Contacts of the strand formed by residues 472 - 478 (chain B) in PDB entry 4X7C
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 472 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470B SER* 2.9 10.5 + - - -
471B ASP* 1.3 94.4 - - + +
473B ALA* 1.3 63.4 + - - +
490B LYS* 3.4 44.0 - - + +
491B LEU 3.5 3.6 - - - +
492B HIS* 3.7 29.4 - - + +
520B TRP* 3.5 3.8 - - - -
521B VAL* 2.9 49.3 + - + +
522B ASN* 4.9 5.8 - - - -
523B GLN 5.9 0.2 - - - +
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Residues in contact with ALA 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B PHE* 4.1 11.0 - - + -
268B THR* 5.5 0.4 - - + -
472B VAL* 1.3 74.1 - - - +
474B LEU* 1.3 62.6 + - - +
475B LEU* 3.5 2.6 + - + -
490B LYS* 3.6 1.2 - - - -
491B LEU* 2.7 52.0 + - + +
517B PHE* 3.5 26.7 - - + -
519B SER 3.7 4.0 - - - -
520B TRP* 3.6 20.5 - - + -
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Residues in contact with LEU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B VAL 3.9 1.8 + - - -
473B ALA* 1.3 71.2 - - - +
475B LEU* 1.3 63.0 + - - +
476B ARG* 3.7 23.8 - - - +
488B GLU* 3.6 20.0 - - + +
489B CYS 3.7 7.4 - - - +
490B LYS* 4.9 3.4 - - + +
517B PHE* 3.7 1.0 - - - -
518B ASP* 2.9 27.6 + - + -
519B SER* 2.7 20.9 + - - +
521B VAL* 3.7 16.5 - - + +
525B TYR* 3.6 40.2 - - + +
527B LEU* 3.7 18.8 - - + -
31D ILE* 4.0 22.4 - - + -
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Residues in contact with LEU 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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229B VAL* 3.9 17.0 - - + -
457B TRP* 3.7 31.4 - - + -
473B ALA* 4.0 10.8 - - + +
474B LEU* 1.3 77.2 - - - +
476B ARG* 1.3 66.1 + - - +
488B GLU* 3.3 3.8 - - - +
489B CYS* 2.8 50.1 + - - -
491B LEU* 3.9 22.2 - - + -
497B VAL* 5.1 1.8 - - + -
515B PHE* 4.0 17.7 - - + -
516B ARG 3.3 4.9 - - - +
517B PHE* 3.7 31.2 - - + +
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Residues in contact with ARG 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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474B LEU* 3.7 17.0 - - - +
475B LEU* 1.3 82.2 - - - +
477B PHE* 1.3 61.1 + - - +
478B VAL* 3.6 5.7 + - + +
485B VAL* 3.7 32.0 - - + +
487B PHE 3.7 2.2 - - - -
488B GLU* 2.9 30.9 + - + +
515B PHE* 4.5 2.2 - - - -
516B ARG* 2.8 45.3 + - - +
518B ASP* 2.8 49.3 + - - +
525B TYR* 3.2 12.9 + - - -
31D ILE* 4.2 12.7 - - - +
53D SER* 4.6 5.3 + - - -
54D GLY* 4.2 11.7 - - - +
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Residues in contact with PHE 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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234B VAL* 4.5 4.5 - - + -
249B LEU* 4.4 6.1 - - + -
475B LEU 4.2 0.4 + - - -
476B ARG* 1.3 69.6 - - - +
478B VAL* 1.3 56.0 + - - +
485B VAL* 3.6 1.4 - - - -
486B LEU* 2.7 46.2 + - + +
487B PHE* 2.9 47.6 + + + +
489B CYS* 5.8 0.2 - - - -
509B ILE* 3.8 37.7 - - + -
510B PRO* 4.3 2.7 - - + -
513B GLY* 3.4 33.9 - - - -
514B TYR* 3.5 18.2 - - - -
515B PHE* 3.7 40.3 - + + +
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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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476B ARG* 3.6 17.0 - - + +
477B PHE* 1.3 77.5 - - - +
479B ASN* 1.3 75.9 + - - +
480B PRO* 3.4 7.6 - - + +
483B GLY* 4.2 12.8 - - - +
484B ARG 3.7 8.7 - - - +
485B VAL* 4.4 4.9 - - + -
486B LEU* 4.8 0.2 - - - -
513B GLY* 3.1 7.2 - - - -
514B TYR* 2.8 51.4 + - + +
516B ARG* 3.7 44.6 - - + +
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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