Contacts of the strand formed by residues 4241 - 4246 (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 ILE4241 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4201C VAL* 4.0 18.0 - - + +
4205C GLY* 2.8 32.2 + - - +
4208C VAL* 3.7 10.8 - - + -
4236C LEU* 3.7 31.9 - - + +
4239C ILE* 3.8 27.8 - - + -
4240C GLY* 1.3 71.7 - - - -
4242C LYS* 1.3 63.1 + - - +
4243C LYS 3.7 19.1 - - - +
4244C VAL* 4.0 16.8 - - + -
4253C ALA* 4.4 8.5 - - + -
4254C LEU 3.6 12.3 - - - +
4255C THR* 4.3 8.3 - - + -
4256C LYS* 3.8 7.7 - - - -
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Residues in contact with LYS4242 (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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4190C GLN* 4.2 6.3 - - - +
4201C VAL* 5.6 2.5 - - - +
4240C GLY 3.8 2.8 + - - -
4241C ILE* 1.3 75.1 - - - +
4243C LYS* 1.3 65.2 + - + +
4254C LEU* 2.8 29.6 + - + +
4255C THR 4.0 13.5 - - - +
4256C LYS* 3.9 17.7 - - + +
4293C ILE 5.0 1.2 + - - +
4294C GLU* 2.7 43.6 + - - +
4295C ASP* 5.9 0.9 - - - -
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Residues in contact with LYS4243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4190C GLN* 3.3 16.6 - - - +
4241C ILE* 3.7 3.3 - - - +
4242C LYS* 1.3 91.4 - - + +
4244C VAL* 1.3 82.6 + - - +
4245C ALA* 5.0 4.7 - - - -
4253C ALA* 3.5 1.9 - - - -
4254C LEU* 2.8 40.8 + - + +
4295C ASP* 3.0 34.4 + - - +
4296C VAL* 3.2 26.6 + - + +
4297C ALA* 5.3 1.0 - - - +
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Residues in contact with VAL4244 (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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4190C GLN* 2.9 38.6 + - + +
4191C VAL 4.9 0.4 - - - -
4192C ALA* 3.7 20.7 - - + +
4199C LEU* 4.0 25.1 - - + +
4201C VAL* 3.4 29.2 - - + -
4208C VAL* 4.3 14.1 - - + -
4236C LEU* 5.8 0.4 - - + -
4241C ILE* 4.0 8.5 - - + -
4243C LYS* 1.3 88.2 - - - +
4245C ALA* 1.3 61.8 + - - +
4252C VAL 3.3 11.2 - - - +
4253C ALA* 4.3 9.2 - - + -
4296C VAL* 5.7 0.4 - - - -
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Residues in contact with ALA4245 (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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4192C ALA* 3.8 7.4 - - - -
4199C LEU* 3.9 4.0 - - - +
4243C LYS* 5.0 6.3 - - - -
4244C VAL* 1.3 76.5 - - - +
4246C CYS* 1.3 63.4 + - - +
4251C SER* 3.5 2.6 - - - -
4252C VAL* 2.8 35.9 + - + +
4296C VAL* 4.8 10.5 - - + +
4298C VAL* 3.4 33.4 - - + +
4402C UNX 4.3 6.1 - - - +
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Residues in contact with CYS4246 (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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4192C ALA 3.7 19.7 - - - -
4193C CYS* 3.7 6.0 - - - +
4194C GLY* 3.5 26.5 - - - +
4197C HIS* 3.4 27.1 - - + -
4199C LEU* 3.5 30.1 - - - -
4245C ALA* 1.3 73.7 - - - +
4247C GLY* 1.3 58.9 + - - +
4250C PHE* 3.6 4.7 - - - -
4251C SER* 4.5 0.2 - - - +
4298C VAL* 3.5 16.1 - - - +
4299C GLY 4.1 3.1 - - - +
4402C UNX 3.5 14.9 + - - +
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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