Contacts of the strand formed by residues 189 - 196 (chain C) in PDB entry 2PJ7
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 ILE 189 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ALA* 3.4 6.5 - - + -
63C PHE* 3.9 31.6 - - + +
106C TYR* 4.4 12.3 - - + -
182C PHE* 4.3 4.5 - - + -
183C ILE* 4.1 25.8 - - + -
186C ASN* 3.1 31.6 + - + +
187C SER* 4.0 6.5 + - - +
188C SER* 1.3 78.2 - - - +
190C LYS* 1.3 68.3 + - - +
191C ALA 3.4 24.2 - - - +
192C TYR* 5.2 1.3 - - + -
263C ILE* 3.8 32.2 - - + +
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Residues in contact with LYS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PRO* 4.2 7.0 - - + -
61C ALA 2.9 10.4 + - - +
187C LEU 4.4 16.7 + - - -
188C SER 3.4 14.1 - - - +
189C ILE* 1.3 89.6 - - - +
191C ALA* 1.3 60.8 + - - +
262C GLY 5.5 5.5 + - - -
263C ILE* 3.6 14.7 - - - +
264C LYS* 4.2 2.8 + - - +
265C TYR* 3.7 20.6 + - + -
304C VAL* 4.5 6.3 - - + -
307C HIS 6.0 0.7 - - - +
308C LEU* 3.7 53.7 + - + +
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Residues in contact with ALA 191 (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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61C ALA 3.8 3.4 + - - -
62C ILE* 4.0 25.4 - - + -
63C PHE 3.0 25.4 + - - -
189C ILE* 3.4 7.1 - - - +
190C LYS* 1.3 81.4 - - - +
192C TYR* 1.3 61.5 + - - +
193C LEU* 5.0 5.8 - - + -
263C ILE* 3.6 4.9 - - - -
265C TYR* 3.1 22.4 - - + +
300C VAL* 5.7 1.3 - - + -
304C VAL* 4.1 13.0 - - + -
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Residues in contact with TYR 192 (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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63C PHE* 3.5 27.4 - + + -
65C ASP* 2.5 30.4 + - - -
68C PHE* 3.8 1.9 - - - -
179C LEU* 4.3 1.6 - - + +
183C ILE* 4.0 21.8 - - + -
189C ILE* 5.3 0.4 - - + -
191C ALA* 1.3 75.8 - - - +
193C LEU* 1.3 66.1 + - - +
194C THR* 3.5 20.1 + - + -
254C SER* 2.6 38.0 + - - -
255C ASP* 3.7 13.7 - - + -
258C ALA* 3.7 21.1 - - + -
263C ILE* 3.7 10.5 - - + +
265C TYR 2.8 9.3 + - - -
266C SER* 3.3 19.9 - - - +
267C PHE 2.9 25.5 + - - -
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Residues in contact with LEU 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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62C ILE* 4.0 22.4 - - + -
63C PHE 2.8 13.8 + - - +
64C MET* 3.1 22.1 - - + +
65C ASP* 3.0 24.9 + - - +
105C PHE* 5.7 0.7 - - + -
191C ALA* 5.0 3.4 - - + -
192C TYR* 1.3 88.5 - - - +
194C THR* 1.3 60.5 + - - +
195C ILE* 4.8 5.6 - - + -
265C TYR 5.0 1.3 - - - +
267C PHE* 3.5 31.0 - - + +
269C PHE* 4.4 9.2 - - + -
297C ILE* 3.9 33.9 - - + -
300C VAL* 4.6 15.5 - - + -
301C THR* 5.3 2.9 - - - +
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Residues in contact with THR 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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65C ASP* 2.7 22.5 + - - -
68C PHE* 4.0 4.5 - - - -
144C ASN* 5.9 0.9 - - - +
192C TYR* 3.5 26.6 + - + -
193C LEU* 1.3 75.2 - - - +
195C ILE* 1.3 62.2 + - - +
196C HIS* 3.5 18.1 + - + +
254C SER* 4.0 7.8 + - - +
255C ASP* 4.3 2.9 - - + -
267C PHE 3.0 8.9 + - - +
268C THR* 3.2 30.1 - - + +
269C PHE* 2.9 25.0 + - - +
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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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64C MET* 3.9 27.4 - - + -
65C ASP* 2.9 19.0 + - - +
66C CYS* 3.6 25.3 - - - -
67C GLY 4.1 2.6 + - - -
68C PHE* 4.9 2.6 + - - +
72C GLU* 4.7 0.3 - - - +
75C SER* 2.7 32.8 + - - +
78C PHE* 4.3 13.0 - - + -
193C LEU* 4.8 0.9 - - + -
194C THR* 1.3 78.2 + - - +
196C HIS* 1.3 66.1 + - - +
269C PHE* 3.8 27.4 - - + -
271C LEU* 3.8 35.0 - - + -
293C THR* 5.5 0.2 - - + -
297C ILE* 4.7 4.5 - - + -
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Residues in contact with HIS 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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68C PHE* 3.7 21.1 - - + +
69C HIS* 3.4 17.0 - + - -
72C GLU* 3.1 8.1 + - - +
75C SER* 4.4 6.5 - - - -
144C ASN* 3.7 22.0 + - - -
194C THR* 3.5 22.8 + - - +
195C ILE* 1.3 81.0 - - - +
197C SER* 1.3 63.2 + - - +
268C THR* 3.9 17.0 - - + -
269C PHE 2.7 10.4 + - - +
270C GLU* 3.3 20.9 - - - +
271C LEU* 3.0 27.5 + - - +
600C ZN 2.1 31.3 - - - -
601C 235 3.4 5.2 + - + +
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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