Contacts of the helix formed by residues 192 - 198 (chain C) in PDB entry 1JZ3
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 SER 192 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C TRP* 3.4 19.7 - - - -
114C VAL* 3.5 13.4 - - - +
148C SER* 3.0 21.2 + - - -
149C ALA* 3.7 24.8 - - - +
163C GLN* 4.4 4.0 - - - -
191C TRP* 1.3 77.1 - - - +
193C ASP* 1.3 55.4 + - - +
194C GLY* 3.1 15.4 + - - -
195C SER* 2.7 30.8 + - - -
196C TYR* 4.0 1.7 + - - -
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Residues in contact with ASP 193 (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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16C TRP 2.9 21.3 + - - -
18C ASN 2.8 24.5 + - - +
19C PRO* 3.2 16.7 - - - +
22C THR* 4.9 0.3 - - - +
112C PRO* 3.8 26.7 - - + +
114C VAL* 4.1 0.2 - - - +
163C GLN* 3.0 21.2 + - - +
192C SER* 1.3 71.6 - - - +
194C GLY* 1.3 63.3 + - - +
196C TYR* 3.1 28.7 + - - +
197C LEU 4.1 0.2 + - - -
432C TRP* 3.7 16.5 - - + -
435C ALA* 5.7 0.9 - - - +
3002C MG 2.4 25.7 - - - -
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Residues in contact with GLY 194 (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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148C SER* 5.4 2.0 - - - -
163C GLN* 3.6 11.9 - - - +
192C SER* 2.9 12.0 + - - -
193C ASP* 1.3 84.3 + - - +
195C SER* 1.4 54.6 + - - +
197C LEU* 2.8 23.9 + - - +
198C GLU* 3.2 21.2 - - - +
432C TRP* 5.7 0.2 - - - -
439C ARG* 3.5 21.0 + - - -
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Residues in contact with SER 195 (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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105C TYR* 3.6 14.7 - - - -
106C PRO* 6.3 0.4 - - - -
107C ILE* 4.5 11.9 - - - -
148C SER* 3.7 9.2 + - - -
190C ARG 4.0 0.7 + - - -
191C TRP* 3.6 27.3 - - - -
192C SER* 2.7 33.3 + - - -
194C GLY* 1.4 77.9 - - - +
196C TYR* 1.3 60.8 + - - +
198C GLU* 3.0 26.7 + - - +
204C ARG* 5.8 0.2 + - - -
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Residues in contact with TYR 196 (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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105C TYR* 2.7 44.3 + + - -
107C ILE* 4.3 16.3 - - + +
108C THR 3.4 6.9 + - - -
109C VAL* 4.4 12.3 - - + -
110C ASN 2.9 25.0 + - - -
111C PRO* 3.5 33.4 - - + -
112C PRO* 3.7 8.1 - - + -
113C PHE 2.7 29.3 + - - -
114C VAL* 4.6 1.1 - - + -
192C SER 4.3 1.1 - - - -
193C ASP* 3.1 25.5 + - - +
194C GLY 3.1 1.0 - - - -
195C SER* 1.3 79.8 - - - +
197C LEU* 1.3 59.1 + - - +
198C GLU 3.4 0.2 - - - -
416C GLU 3.6 0.9 - - - +
417C THR* 3.4 10.0 - - - +
420C MET* 4.6 6.3 - - - -
426C LEU* 3.9 7.1 - - + +
432C TRP* 3.8 21.3 - + + -
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Residues in contact with LEU 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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193C ASP 4.7 1.6 - - - +
194C GLY* 2.8 11.7 + - - +
196C TYR* 1.3 80.1 - - - +
198C GLU* 1.3 60.5 + - - +
200C GLN* 4.5 0.2 + - - -
414C ASN* 3.5 4.0 - - - +
415C ILE* 3.5 16.6 - - + -
416C GLU 3.0 27.2 + - - -
417C THR* 3.5 22.4 - - + -
426C LEU* 4.2 7.9 - - + -
432C TRP* 3.9 27.1 - - + -
435C ALA* 3.9 24.7 - - + -
436C MET* 4.3 16.6 - - + -
439C ARG* 3.6 37.2 - - - +
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Residues in contact with GLU 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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147C ASN* 4.3 3.1 - - - +
148C SER* 3.8 12.6 - - - +
164C ASP* 3.8 0.3 + - - -
165C SER* 2.8 35.2 + - - -
194C GLY* 3.2 19.1 - - - +
195C SER* 3.0 16.2 + - - +
196C TYR 3.4 0.2 - - - -
197C LEU* 1.3 83.1 - - - +
199C ASP* 1.3 55.6 + - - +
200C GLN* 3.0 21.4 + - - +
202C MET* 5.4 4.4 - - + +
204C ARG* 3.7 13.0 + - - -
414C ASN* 3.0 19.4 + - - +
439C ARG* 3.0 27.9 + - - +
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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