Contacts of the helix formed by residues 2542 - 2546 (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 TYR2542 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2368B ARG* 5.7 6.3 - - - +
2371B PHE* 3.9 52.7 + + + +
2373B GLU* 6.1 2.6 - - + +
2540B GLN 3.8 0.6 + - - -
2541B CYS* 1.3 74.9 - - - +
2543B ILE* 1.3 77.6 + - + +
2544B GLY* 3.2 29.2 - - - -
2545B TRP* 3.0 28.2 + - + +
2546B CYS 3.9 1.6 + - - -
2547B PRO* 4.3 1.7 - - - +
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Residues in contact with ILE2543 (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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2265B HIS* 3.6 50.2 - - + +
2268B MET* 3.9 24.7 - - + -
2275B TYR* 4.9 9.6 - - + -
2276B ASP* 5.5 6.9 + - - +
2371B PHE* 5.4 1.6 - - - -
2541B CYS 3.5 4.0 + - - +
2542B TYR* 1.3 87.5 - - + +
2544B GLY* 1.3 60.9 + - - +
2546B CYS* 3.1 25.2 + - - +
2547B PRO* 4.9 4.3 - - + -
2548B PHE* 3.8 28.1 - - + -
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Residues in contact with GLY2544 (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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2340B HIS* 4.1 5.3 - - - +
2341B PRO* 4.0 7.4 - - - +
2542B TYR* 3.2 21.0 - - - -
2543B ILE* 1.3 84.6 - - - +
2545B TRP* 1.3 59.9 + - - +
2546B CYS* 3.3 13.1 + - - -
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Residues in contact with TRP2545 (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* 4.5 2.7 - - - -
2339B ARG* 3.4 26.8 - - + +
2340B HIS* 3.8 23.1 - - + -
2341B PRO* 3.4 2.9 - - - +
2373B GLU* 3.8 27.0 + - - +
2375B ILE* 4.2 19.7 - - + -
2377B PHE 5.1 0.2 - - - -
2378B ARG* 2.4 80.0 + - + -
2379B LEU 5.2 0.2 - - - -
2380B THR* 5.1 3.6 - - - -
2538B LEU* 3.7 31.2 - - + -
2541B CYS* 3.7 22.0 - - + -
2542B TYR* 3.0 26.6 + - + +
2544B GLY* 1.3 75.5 - - - +
2546B CYS* 1.3 54.3 + - - +
2547B PRO* 3.7 20.2 - - + -
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Residues in contact with CYS2546 (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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2247B HIS* 5.8 0.2 - - - -
2262B ASN* 5.3 4.3 - - - -
2341B PRO* 3.8 14.8 - - + -
2378B ARG* 3.0 15.9 + - - -
2380B THR* 4.1 0.2 + - - -
2543B ILE 3.1 16.7 + - - -
2544B GLY* 3.5 15.3 - - - -
2545B TRP* 1.3 76.6 - - - +
2547B PRO* 1.3 69.4 - - - +
2548B PHE* 3.1 17.4 + - + -
2549B TRP* 3.3 52.0 + - + +
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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