Contacts of the helix formed by residues 4054 - 4058 (chain C) in PDB entry 4O2W
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 GLY4054 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4052C GLY 3.4 1.0 + - - -
4053C GLU* 1.3 72.3 - - - +
4055C SER* 1.3 66.3 + - - +
4057C GLY* 3.2 13.7 + - - -
4058C ARG 3.4 6.1 + - - -
4059C LEU* 3.9 10.7 + - - -
4063C ASN 3.9 0.9 - - - +
4064C SER* 3.2 20.5 - - - -
4065C ASP 3.3 22.4 - - - -
4066C ASP* 2.8 13.7 + - - -
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Residues in contact with SER4055 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4176A LEU* 5.0 10.1 - - - +
4053C GLU* 2.9 31.9 + - - +
4054C GLY* 1.3 76.1 + - - +
4056C TYR* 1.3 91.7 + - - +
4057C GLY 3.2 0.2 + - - -
4058C ARG* 3.4 23.6 + - - +
4064C SER* 3.8 8.6 + - - -
4066C ASP* 4.9 1.7 + - - -
4091C ASP 4.3 0.3 - - - +
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Residues in contact with TYR4056 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4117A GLY* 3.7 23.6 - - - -
4175A LYS* 3.7 23.8 + - - +
4176A LEU* 3.5 36.6 + - + +
4054C GLY 3.5 0.2 + - - -
4055C SER* 1.3 82.3 - - - +
4057C GLY* 1.3 56.5 + - - +
4058C ARG* 4.1 2.2 - - - -
4064C SER* 3.5 9.5 + - - -
4091C ASP* 3.4 45.2 + - + +
4107C GLY* 3.2 26.0 - - - +
4108C ASP* 3.8 17.5 - - + +
4121C ARG* 3.3 45.0 - - - +
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Residues in contact with GLY4057 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4054C GLY 3.2 3.4 + - - -
4055C SER 3.2 1.4 - - - -
4056C TYR* 1.3 77.9 - - - +
4058C ARG* 1.3 64.9 + - - +
4059C LEU 3.2 2.5 - - - -
4060C GLY* 3.1 14.9 + - - -
4063C ASN 3.5 20.6 - - - -
4064C SER* 3.6 5.7 + - - -
4106C TRP* 3.4 10.6 - - - -
4107C GLY* 3.9 4.8 + - - -
4122C GLN 4.0 0.5 - - - +
4123C ARG* 3.9 21.8 - - - +
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Residues in contact with ARG4058 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4036C GLN* 2.9 45.5 + - - +
4038C CYS* 3.6 22.7 - - + -
4040C PHE* 3.6 8.5 - - + -
4053C GLU* 3.2 50.4 + - - +
4054C GLY 3.4 4.5 + - - -
4055C SER* 3.5 26.8 + - - +
4056C TYR* 3.3 4.9 - - - -
4057C GLY* 1.3 76.8 - - - +
4059C LEU* 1.3 54.4 + - - +
4060C GLY 3.3 0.2 - - - -
4086C THR* 5.5 1.3 - - - +
4090C SER 4.6 2.2 + - - -
4091C ASP* 2.7 36.1 + - - +
4092C GLY* 4.0 11.6 - - - -
4093C HIS* 5.5 0.4 - - - +
4094C SER* 4.3 6.2 + - - +
4106C TRP* 2.7 24.6 + - - -
4107C GLY* 4.4 9.6 - - - -
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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