Contacts of the helix formed by residues 2428 - 2433 (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 ASN2428 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2422B VAL 2.9 23.0 - - - +
2423B TYR* 4.4 4.8 + - - +
2424B ASP 2.7 23.1 + - - +
2425B PRO* 3.5 19.7 + - - +
2426B LEU 3.8 0.8 - - - -
2427B LEU* 1.3 76.9 - - - +
2429B TRP* 1.3 63.3 + - - +
2430B ARG 3.1 1.8 + - - -
2431B LEU* 3.1 30.5 + - + +
2432B MET 3.9 3.1 + - - -
2493B LEU* 4.4 28.2 - - + +
2497B ALA* 5.2 5.4 - - - +
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Residues in contact with TRP2429 (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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2191B ASP* 3.4 39.6 + - + -
2193B ARG* 4.9 5.4 - - - -
2194B GLN* 3.3 22.9 - - - +
2426B LEU 4.1 8.7 + - - +
2427B LEU* 3.2 21.3 - - - +
2428B ASN* 1.3 77.7 - - - +
2430B ARG* 1.3 69.3 + - - +
2431B LEU 3.2 1.3 + - - -
2432B MET* 3.7 15.4 + - - +
2433B ASP* 3.9 11.1 + - - +
2493B LEU* 5.9 0.4 - - - -
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Residues in contact with ARG2430 (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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2194B GLN* 3.3 57.9 + - - +
2197B ARG* 5.5 0.4 - - - +
2198B VAL* 5.3 0.8 - - - +
2359B GLY 5.0 6.5 - - - +
2361B CYS* 4.4 15.3 - - - +
2362B PHE* 4.2 22.4 - - - -
2364B VAL* 4.0 20.2 - - + +
2421B PHE* 3.0 47.9 + - - -
2422B VAL* 5.7 0.4 - - - +
2427B LEU* 3.2 34.9 + - - +
2429B TRP* 1.3 82.5 - - - +
2431B LEU* 1.3 80.2 + - + +
2433B ASP* 3.9 16.0 - - - +
2434B THR 5.0 0.2 + - - -
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Residues in contact with LEU2431 (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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2362B PHE* 4.4 13.7 - - + -
2364B VAL* 4.5 13.5 - - + -
2422B VAL* 4.5 19.1 - - + +
2427B LEU 5.4 0.4 - - - +
2428B ASN* 3.1 23.4 + - - +
2430B ARG* 1.3 100.7 - - + +
2432B MET* 1.3 60.2 + - - +
2433B ASP 3.2 2.2 - - - -
2434B THR* 2.8 27.1 + - - -
2493B LEU* 4.3 8.7 - - + +
2496B LYS* 4.3 23.6 - - + +
2497B ALA* 4.8 7.6 - - + +
2500B ILE* 3.4 33.2 - - + -
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Residues in contact with MET2432 (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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2428B ASN 3.9 3.5 + - - +
2429B TRP* 3.7 11.1 + - - +
2430B ARG 3.6 0.2 - - - -
2431B LEU* 1.3 73.1 - - - +
2433B ASP* 1.3 58.1 + - - +
2434B THR* 3.1 10.8 + - - -
2435B ASN* 2.8 48.0 + - + +
2493B LEU* 4.1 27.7 - - + +
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Residues in contact with ASP2433 (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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2364B VAL* 5.9 7.5 - - + +
2368B ARG* 6.1 0.2 - - - -
2429B TRP 3.9 9.5 + - - +
2430B ARG* 3.9 14.8 - - - +
2431B LEU 3.2 1.6 - - - -
2432B MET* 1.3 78.4 - - - +
2434B THR* 1.3 62.5 + - - +
2435B ASN* 3.1 4.7 + - - +
2436B THR* 3.4 29.8 + - - +
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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