Contacts of the strand formed by residues 195 - 200 (chain C) in PDB entry 4JZJ
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 THR 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C CYS* 4.0 2.5 - - - -
104C TRP* 4.2 4.3 - - + -
107C ALA* 2.7 41.0 + - - +
108C GLU* 5.4 1.6 - - - +
109C ASN 5.9 0.4 - - - +
110C LEU* 4.1 29.6 - - + +
182C LEU* 3.6 2.1 - - - +
183C VAL* 2.8 34.0 + - - +
194C CYS* 1.3 76.0 + - - +
196C ASP* 1.3 71.6 + - - +
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Residues in contact with ASP 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C SER* 5.6 2.8 - - - -
75C LEU* 4.5 10.4 + - - +
76C CYS* 3.1 25.4 + - - +
77C GLU 4.9 1.2 + - - -
110C LEU* 4.0 4.5 - - - -
180C HIS* 2.7 28.2 + - - +
181C ILE 3.2 14.1 - - - +
182C LEU* 3.7 10.3 - - + -
195C THR* 1.3 84.4 - - - +
197C LYS* 1.3 63.3 + - - +
198C PHE* 4.5 6.7 - - - -
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Residues in contact with LYS 197 (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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110C LEU* 3.3 42.0 + - + +
111C THR* 4.6 9.9 - - - +
112C CYS* 4.9 5.2 - - - +
180C HIS* 3.6 3.0 - - - -
181C ILE* 2.9 34.4 + - + +
196C ASP* 1.3 77.8 - - - +
198C PHE* 1.3 71.1 - - - +
199C VAL* 3.9 19.3 + - + -
204C ILE* 6.1 2.9 - - - -
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Residues in contact with PHE 198 (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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75C LEU* 6.1 1.3 - - + -
144C LYS* 6.3 5.2 - - + -
178C SER* 6.1 1.3 - - - -
179C SER* 3.5 9.6 - - - +
180C HIS* 3.4 53.6 - + + -
196C ASP* 4.5 5.2 - - - -
197C LYS* 1.3 78.6 - - - +
199C VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 199 (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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112C CYS* 4.4 13.7 - - + +
120C LEU* 5.5 0.4 - - + -
178C SER* 3.2 8.5 - - - -
179C SER* 2.9 41.3 + - - +
181C ILE* 4.3 19.7 - - + -
197C LYS* 4.3 20.9 - - + -
198C PHE* 1.3 79.0 - - - +
200C VAL* 1.3 61.4 + - - +
201C PHE* 3.9 25.4 - - + -
204C ILE* 3.8 33.7 - - + -
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Residues in contact with VAL 200 (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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177C GLN* 3.6 11.9 - - + +
178C SER* 4.3 10.1 - - - -
199C VAL* 1.3 76.3 - - - +
201C PHE* 1.3 68.4 + - - +
202C SER* 3.5 25.4 - - - +
203C GLN* 2.9 29.6 + - + +
204C ILE* 3.4 12.9 + - - +
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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