Contacts of the strand formed by residues 189 - 198 (chain C) in PDB entry 3I5D
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 189 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C LYS 3.9 1.0 - - - +
71C VAL* 3.4 3.2 - - - -
72C LYS* 2.8 52.2 + - + +
187C ASN 4.8 3.1 - - - +
188C PHE* 1.3 80.9 - - - +
190C VAL* 1.3 61.7 + - - +
191C LEU 4.2 0.4 + - - -
221C VAL* 5.1 6.7 - - - +
232C ILE* 2.9 30.9 + - + +
233C PHE 3.2 13.1 + - - -
234C ARG* 4.1 4.9 + - - -
235C LEU* 4.4 1.8 - - - +
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Residues in contact with VAL 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C THR* 4.0 7.6 - - - -
70C LYS 3.6 3.4 - - - +
71C VAL* 3.7 19.7 - - + +
102C PHE* 3.7 27.6 - - + -
189C THR* 1.3 72.8 - - - +
191C LEU* 1.3 74.5 + - - +
192C ILE* 3.7 24.4 + - + +
231C PRO 3.6 1.6 - - - +
232C ILE* 3.5 2.8 - - - -
233C PHE* 2.8 40.0 + - + +
235C LEU* 4.1 17.2 - - + +
238C ILE* 4.2 9.4 - - + -
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Residues in contact with LEU 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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291B VAL* 4.0 22.0 - - + -
292B ALA* 3.8 29.2 - - + -
68C THR 3.5 0.9 - - - +
69C THR* 3.2 6.9 - - - -
70C LYS* 2.9 43.8 + - + +
189C THR 4.2 0.8 - - - -
190C VAL* 1.3 74.1 - - - +
192C ILE* 1.3 66.6 + - - +
193C LYS* 3.9 23.3 - - + -
208C ILE* 5.9 1.1 - - + -
231C PRO* 3.9 17.9 - - + +
232C ILE* 3.7 32.3 - - + +
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Residues in contact with ILE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C VAL* 5.3 1.3 - - + -
68C THR 3.5 4.5 - - - +
69C THR* 4.5 6.5 - - + -
102C PHE* 5.2 2.5 - - + -
190C VAL* 3.9 27.4 - - + +
191C LEU* 1.3 79.1 - - - +
193C LYS* 1.3 61.8 + - - +
194C ASN* 5.2 0.7 - - + -
207C ASN* 2.7 29.0 + - - +
231C PRO* 3.2 18.3 + - - +
233C PHE* 3.8 25.8 - - + -
238C ILE* 5.1 1.1 - - + -
258C VAL* 4.3 24.0 - - + -
260C ILE* 4.4 21.8 - - + -
277C TYR* 5.8 0.4 - - + -
324C VAL* 4.5 22.9 - - + -
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Residues in contact with LYS 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ASP* 4.9 9.2 - - - +
284B ASN* 4.8 12.7 + - - +
290B ASN* 3.5 17.8 - - - +
291B VAL 3.5 24.8 + - - +
292B ALA* 4.1 12.2 + - + +
293B PRO* 5.3 0.4 - - - +
294B GLY 5.4 1.8 + - - +
67C VAL* 3.4 5.6 - - - +
68C THR* 2.8 55.0 + - + +
191C LEU* 3.9 24.7 - - + -
192C ILE* 1.3 77.1 - - - +
194C ASN* 1.3 61.2 + - - +
195C ASN 4.3 0.4 - - - -
207C ASN* 3.6 5.4 - - - +
208C ILE* 3.6 26.2 - - + +
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Residues in contact with ASN 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 SER* 3.2 18.2 + - - -
66C SER 2.9 19.2 + - - -
67C VAL* 3.7 12.7 - - + +
192C ILE* 5.1 0.7 - - + +
193C LYS* 1.3 76.2 - - - +
195C ASN* 1.3 64.3 + - - +
196C ILE* 3.4 5.2 + - - +
206C ARG* 3.5 3.6 - - - -
207C ASN* 2.6 47.6 + - + +
260C ILE* 3.8 15.1 - - + +
262C TRP* 3.0 27.5 + - - -
326C VAL* 3.5 14.2 - - - +
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Residues in contact with ASN 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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281B ARG 4.9 0.8 + - - -
282B LEU* 2.9 57.3 + - + +
64C LEU 4.2 0.5 - - - +
65C SER 4.0 0.7 - - - -
66C SER* 3.1 36.6 + - - +
193C LYS 4.3 0.4 - - - -
194C ASN* 1.3 74.6 + - - +
196C ILE* 1.3 87.9 + - - +
197C ARG* 5.3 0.7 - - - +
204C ASN* 4.6 4.5 - - - +
205C LYS 3.5 9.2 + - - +
206C ARG* 4.3 21.0 + - + +
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Residues in contact with ILE 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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63C VAL* 3.4 22.4 - - + -
64C LEU 3.6 4.3 - - - -
65C SER* 3.7 11.7 - - - +
194C ASN* 3.4 18.6 - - - +
195C ASN* 1.3 84.4 + - - +
197C ARG* 1.3 63.2 - - - +
198C TYR* 4.2 23.1 - - + -
203C PHE* 5.1 2.0 - - + -
204C ASN* 3.0 6.5 - - - +
205C LYS* 2.9 50.9 + - + +
262C TRP* 3.5 52.0 - - + +
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Residues in contact with ARG 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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259B GLN* 3.7 32.5 + - - +
327B PHE* 5.4 2.6 - - - -
63C VAL* 3.8 2.2 - - - -
64C LEU* 2.8 49.8 + - + +
195C ASN* 5.3 0.4 - - - +
196C ILE* 1.3 79.5 - - - +
198C TYR* 1.3 71.8 - - - +
199C PRO* 3.5 27.3 + - + +
202C ASN* 3.5 36.1 + - - +
203C PHE 3.4 12.3 - - - +
204C ASN* 3.2 24.4 + - + +
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Residues in contact with TYR 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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61C ASP* 3.3 36.6 - - - +
62C THR 3.7 8.7 - - - -
63C VAL* 3.3 26.9 - - + +
196C ILE* 4.2 13.5 - - + -
197C ARG* 1.3 73.6 - - - +
199C PRO* 1.3 70.8 - - - +
200C LYS 3.3 0.7 - - - -
201C PHE* 3.3 14.4 + + + -
202C ASN* 3.1 18.0 + - - -
203C PHE* 2.7 48.5 + + + +
262C TRP* 2.7 34.4 + - + +
264C CYS* 4.3 8.4 + - + -
329C GLN 3.7 3.4 + - - -
330C ALA* 3.7 26.5 - - + +
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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