5 + - + +
436B VAL* 3.9 6.3 - - + -
462B ILE* 3.9 26.2 - - + -
465B ALA 5.2 1.4 + - - -
466B PRO 4.4 0.2 + - - -
467B ARG* 3.9 1.6 - - - -
468B GLY 3.2 25.1 + - - -
470B PRO* 3.4 33.3 - - + +
472B ILE* 5.2 0.7 - - + -
9C ARG* 3.3 13.1 - - - +
10C LEU 4.2 3.1 - - - -
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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