Contacts of the strand formed by residues 192 - 197 (chain C) in PDB entry 4JHN
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 VAL 192 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C LYS* 5.1 1.2 + - - +
155C LEU* 3.4 31.1 - - + +
156C THR 4.7 0.7 - - - +
159C GLY* 2.9 29.5 + - - +
161C LEU* 4.1 20.4 - - + +
186C VAL 4.9 3.6 - - - +
187C THR* 5.9 2.2 - - - -
188C ILE* 5.8 0.2 - - + -
190C LYS 3.8 12.8 - - - +
191C PRO* 1.3 73.2 - - - +
193C SER* 1.3 61.5 + - - +
194C TRP 3.5 17.7 - - - +
204C PHE* 3.8 34.5 - - + -
205C VAL 3.4 12.3 - - - +
206C THR* 4.2 1.1 - - + +
207C THR* 4.3 3.3 - - - +
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Residues in contact with SER 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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143C LYS* 2.8 37.3 + - - +
144C GLN* 4.3 0.7 - - - +
155C LEU* 3.6 7.3 - - - +
191C PRO 4.1 0.6 + - - -
192C VAL* 1.3 74.8 - - - +
194C TRP* 1.3 70.3 + - - +
205C VAL* 2.8 23.0 + - - +
206C THR 3.3 12.5 + - - -
207C THR* 3.9 21.0 - - - -
246C ILE 4.7 2.6 + - - -
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Residues in contact with TRP 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LYS* 5.2 6.1 - - - -
144C GLN* 3.4 28.3 - - - +
155C LEU* 3.6 2.3 - - - +
192C VAL* 3.5 3.7 - - - +
193C SER* 1.3 89.4 - - - +
195C ILE* 1.3 75.8 + - - +
196C SER* 5.3 0.4 - - - -
204C PHE* 3.1 7.4 - - - +
205C VAL* 2.8 45.5 + - + -
246C ILE* 3.9 13.7 - - + +
247C GLN* 3.6 45.0 - - + +
248C VAL* 3.3 35.1 + - + +
299C TYR* 4.0 22.4 - + - -
300C ILE 5.5 1.6 - - - -
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Residues in contact with ILE 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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144C GLN* 2.9 38.6 + - + +
146C SER* 4.0 11.5 - - - +
153C ALA* 3.9 16.4 - - + -
155C LEU* 4.1 14.1 - - + +
161C LEU* 3.3 51.8 - - + -
163C MET* 3.8 26.7 - - + -
194C TRP* 1.3 81.0 + - - +
196C SER* 1.3 73.8 + - - +
197C CYS 4.7 0.4 - - - +
203C ALA 3.4 15.3 - - - +
204C PHE* 4.2 3.8 - - + +
214C PHE* 4.9 0.7 - - + -
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Residues in contact with SER 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C SER* 3.6 5.4 + - - -
194C TRP* 5.1 0.4 - - - -
195C ILE* 1.3 76.4 - - - +
197C CYS* 1.3 63.7 + - - +
198C GLY 3.9 0.2 - - - -
202C SER* 3.3 4.5 - - - -
203C ALA 2.9 33.9 + - - +
248C VAL* 3.3 26.6 - - - +
249C ALA* 3.5 2.9 - - - +
250C CYS* 2.8 36.9 + - - +
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Residues in contact with CYS 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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146C SER* 2.9 25.1 + - - +
147C ALA 3.7 12.5 - - - +
148C GLY* 3.5 20.0 - - - +
151C THR* 3.8 13.0 - - - +
152C SER 4.2 5.2 - - - -
153C ALA* 3.7 20.6 - - - -
163C MET* 3.6 30.5 - - - -
195C ILE* 4.7 0.2 - - - -
196C SER* 1.3 75.1 + - - +
198C GLY* 1.3 62.0 + - - +
202C SER* 3.6 7.6 - - - +
250C CYS 4.1 4.0 - - - +
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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