Contacts of the strand formed by residues 423 - 430 (chain B) in PDB entry 4J15
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 GLU 423 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B THR* 5.8 9.4 - - + +
373B GLU* 5.2 2.7 - - - -
374B LYS* 5.1 12.1 + - + -
419B PHE* 3.2 4.9 - - - +
420B MET 2.8 37.0 + - - +
421B ARG* 4.2 6.3 - - - +
422B GLY* 1.3 84.7 - - - +
424B GLU* 1.3 64.4 + - - +
425B ILE* 3.4 2.8 + - - +
475B ARG* 3.7 26.2 + - - +
478B MET* 4.7 5.5 - - - +
479B LEU* 3.4 26.4 - - + +
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Residues in contact with GLU 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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373B GLU* 3.8 23.8 + - - +
417B ASP* 3.5 26.7 - - + +
418B MET 3.5 8.3 - - - +
419B PHE* 3.6 6.2 - - + -
423B GLU* 1.3 71.2 - - - +
425B ILE* 1.3 62.7 + - - +
426B LEU* 3.5 30.8 + - - +
427B SER* 3.8 11.4 + - - -
475B ARG* 2.8 34.6 + - - +
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Residues in contact with ILE 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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310B MET* 4.1 21.8 - - + -
388B PHE* 4.2 14.4 - - + -
418B MET* 2.9 23.4 + - + +
419B PHE 4.2 0.2 - - - +
420B MET* 3.8 35.9 - - + -
423B GLU 3.9 3.4 - - - +
424B GLU* 1.3 78.6 - - - +
426B LEU* 1.3 62.8 + - + +
470B GLY 3.2 13.2 - - - +
471B ILE* 3.4 23.3 - - + -
472B GLY 4.2 3.0 + - - +
475B ARG* 4.5 8.1 - - + +
476B VAL* 4.0 14.4 - - + -
479B LEU* 3.5 31.9 - - + -
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Residues in contact with LEU 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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291B ILE* 6.1 0.4 - - + -
306B ILE* 3.6 26.0 - - + -
310B MET* 5.9 1.3 - - + -
416B TYR* 3.8 24.0 - - + -
417B ASP* 3.0 10.0 - - - +
418B MET* 2.9 48.2 + - + +
424B GLU* 3.5 5.8 + - - +
425B ILE* 1.3 86.5 - - + +
427B SER* 1.3 65.1 + - - +
428B GLY 3.8 14.6 - - - +
469B GLY* 3.7 23.8 - - - +
470B GLY 3.5 19.3 - - - +
471B ILE* 4.2 9.9 - - + -
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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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399B ARG* 3.2 13.8 + - - -
416B TYR 3.4 0.2 - - - -
417B ASP* 3.0 21.9 + - - -
424B GLU* 3.8 15.2 + - - -
426B LEU* 1.3 78.0 - - - +
428B GLY* 1.3 58.5 + - - +
431B ARG* 5.1 2.8 + - - -
469B GLY* 4.3 6.9 - - - -
470B GLY 4.3 4.2 + - - +
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Residues in contact with GLY 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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399B ARG* 3.3 6.3 + - - -
416B TYR* 2.8 51.7 + - - +
426B LEU* 3.8 3.8 - - - +
427B SER* 1.3 76.4 - - - +
429B ALA* 1.3 61.6 + - - +
431B ARG* 4.5 4.9 - - - -
468B GLY 3.2 18.6 - - - -
469B GLY* 4.2 2.0 - - - -
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Residues in contact with ALA 429 (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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399B ARG* 5.3 0.7 - - - +
402B TYR* 5.9 0.9 - - + -
403B THR* 3.7 26.0 - - + +
414B ASN 3.1 15.5 - - - +
415B SER* 3.8 3.4 - - - -
416B TYR* 3.5 8.9 - - - -
428B GLY* 1.3 75.2 - - - +
430B GLN* 1.3 72.3 + - - +
431B ARG* 3.6 17.2 + - - +
467B ALA* 3.3 22.7 - - - +
468B GLY 3.4 6.3 + - - -
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Residues in contact with GLN 430 (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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35A ILE 2.9 23.6 - - - +
36A GLN 3.6 5.3 - - - -
37A SER* 2.6 28.5 + - - -
295B PHE* 3.5 17.3 - - + -
299B TYR* 3.7 14.0 - - + +
403B THR* 3.9 0.9 - - - -
404B MET* 3.2 37.0 + - + +
414B ASN* 2.8 35.1 + - + +
416B TYR* 4.3 2.0 - - - -
429B ALA* 1.3 80.0 - - - +
431B ARG* 1.3 72.0 + - - +
433B HIS* 4.2 0.2 - - - -
465B PRO* 4.1 6.1 - - - +
466B HIS 3.5 11.2 - - - +
467B ALA* 3.8 5.9 - - - +
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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