Contacts of the strand formed by residues 188 - 198 (chain C) in PDB entry 5NXR
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 188 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C GLU* 3.4 3.5 - - - +
184C LEU* 3.0 52.9 + - + -
185C GLY 2.9 12.6 + - - +
186C TRP* 4.0 9.2 - - + +
187C GLY* 1.3 77.4 - - - +
189C THR* 1.3 71.2 + - - +
190C LEU* 4.6 7.0 - - + -
231C LYS 3.4 7.6 - - - +
232C PHE* 3.7 24.9 - - + -
418C LDA 4.1 37.2 - - + -
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Residues in contact with THR 189 (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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107C TRP* 3.6 28.1 - - + -
181C ALA* 4.2 6.5 - - + -
182C TYR 3.3 17.0 - - - +
183C GLU* 3.9 18.1 + - + +
187C GLY 4.9 2.4 + - - -
188C VAL* 1.3 79.1 + - - +
190C LEU* 1.3 68.9 + - - +
230C GLY* 3.1 4.9 - - - -
231C LYS* 3.0 56.7 + - - -
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Residues in contact with LEU 190 (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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107C TRP* 3.7 3.6 - - - -
181C ALA* 3.3 3.5 - - - +
182C TYR* 2.8 36.1 + - + +
184C LEU* 3.7 34.1 - - + -
188C VAL* 4.6 11.0 - - + -
189C THR* 1.3 79.8 - - - +
191C GLY* 1.3 60.2 + - - +
229C GLY 3.6 5.4 - - - +
230C GLY* 4.3 10.5 - - - -
413C LDA 5.5 6.5 - - + -
418C LDA 5.8 5.6 - - + -
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Residues in contact with GLY 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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104C THR* 4.0 7.0 - - - -
107C TRP* 3.6 10.1 - - - -
180C THR* 3.2 14.4 - - - -
181C ALA* 4.1 0.4 - - - -
190C LEU* 1.3 76.8 - - - +
192C GLY* 1.3 56.9 + - - -
228C VAL* 3.5 3.8 - - - +
229C GLY 2.9 34.2 + - - +
429C LDA 4.3 7.2 - - - +
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Residues in contact with GLY 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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104C THR* 3.3 13.7 + - - -
178C PHE* 5.1 0.4 - - - -
179C SER* 3.3 2.8 - - - -
180C THR* 2.9 33.3 + - - +
191C GLY* 1.3 74.7 - - - -
193C GLY* 1.3 58.0 + - - -
227C ASN 3.0 14.4 - - - -
228C VAL* 4.1 0.2 - - - -
429C LDA 3.7 22.0 - - - +
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Residues in contact with GLY 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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100C VAL 4.6 5.4 - - - -
101C VAL* 4.8 3.8 - - - -
104C THR* 4.5 0.9 - - - -
178C PHE* 3.2 13.0 - - - -
179C SER* 3.9 7.2 - - - -
192C GLY* 1.3 74.3 - - - -
194C TYR* 1.3 60.8 + - - +
226C TRP* 3.2 5.8 - - - +
227C ASN* 2.9 41.3 + - - +
429C LDA 4.0 6.2 - - - +
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Residues in contact with TYR 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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100C VAL* 4.3 0.2 - - - +
101C VAL* 4.0 6.2 - - - +
176C TYR* 4.7 13.9 + + - -
177C GLY* 3.1 3.1 - - - -
178C PHE* 2.8 62.4 + + + +
193C GLY* 1.3 74.8 - - - +
195C SER* 1.3 78.5 + - - +
196C SER* 3.5 19.7 - - - -
224C GLN* 3.2 40.0 + - + -
225C ALA 3.5 5.2 - - - -
226C TRP* 3.7 17.7 - - + -
429C LDA 3.9 24.0 - - + -
430C LDA 3.7 36.6 - - + +
440C LDA 6.1 0.7 - - + -
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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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101C VAL* 3.6 19.7 - - - +
125C PHE* 5.1 3.3 - - - +
126C MET* 3.7 27.4 + - - +
127C THR* 6.0 0.2 - - - +
176C TYR 3.3 12.3 - - - -
177C GLY* 3.9 3.6 - - - -
194C TYR* 1.3 82.8 - - - +
196C SER* 1.3 60.0 + - - +
197C SER* 4.5 2.3 + - - -
223C ALA 5.0 0.7 + - - -
224C GLN* 3.4 11.4 - - - +
225C ALA* 2.8 38.3 + - - +
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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
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175C GLY* 3.3 1.7 - - - -
176C TYR* 2.8 59.9 + - - +
194C TYR* 3.5 22.9 + - - -
195C SER* 1.3 74.2 - - - +
197C SER* 1.3 61.6 + - - +
222C ARG* 3.1 26.6 + - - +
223C ALA 3.6 6.4 + - - -
224C GLN* 4.6 4.8 + - - +
430C LDA 5.2 6.3 - - - -
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Residues in contact with SER 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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125C PHE* 3.6 31.1 - - - -
126C MET* 3.2 30.8 - - - +
155C GLN* 4.8 0.5 + - - -
173C GLY 4.4 1.8 - - - -
174C ASP 3.4 13.9 - - - -
175C GLY* 3.4 3.8 - - - -
195C SER* 4.5 2.1 + - - -
196C SER* 1.3 73.9 + - - +
198C SER* 1.3 58.1 + - - +
222C ARG* 3.5 13.9 - - - +
223C ALA 2.8 35.0 + - - +
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Residues in contact with SER 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PHE* 3.7 6.9 - - - -
173C GLY* 3.0 22.9 + - - -
174C ASP* 2.8 30.3 + - - +
197C SER* 1.3 77.2 - - - +
199C ARG* 1.3 65.0 + - - +
204C LYS* 5.9 1.8 - - - -
221C LYS* 3.9 7.9 - - - -
222C ARG* 3.6 20.2 - - - +
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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