Contacts of the strand formed by residues 468 - 476 (chain B) in PDB entry 3H60
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 ASP 468 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465B GLN* 2.9 35.0 + - + +
466B GLY 3.2 1.4 - - - -
467B SER* 1.3 88.5 + - - +
469B LEU* 1.3 58.7 + - - +
470B ARG* 3.0 64.3 + - - +
472B GLN* 5.3 2.6 + - - -
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Residues in contact with LEU 469 (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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231B LEU* 4.3 4.7 - - + -
344B ILE* 4.1 24.2 - - + +
345B ASN* 3.9 26.5 - - + +
347B LYS* 3.8 31.2 - - + -
348B VAL* 4.1 13.9 - - + +
421B ASP* 5.1 4.5 - - - +
422B TYR* 2.7 33.2 + - + -
464B LEU* 3.4 15.2 - - + +
465B GLN 3.3 21.5 - - - +
466B GLY* 4.5 5.8 - - - +
468B ASP* 1.3 72.5 + - - +
470B ARG* 1.3 55.9 + - - +
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Residues in contact with ARG 470 (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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422B TYR* 4.7 3.4 - - + -
463B HIS 3.8 6.4 - - - +
464B LEU* 4.0 0.7 - - - +
468B ASP* 3.0 41.2 + - - +
469B LEU* 1.3 79.2 - - - +
471B PRO* 1.3 75.1 - - + +
472B GLN* 3.4 11.1 + - - +
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Residues in contact with PRO 471 (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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422B TYR* 3.4 33.2 - - + +
436B VAL* 5.7 1.8 - - + -
443B VAL* 4.3 8.7 - - + -
462B ILE* 4.1 17.0 - - + -
463B HIS 4.0 0.2 - - - +
464B LEU* 3.8 10.3 - - + -
470B ARG* 1.3 89.8 - - + +
472B GLN* 1.3 60.0 + - - +
473B PHE* 3.9 36.1 - - + -
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Residues in contact with GLN 472 (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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462B ILE* 3.2 5.6 - - - -
463B HIS* 2.8 49.8 + - + +
465B GLN* 2.9 43.1 + - - +
468B ASP* 5.3 3.2 + - - -
470B ARG 4.0 7.6 + - - +
471B PRO* 1.3 75.6 - - - +
473B PHE* 1.3 62.0 + - - +
474B HIS* 3.6 21.3 + - + -
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Residues in contact with PHE 473 (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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434B TYR* 3.5 57.9 - + + -
436B VAL* 3.6 32.1 - - + -
443B VAL* 3.8 18.4 - - + -
460B SER* 4.3 5.6 - - - +
461B TYR 3.7 1.3 - - - +
462B ILE* 3.7 26.5 - - + -
471B PRO* 3.9 28.0 - - + -
472B GLN* 1.3 72.9 - - - +
474B HIS* 1.3 67.2 + - - +
475B GLN* 4.1 3.1 + - + +
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Residues in contact with HIS 474 (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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460B SER* 3.0 5.3 - - - -
461B TYR* 2.8 74.6 + + + +
463B HIS* 3.1 41.6 + + + -
472B GLN* 3.6 28.0 + - + -
473B PHE* 1.3 76.2 - - - +
475B GLN* 1.3 63.4 + - - +
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Residues in contact with GLN 475 (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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256B LEU* 5.1 1.7 - - - +
432B GLU* 2.9 58.0 + - - +
434B TYR* 3.8 19.0 + - + -
458B LYS* 3.6 18.9 - - + +
459B ALA 3.3 6.3 - - - +
460B SER* 4.2 3.4 - - - -
461B TYR* 5.6 0.5 - - - -
473B PHE* 4.1 3.5 + - + -
474B HIS* 1.3 77.3 - - - +
476B PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 476 (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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249B ASP* 4.2 7.9 - - + -
252B ASN* 4.0 11.7 - - - +
253B ILE* 3.5 27.4 - - + -
256B LEU* 3.4 23.6 - - + -
447B SER* 3.7 11.9 - - - -
449B PRO* 3.7 21.8 - - + -
458B LYS* 3.5 6.2 - - - +
459B ALA* 2.8 55.8 + - + -
460B SER* 3.7 12.3 - - - -
461B TYR* 3.7 33.0 - + - -
475B GLN* 1.3 78.2 - - - +
477B THR* 1.3 74.0 + - - +
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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