Contacts of the helix formed by residues 497 - 502 (chain A) in PDB entry 2W93
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 SER 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A ASP* 2.9 32.5 + - - -
495A HIS 3.1 1.0 - - - -
496A LEU* 1.3 78.8 - - - +
498A LEU* 1.3 62.9 + - - +
499A LEU 3.4 0.4 - - - -
500A PRO* 3.3 11.4 - - - +
501A THR* 2.9 28.4 + - - -
501B THR* 3.4 20.4 - - - -
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Residues in contact with LEU 498 (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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447A LEU* 3.9 20.9 - - + -
451A VAL* 3.6 34.1 - - + -
454A ILE* 4.7 3.4 - - + -
493A TRP* 4.5 10.8 - - + -
494A ASP 3.9 0.4 + - - +
495A HIS* 2.9 34.2 + - + +
497A SER* 1.3 76.5 - - - +
499A LEU* 1.3 65.5 + - - +
501A THR* 3.2 5.5 + - - -
502A PHE* 2.9 47.7 + - + -
535A MET* 4.0 15.0 - - + -
501B THR* 3.7 21.3 - - + -
502B PHE* 4.6 5.4 - - + -
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Residues in contact with LEU 499 (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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454A ILE* 3.6 27.6 - - + -
458A ILE* 3.7 15.1 - - + +
466A LEU* 4.9 2.0 - - + -
495A HIS 4.6 0.6 + - - -
496A LEU 4.3 1.4 + - - -
498A LEU* 1.3 78.5 - - - +
500A PRO* 1.4 70.2 - - + +
502A PHE* 3.1 9.9 + - - -
503A GLY 3.3 0.5 + - - -
504A ALA* 3.0 24.2 + - + +
507A TYR* 4.0 30.7 - - + -
508A GLU 4.1 2.2 - - - +
509A THR* 4.1 4.7 - - + -
533A ILE* 3.9 26.0 - - + -
534A ARG 4.3 4.0 - - - -
535A MET* 3.9 41.3 - - + +
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Residues in contact with PRO 500 (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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496A LEU 3.7 10.5 - - - +
497A SER* 3.3 23.3 - - - +
499A LEU* 1.4 95.0 - - + +
501A THR* 1.3 56.8 + - - +
503A GLY* 2.9 18.9 + - - -
504A ALA* 4.1 12.7 - - - +
507A TYR* 3.5 29.8 - - + +
494B ASP* 4.1 10.8 - - - +
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Residues in contact with THR 501 (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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497A SER* 2.9 21.1 + - - -
498A LEU* 3.6 6.7 - - + -
500A PRO* 1.3 77.6 - - - +
502A PHE* 1.3 64.2 + - + +
493B TRP* 3.6 5.2 - - + +
494B ASP* 2.8 30.3 + - - +
497B SER* 2.8 29.7 + - - +
498B LEU* 3.6 32.1 - - + +
501B THR* 2.8 27.6 + - + +
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Residues in contact with PHE 502 (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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451A VAL* 3.5 30.3 - - + -
452A GLN* 4.1 14.6 - - + -
454A ILE* 4.0 12.3 - - + -
455A SER* 3.9 17.5 - - - -
458A ILE* 3.6 17.8 - - + +
498A LEU* 2.9 39.2 + - + +
499A LEU 3.1 0.6 + - - -
501A THR* 1.3 82.2 - - + +
503A GLY* 1.3 57.4 + - - +
504A ALA 3.4 2.8 + - - -
451B VAL* 4.8 2.9 - - + -
491B GLN* 3.0 29.5 + - - +
492B GLY 3.6 0.6 - - - +
493B TRP* 3.4 52.5 - + - +
498B LEU* 4.4 13.5 - - + -
502B PHE* 5.6 1.8 - + - -
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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