Contacts of the strand formed by residues 473 - 480 (chain B) in PDB entry 5XOU
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 LEU 473 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471B ALA* 3.3 4.9 - - - +
472B GLU* 1.3 81.8 - - - +
474B ALA* 1.3 60.5 + - - +
475B VAL* 4.0 6.7 - - + -
492B CYS* 4.2 15.0 - - + -
493B ALA 3.4 16.8 - - - +
494B VAL* 4.0 20.9 - - + -
523B LEU* 5.3 0.7 - - + -
526B THR* 3.9 23.3 - - - +
527B LEU* 3.9 24.9 - - + -
530B PHE* 4.2 6.3 - - + -
538B PRO* 4.1 13.7 - - + -
540B ARG 3.9 1.6 + - - -
541B VAL* 3.3 30.7 - - + +
542B LEU 2.8 23.7 + - - -
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Residues in contact with ALA 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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472B GLU 4.4 0.2 - - - -
473B LEU* 1.3 74.5 - - - +
475B VAL* 1.3 63.5 - - - +
492B CYS* 3.3 3.6 - - - +
493B ALA* 2.9 40.8 + - + +
542B LEU* 3.2 16.8 - - + +
544B LEU* 5.1 1.8 - - + -
634B GLN* 4.8 5.6 - - - +
638B LEU* 3.9 28.3 - - + -
655B PRO* 3.8 12.5 - - + +
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Residues in contact with VAL 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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473B LEU* 4.0 14.4 - - + +
474B ALA* 1.3 79.9 - - - +
476B GLY* 1.3 62.0 - - - +
477B PHE* 3.6 25.2 - - + -
490B ALA* 4.1 4.9 - - + -
491B ALA 3.5 11.2 - - - +
492B CYS* 3.9 8.1 - - + -
523B LEU* 4.3 7.4 - - + -
526B THR* 3.4 37.0 - - + +
541B VAL* 5.5 0.7 - - + -
542B LEU 2.6 10.7 + - - +
543B LEU* 3.4 13.8 - - + -
544B LEU* 2.6 35.1 + - - +
655B PRO* 4.1 3.8 - - - -
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Residues in contact with GLY 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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475B VAL* 1.3 75.1 - - - +
477B PHE* 1.3 61.8 + - - -
490B ALA* 3.0 9.0 - - - +
491B ALA 2.9 33.6 + - - -
544B LEU* 3.3 7.0 - - - -
655B PRO* 3.7 13.5 - - - +
656B LEU* 3.6 16.8 - - - -
659B ALA* 3.7 4.6 - - - +
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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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475B VAL* 3.6 26.5 - - + -
476B GLY* 1.3 74.1 - - - -
478B ASP* 1.3 61.6 + - - +
489B GLY 3.2 7.4 - - - +
490B ALA* 4.1 17.3 - - + -
514B ILE* 4.3 13.2 - - + -
519B VAL* 3.9 31.4 - - + -
522B LEU* 4.2 13.2 - - + -
523B LEU* 4.3 13.9 - - + -
543B LEU* 3.9 15.3 - - + -
544B LEU 2.9 19.1 + - - +
545B ARG* 3.7 17.6 - - - -
546B ASN* 3.1 25.8 + - - +
554B PHE* 3.6 31.9 - + + -
656B LEU* 3.6 2.4 - - - +
659B ALA* 4.6 0.2 - - - -
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Residues in contact with ASP 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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477B PHE* 1.3 74.8 - - - +
479B ALA* 1.3 78.6 + - - +
488B GLY* 3.4 3.6 - - - -
489B GLY 2.9 31.5 + - - +
512B GLU* 4.5 2.8 - - - +
514B ILE* 4.1 4.3 - - - +
545B ARG* 4.2 8.2 + - - +
546B ASN* 3.3 33.5 + - + +
656B LEU* 5.2 0.7 - - + -
659B ALA* 4.3 4.9 - - + +
660B ASP* 3.1 46.2 - - - +
663B VAL* 3.7 10.8 - - + +
9F C 4.6 1.9 - - - +
10F T 3.2 10.8 + - - -
11F A 5.5 0.2 + - - -
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Residues in contact with ALA 479 (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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478B ASP* 1.3 91.5 + - - +
480B GLY* 1.3 57.9 + - - +
486B ARG* 4.3 10.7 + - + +
487B PHE 3.1 6.7 - - - +
509B GLN* 3.7 26.2 - - - +
512B GLU* 3.6 31.1 + - - +
514B ILE* 5.0 2.0 - - + -
663B VAL* 3.7 4.2 - - - +
10F T 3.9 18.4 - - - +
11F A 5.1 0.3 + - - -
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Residues in contact with GLY 480 (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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479B ALA* 1.3 73.6 - - - +
481B GLY* 1.3 62.4 + - - -
486B ARG* 3.1 10.1 - - - -
487B PHE* 2.9 34.8 + - - +
663B VAL* 3.5 26.0 - - - +
10F T 4.1 4.7 - - - -
11F A 3.7 7.0 - - - -
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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