Contacts of the strand formed by residues 468 - 474 (chain A) 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 VAL 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.8 9.6 - - + -
442A ASN* 5.7 3.1 - - + -
443A ASP* 5.6 8.3 - - + +
444A LEU* 3.8 38.8 - - + -
462A ASN* 4.0 6.3 - - - +
464A SER* 4.9 4.3 - - - +
466A LYS* 3.7 14.1 - - + +
467A ASP* 1.3 79.2 - - - +
469A PRO* 1.3 71.9 - - + +
470A LEU* 3.5 2.1 + - - +
483A ILE* 4.4 0.9 - - - -
484A SER* 2.8 38.6 + - - +
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Residues in contact with PRO 469 (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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64A GLY* 4.4 12.2 - - - -
65A LEU* 3.8 18.6 + - - +
467A ASP* 3.4 13.0 - - + +
468A VAL* 1.3 93.2 - - + +
470A LEU* 1.3 58.5 + - - +
482A THR 3.8 7.2 - - - +
483A ILE* 4.1 14.8 - - + -
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Residues in contact with LEU 470 (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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65A LEU* 3.6 37.9 - - + -
67A LEU* 3.8 19.5 - - + -
444A LEU* 4.0 6.7 - - + -
460A VAL* 3.7 37.7 - - + -
468A VAL 3.7 8.7 - - - +
469A PRO* 1.3 75.5 - - - +
471A THR* 1.3 74.1 + - - +
472A ILE* 4.3 5.6 - - + -
481A GLU* 4.0 0.9 - - - +
482A THR* 2.8 59.1 + - + +
484A SER* 4.5 7.2 - - - +
492A TYR* 4.9 1.8 - - + -
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Residues in contact with THR 471 (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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60A HIS* 3.5 29.3 + - + -
62A GLY* 4.5 3.3 - - - -
64A GLY 5.8 1.0 + - - -
65A LEU 3.0 14.9 + - - -
66A LEU* 3.2 22.6 - - + +
67A LEU 2.9 28.1 + - - +
470A LEU* 1.3 75.3 + - - +
472A ILE* 1.3 63.6 + - - +
479A PHE* 3.8 20.0 - - + -
480A LEU 3.2 8.7 - - - +
481A GLU* 2.9 21.9 + - - +
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Residues in contact with ILE 472 (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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67A LEU* 3.1 22.9 - - + +
69A LEU* 5.2 1.3 - - + +
436A LEU* 4.9 5.4 - - + -
458A VAL* 4.6 13.2 - - + -
460A VAL* 4.5 6.1 - - + -
470A LEU* 4.3 16.6 - - + -
471A THR* 1.3 77.7 - - - +
473A LYS* 1.3 65.0 + - - +
478A GLY 3.9 0.3 - - - +
479A PHE* 3.5 1.6 - - - -
480A LEU* 2.8 52.2 + - + +
482A THR* 4.6 4.3 - - + -
492A TYR* 3.8 38.8 - - + -
494A TRP* 3.7 27.8 - - + -
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Residues in contact with LYS 473 (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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66A LEU* 3.9 13.9 - - + -
67A LEU 2.7 9.9 + - - -
68A THR* 3.5 24.5 - - + +
69A LEU* 2.8 34.8 + - - +
471A THR 3.7 1.4 + - - -
472A ILE* 1.3 75.0 - - - +
474A ASP* 1.3 61.6 + - - +
475A PRO* 3.4 32.7 - - - +
478A GLY 3.4 6.7 - - - +
479A PHE* 3.4 44.2 - - + -
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Residues in contact with ASP 474 (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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56A ILE* 6.1 0.4 - - + -
69A LEU* 3.6 8.9 - - + +
472A ILE 4.0 1.0 + - - +
473A LYS* 1.3 73.5 - - - +
475A PRO* 1.3 63.0 - - - +
476A ALA* 2.8 8.3 + - - +
477A VAL* 2.8 19.3 + - + +
478A GLY* 2.7 40.4 + - - +
480A LEU* 5.8 2.2 - - + +
494A TRP* 2.8 39.0 + - + +
496A ARG* 2.5 48.6 + - - -
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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