Contacts of the strand formed by residues 425 - 431 (chain D) in PDB entry 5J87
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 TYR 425 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420D LYS* 3.2 2.6 - - - -
421D TRP* 2.7 80.1 + + + +
422D ARG* 4.0 29.5 + - + -
424D GLN* 1.3 98.6 - - + +
426D ASP* 1.3 64.4 + - - +
427D VAL* 3.6 7.7 + - + +
461D TYR* 4.2 19.3 - + + -
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Residues in contact with ASP 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D TYR* 2.7 37.5 + - + -
419D GLY 2.9 4.2 - - - +
420D LYS* 2.7 42.7 - - - +
424D GLN 3.5 5.8 + - - +
425D TYR* 1.3 73.7 - - - +
427D VAL* 1.3 57.8 + - - +
461D TYR* 4.6 5.7 + - - -
476D TYR* 3.3 26.1 + - + +
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Residues in contact with VAL 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D LEU* 5.0 1.3 - - + -
418D TYR* 3.2 10.4 - - - -
419D GLY* 2.9 48.0 + - - +
420D LYS 4.0 1.8 - - - -
421D TRP* 3.6 34.3 - - + +
425D TYR* 3.7 4.0 - - + +
426D ASP* 1.3 76.6 - - - +
428D ALA* 1.3 59.9 + - - +
429D ILE* 4.2 13.5 - - + -
461D TYR* 3.9 22.0 - - + -
473D ILE* 3.8 22.9 - - + -
474D THR 3.5 8.5 - - - +
476D TYR* 4.1 3.4 - - - -
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Residues in contact with ALA 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D LEU* 3.8 10.3 - - + -
416D VAL* 4.3 2.9 - - + -
417D LYS 3.2 11.2 - - - +
418D TYR* 4.3 0.2 - - - +
427D VAL* 1.3 74.5 - - - +
429D ILE* 1.3 63.2 + - - +
430D LYS* 4.0 1.0 - - - +
472D ILE 3.4 4.2 - - - +
473D ILE* 3.7 1.4 - - - -
474D THR* 3.0 31.5 + - - +
475D GLU 4.5 0.4 - - - +
476D TYR* 4.5 1.7 - - + +
701D N42 3.1 44.4 - - + +
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Residues in contact with ILE 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D LEU* 4.9 6.1 - - + -
403D THR 4.9 1.6 - - - +
404D PHE* 3.6 41.3 - - + -
416D VAL* 3.3 4.2 - - - -
417D LYS* 2.8 38.1 + - + +
418D TYR 4.4 2.5 - - - -
419D GLY* 4.1 25.1 - - - +
427D VAL* 4.2 11.0 - - + -
428D ALA* 1.3 75.0 - - - +
430D LYS* 1.3 74.4 - - - +
431D MET* 3.8 1.4 + - + -
471D PHE* 3.6 33.2 - - + -
472D ILE 3.6 2.9 - - - +
473D ILE* 3.3 22.4 - - + -
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Residues in contact with LYS 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413D PHE* 5.2 7.9 - - + -
415D VAL 3.8 6.5 - - - +
416D VAL* 4.5 11.8 - - + +
428D ALA 5.3 1.3 - - - +
429D ILE* 1.3 76.3 - - - +
431D MET* 1.3 61.8 + - - +
432D ILE* 4.0 16.1 - - + +
470D ILE 3.5 0.7 - - - +
471D PHE* 3.2 8.8 - - - -
472D ILE* 3.1 55.8 + - + +
474D THR* 4.6 13.4 + - + +
539D ASP* 2.9 28.0 + - - -
542D LEU* 4.0 17.5 - - + -
701D N42 3.3 37.3 + - + +
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Residues in contact with MET 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404D PHE* 4.3 7.9 - - + -
413D PHE* 3.1 16.3 - - - +
414D GLY* 4.5 0.2 - - - -
415D VAL* 3.1 29.6 + - + +
417D LYS* 2.6 45.8 - - - +
429D ILE* 4.4 6.7 - - + +
430D LYS* 1.3 78.1 - - - +
432D ILE* 1.3 59.8 + - - +
433D LYS* 3.2 3.7 + - - +
469D PRO* 4.5 17.7 - - + -
470D ILE 3.6 4.5 - - - +
471D PHE* 4.0 27.8 - - + -
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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