Contacts of the strand formed by residues 467 - 478 (chain B) in PDB entry 4U7C
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 467 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459B LYS* 3.8 32.3 - - + -
460B LEU 3.4 7.0 - - - +
461B LYS* 3.6 31.9 - - + +
465B PHE 3.5 6.7 + - - +
466B GLU* 1.3 76.3 - - - +
468B LYS* 1.3 69.8 + - - +
469B THR* 4.9 4.7 - - + -
8P G 4.7 7.8 + - - +
9P A 5.1 6.8 + - - -
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Residues in contact with LYS 468 (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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458B ILE 4.1 0.2 - - - +
459B LYS* 3.7 1.4 - - - +
460B LEU* 2.9 52.8 + - + +
462B ASN* 6.1 3.6 - - - +
466B GLU* 5.2 4.3 - - - +
467B VAL* 1.3 78.9 - - - +
469B THR* 1.3 64.9 + - - +
470B ARG* 3.7 26.9 - - + +
495B GLU* 4.0 16.7 + - - +
499B ASP* 4.9 9.9 + - - -
504B LEU* 6.2 2.0 - - - +
8P G 3.5 21.8 - - - +
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Residues in contact with THR 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B THR* 3.8 15.2 - - + +
458B ILE 3.2 11.9 - - - +
459B LYS* 4.2 22.0 - - + -
467B VAL* 4.9 5.4 - - + -
468B LYS* 1.3 78.4 - - - +
470B ARG* 1.3 86.5 + - - +
7P G 3.5 20.1 + - - +
8P G 3.1 21.8 + - + +
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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
----------------------------------------------------------
457B THR* 3.2 2.7 - - - -
458B ILE* 2.9 46.9 + - + +
460B LEU* 5.4 2.7 - - + -
468B LYS* 3.7 30.4 - - + +
469B THR* 1.3 89.8 + - - +
471B ALA* 1.3 61.9 + - - +
491B LEU* 3.8 19.3 - - + +
495B GLU* 3.0 42.1 + - + +
7P G 3.3 41.1 + - - +
8P G 3.4 11.5 + - - -
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Residues in contact with ALA 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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455B THR* 4.4 5.8 - - + -
456B VAL 3.2 5.6 - - - +
457B THR* 3.4 24.7 - - + +
470B ARG* 1.3 75.1 - - - +
472B SER* 1.3 69.6 + - - +
491B LEU* 3.6 7.2 - - - +
6P C 4.0 28.9 + - + +
7P G 2.5 21.7 + - + +
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Residues in contact with SER 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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454B ARG 3.8 1.0 - - - +
455B THR* 3.4 1.8 - - - -
456B VAL* 2.9 31.5 + - - +
471B ALA* 1.3 80.7 + - - +
473B THR* 1.3 65.7 + - - +
474B VAL* 4.1 6.5 + - - +
487B ILE* 3.6 25.7 - - - +
490B GLU* 5.6 2.6 - - - +
491B LEU* 3.2 17.9 - - - +
6P C 3.2 4.7 - - - -
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Residues in contact with THR 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ARG* 3.2 37.9 - - - +
455B THR* 2.8 24.5 + - - +
472B SER* 1.3 74.1 - - - +
474B VAL* 1.3 64.8 + - - +
515B SER* 4.9 0.7 - - - +
5P G 3.4 25.9 + - - +
6P C 2.6 33.7 + - - -
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Residues in contact with VAL 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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454B ARG* 2.8 43.2 + - + +
472B SER* 4.6 6.3 - - - +
473B THR* 1.3 80.8 - - - +
475B SER* 1.3 67.3 + - - +
476B SER 3.3 21.3 - - - +
478B VAL* 4.4 15.0 - - + -
487B ILE* 3.9 27.8 - - + -
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Residues in contact with SER 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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454B ARG* 3.8 13.1 + - - +
474B VAL* 1.3 77.3 - - - +
476B SER* 1.3 65.8 + - - +
477B VAL 4.2 0.2 + - - -
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Residues in contact with SER 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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454B ARG* 3.8 3.1 - - - +
474B VAL* 3.3 21.9 - - - +
475B SER* 1.3 82.9 - - - +
477B VAL* 1.3 71.3 + - - +
478B VAL* 4.1 2.3 - - - +
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Residues in contact with VAL 477 (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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452B LYS* 3.7 53.1 - - + +
453B GLY* 3.5 14.8 - - - +
454B ARG* 4.0 12.6 - - + -
475B SER 4.2 0.6 + - - -
476B SER* 1.3 82.1 - - - +
478B VAL* 1.3 61.7 + - - +
483B GLU* 5.4 0.9 - - - +
515B SER 5.2 0.7 - - - +
517B PRO* 4.4 16.6 - - + -
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Residues in contact with VAL 478 (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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452B LYS* 3.6 3.0 - - - -
453B GLY 2.7 34.4 + - - +
454B ARG* 5.1 0.4 - - - -
456B VAL* 4.9 2.5 - - + -
474B VAL* 4.4 13.5 - - + -
476B SER 4.1 7.6 - - - +
477B VAL* 1.3 80.2 - - - +
479B SER* 1.3 66.4 + - - +
483B GLU* 3.4 36.3 - - + +
484B ILE* 3.7 24.2 - - + +
487B ILE* 4.5 13.5 - - + -
513B ILE* 3.8 10.3 - - + +
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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