Contacts of the helix formed by residues 2363 - 2368 (chain B) in PDB entry 5WBY
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 GLU2363 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2332B TYR* 5.9 0.6 - - - -
2335B GLY* 4.0 6.1 - - - +
2362B PHE* 1.3 76.0 - - - +
2364B VAL* 1.3 52.3 + - - +
2365B ALA 3.3 1.6 - - - -
2366B MET* 2.8 57.5 + - + +
2367B THR* 2.9 26.0 + - - +
2500B ILE* 5.9 0.8 - - - +
2503B ARG* 2.7 48.8 + - + -
2507B LYS* 3.4 17.5 + - - -
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Residues in contact with VAL2364 (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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2359B GLY 5.8 0.4 - - - +
2360B ASP* 4.1 22.4 - - - +
2361B CYS 3.2 21.3 - - - +
2362B PHE* 2.8 10.8 + - + -
2363B GLU* 1.3 71.2 - - - +
2365B ALA* 1.3 61.5 - - - +
2367B THR* 3.4 6.4 + - - -
2368B ARG* 3.3 24.7 + - + +
2430B ARG* 4.0 26.9 - - + +
2431B LEU* 4.5 16.4 - - + -
2433B ASP* 5.9 8.5 - - + +
2434B THR* 6.1 2.0 - - - +
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Residues in contact with ALA2365 (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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2337B GLY* 3.8 19.7 - - - +
2338B ASP 4.2 1.6 - - - +
2360B ASP* 4.2 12.6 - - + +
2362B PHE 4.4 1.7 + - - +
2363B GLU 3.3 0.6 - - - -
2364B VAL* 1.3 79.4 - - - +
2366B MET* 1.3 62.7 + - + +
2368B ARG* 3.0 36.2 + - - +
2373B GLU* 3.1 41.9 + - + +
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Residues in contact with MET2366 (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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2335B GLY 6.0 1.8 - - - +
2337B GLY* 6.4 0.4 - - - -
2362B PHE 5.8 0.2 - - - +
2363B GLU* 2.8 44.4 + - + +
2365B ALA* 1.3 81.0 - - + +
2367B THR* 1.3 58.6 + - - +
2368B ARG 3.4 0.8 - - - +
2372B PRO* 3.3 20.3 - - - +
2373B GLU* 3.3 33.6 - - + +
2374B LYS* 3.9 8.7 + - - -
2375B ILE 3.8 28.0 - - - +
2376B PRO* 4.8 3.8 - - + -
2503B ARG* 6.0 0.2 - - - -
2531B GLN* 4.1 15.3 - - - +
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Residues in contact with THR2367 (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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2363B GLU* 2.9 28.7 + - - +
2364B VAL* 3.4 6.7 + - - -
2366B MET* 1.3 74.9 - - - +
2368B ARG* 1.3 65.8 + - - +
2369B GLU* 4.2 8.3 - - - +
2434B THR* 3.8 30.8 - - + +
2496B LYS* 5.4 9.7 + - - +
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Residues in contact with ARG2368 (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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2338B ASP* 4.1 9.7 + - - -
2360B ASP* 4.1 12.9 + - - -
2364B VAL* 3.3 13.0 + - + +
2365B ALA* 3.0 29.1 + - - +
2366B MET 4.3 0.2 - - - +
2367B THR* 1.3 82.9 - - - +
2369B GLU* 1.3 63.9 + - - +
2370B LYS 3.2 23.7 + - - +
2371B PHE* 3.4 19.4 + - - +
2372B PRO* 3.5 15.7 - - + +
2373B GLU* 3.0 35.4 + - - +
2433B ASP 6.1 0.2 - - - -
2434B THR* 5.4 4.7 - - - +
2436B THR 4.4 11.0 - - - +
2542B TYR* 5.7 6.6 - - - +
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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