Contacts of the strand formed by residues 505 - 509 (chain A) in PDB entry 2W8D
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 505 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A TYR* 3.4 6.1 - - - -
285A PHE* 3.2 63.5 + - + -
288A PHE* 3.7 37.9 - - + -
467A VAL* 3.9 24.2 - - + -
468A MSE 3.2 15.0 - - - +
469A TYR* 4.2 11.2 - - + -
503A VAL 3.6 0.8 + - - -
504A PRO* 1.3 74.8 - - - +
506A PHE* 1.3 63.9 + - - +
507A ILE* 4.5 7.4 - - + -
526A VAL* 4.3 15.3 - - + -
548A ILE* 4.1 12.1 - - + -
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Residues in contact with PHE 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 4.8 3.8 - - + -
260A ILE* 4.3 6.7 - - + -
273A LEU* 3.5 49.4 - - + -
276A LEU* 3.8 16.2 - - + -
277A ALA* 3.7 11.2 - - + -
282A THR* 4.3 13.2 - - + -
283A PHE 3.3 5.4 - - - +
284A TYR* 3.4 32.5 - + + -
466A ILE 3.8 0.6 - - - +
467A VAL* 3.3 3.6 - - - -
468A MSE 2.8 65.3 + - + +
504A PRO* 3.7 23.8 - - + -
505A LEU* 1.3 76.2 - - - +
507A ILE* 1.3 64.5 + - - +
508A HIS 4.2 0.4 - - - +
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Residues in contact with ILE 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A THR* 3.9 2.6 - - - -
283A PHE* 3.0 50.7 + - + -
285A PHE* 3.7 27.6 - - + -
465A ILE* 3.9 24.2 - - + -
466A ILE 3.3 3.6 - - - +
467A VAL* 4.3 9.2 - - + -
505A LEU* 4.5 9.0 - - + -
506A PHE* 1.3 79.9 - - - +
508A HIS* 1.3 60.9 + - - +
509A ALA 4.3 4.0 - - - +
526A VAL* 5.5 1.3 - - + -
529A THR* 4.1 16.4 - - + -
530A ILE* 3.8 22.2 - - + -
533A LEU* 4.1 16.2 - - + -
549A LEU* 6.0 0.7 - - + -
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Residues in contact with HIS 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLU* 2.7 40.0 + - + +
282A THR* 3.5 28.7 - - + +
452A PHE* 5.3 6.7 - - + -
461A TYR* 3.3 49.4 + + + +
462A ASP* 5.9 0.4 - - - -
464A SER 3.6 1.7 - - - +
465A ILE* 3.3 2.5 - - - -
466A ILE* 2.8 45.9 + - + +
506A PHE* 4.2 0.6 - - - +
507A ILE* 1.3 73.2 - - - +
509A ALA* 1.3 60.6 + - - +
510A ALA* 4.2 24.7 + - + +
512A VAL 5.7 0.6 + - - -
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Residues in contact with ALA 509 (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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242A ALA* 4.4 6.5 - - + -
281A GLU 5.5 1.0 + - - -
283A PHE* 4.7 5.9 - - + -
464A SER 4.0 3.4 - - - -
465A ILE* 4.1 23.6 - - + -
507A ILE* 3.8 10.2 + - + -
508A HIS* 1.3 77.1 + - - +
510A ALA* 1.3 63.9 + - - +
512A VAL* 3.1 44.9 + - + +
533A LEU* 4.5 9.9 - - + -
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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