Contacts of the strand formed by residues 195 - 201 (chain C) in PDB entry 2IK8
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 HIS 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C GLU* 3.7 26.1 - - + +
34C VAL* 3.1 24.5 + - - +
189C PHE 3.5 3.4 - - - -
190C THR* 2.8 34.6 + - + +
193C ASP 6.1 0.7 - - - -
194C LEU* 1.3 70.1 - - - +
196C PHE* 1.3 63.3 + - - +
197C LYS* 3.6 1.8 + - + +
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Residues in contact with PHE 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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34C VAL* 3.5 29.6 - - + -
36C LEU* 4.4 14.4 - - + -
188C HIS* 3.4 8.3 - - - +
189C PHE* 2.6 81.3 + + + +
191C PHE* 3.8 16.6 - + + -
194C LEU* 3.5 42.4 - - + -
195C HIS* 1.3 70.3 - - - +
197C LYS* 1.3 60.9 + - - +
198C MET 3.6 2.9 + - - +
336C PHE* 3.7 23.6 - + - -
340C THR* 4.0 13.0 - - + -
343C ILE* 4.7 8.5 - - + -
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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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33C GLU* 3.2 27.1 - - - +
34C VAL 2.8 13.1 + - - +
35C LYS* 3.4 6.8 - - + -
36C LEU 3.0 22.3 + - - -
187C THR 3.8 5.4 - - - -
188C HIS* 4.0 23.3 - - + +
195C HIS* 4.7 2.5 - - + +
196C PHE* 1.3 72.5 - - - +
198C MET* 1.3 59.0 + - - +
199C PHE* 3.4 25.6 - - + -
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Residues in contact with MET 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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36C LEU* 3.4 39.5 - - + +
38C LEU* 3.9 16.8 - - + -
49C ILE* 5.1 3.4 - - + -
50C VAL* 3.5 37.2 - - + -
53C MET* 3.6 36.1 - - + -
185C VAL 3.9 0.5 - - - +
186C GLU* 3.5 2.8 - - - -
187C THR* 2.9 42.8 + - - +
189C PHE* 3.8 21.3 - - + -
196C PHE* 3.6 1.9 - - + -
197C LYS* 1.3 72.6 - - - +
199C PHE* 1.3 65.0 + - - +
200C ASP 4.8 0.2 - - - +
222C ILE* 5.5 0.4 - - + -
336C PHE* 4.6 1.1 - - + -
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Residues in contact with PHE 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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35C LYS* 4.0 33.2 - - + -
36C LEU 2.6 16.9 + - - +
37C LEU* 3.8 11.4 - - + -
38C LEU* 2.9 30.7 + - - +
184C ILE* 3.8 26.7 - - + -
185C VAL 3.6 2.0 - - - -
186C GLU* 3.8 24.2 - - + -
188C HIS* 6.4 1.1 - + - -
197C LYS* 3.4 31.6 - - + -
198C MET* 1.3 75.2 - - - +
200C ASP* 1.3 60.5 + - - +
201C VAL* 4.6 2.9 - - + +
214C CYS* 4.2 17.9 - - + -
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Residues in contact with ASP 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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38C LEU* 4.1 3.6 - - - +
46C LYS* 3.2 24.8 - - - +
47C SER* 2.8 31.1 + - - -
50C VAL* 3.7 28.8 - - + +
181C THR* 4.0 8.4 + - - +
183C GLY 3.9 0.2 - - - +
184C ILE* 3.4 5.4 - - - +
185C VAL* 2.8 50.5 + - + +
187C THR* 5.9 0.4 - - - +
198C MET* 4.1 0.8 + - - +
199C PHE* 1.3 71.2 - - - +
201C VAL* 1.3 76.7 + - - +
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Residues in contact with VAL 201 (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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38C LEU 3.2 20.6 + - - +
39C LEU* 3.7 18.4 - - + -
46C LYS* 3.0 27.7 - - + -
181C THR* 4.4 5.6 - - - -
183C GLY 3.4 8.1 - - - +
184C ILE* 4.1 22.2 - - + -
199C PHE* 4.6 3.6 - - + +
200C ASP* 1.3 92.6 + - - +
202C GLY* 1.3 61.7 + - - +
211C TRP* 3.6 32.5 - - + +
214C CYS* 4.5 11.7 - - - -
355C ALF 3.8 6.1 - - - -
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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