Contacts of the strand formed by residues 175 - 185 (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 GLY 175 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C MET* 4.0 4.9 - - - -
154C TYR* 3.4 13.0 - - - -
155C GLN* 2.8 35.8 + - - +
173C GLY 3.6 0.8 + - - -
174C ASP* 1.3 76.8 - - - +
176C TYR* 1.3 64.2 + - - -
196C SER 3.3 12.3 - - - -
197C SER* 3.4 11.0 - - - -
222C ARG* 5.0 0.2 - - - -
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Residues in contact with TYR 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C MET* 3.7 7.9 - - - +
153C GLN 3.2 13.5 - - - +
154C TYR* 4.2 5.4 - + + -
175C GLY* 1.3 78.6 - - - +
177C GLY* 1.3 59.9 + - - +
194C TYR* 4.7 11.8 + + - -
195C SER* 3.3 2.9 - - - -
196C SER* 2.8 61.5 + - - +
222C ARG* 3.6 19.3 + - - -
408C LDA 4.0 22.4 - - + -
430C LDA 6.0 2.6 - - - +
440C LDA 3.6 55.3 - - + +
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Residues in contact with GLY 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C VAL* 3.6 12.1 - - - -
126C MET* 4.1 1.4 - - - -
152C LEU* 3.7 2.3 - - - +
153C GLN 2.9 30.5 + - - +
176C TYR* 1.3 82.9 - - - +
178C PHE* 1.3 65.0 + - - +
194C TYR* 3.1 14.4 - - - -
195C SER* 3.9 6.3 - - - -
408C LDA 5.6 0.3 - - - +
440C LDA 5.2 2.7 - - - +
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Residues in contact with PHE 178 (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* 3.5 9.0 - - - +
150C PHE* 6.0 1.6 - - + -
151C ALA 3.1 14.4 - - - +
152C LEU* 4.1 6.5 - - + -
177C GLY* 1.3 76.0 - - - +
179C SER* 1.3 72.6 - - - +
180C THR* 4.1 21.5 - - + -
192C GLY 5.1 1.1 - - - -
193C GLY* 3.2 1.7 - - - -
194C TYR* 2.8 69.5 + + + +
429C LDA 4.7 10.3 - - + -
430C LDA 4.0 39.0 - - + -
440C LDA 3.7 48.7 - - + -
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Residues in contact with SER 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C VAL* 3.4 25.3 - - - +
103C ASP* 2.7 28.2 + - - +
104C THR* 5.2 0.4 - - - -
137C ARG* 4.4 0.2 + - - -
150C PHE* 3.2 4.7 - - - +
151C ALA* 2.8 38.2 + - - +
178C PHE* 1.3 81.1 - - - +
180C THR* 1.3 66.4 + - - +
192C GLY 3.3 13.2 - - - -
193C GLY* 4.0 1.3 - - - -
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Residues in contact with THR 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C THR* 4.8 1.2 + - - -
148C LEU* 3.5 19.6 - - - +
149C SER 3.0 14.9 + - - -
150C PHE* 4.1 7.7 - - - +
178C PHE* 4.1 17.7 - - + -
179C SER* 1.3 79.3 - - - +
181C ALA* 1.3 64.6 + - - +
191C GLY* 3.2 3.1 - - - -
192C GLY 2.9 40.8 + - - +
429C LDA 4.7 11.4 - - + -
430C LDA 4.9 9.9 - - + -
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Residues in contact with ALA 181 (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* 3.9 24.0 - - + -
147C GLY 3.7 0.8 - - - +
148C LEU* 3.5 5.5 - - - +
149C SER* 2.8 45.3 + - - +
180C THR* 1.3 75.8 + - - +
182C TYR* 1.3 60.8 + - - +
183C GLU* 6.0 0.4 - - - -
189C THR* 4.2 6.3 - - + -
190C LEU 3.3 10.8 - - - +
191C GLY* 4.1 0.2 - - - -
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Residues in contact with TYR 182 (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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145C VAL* 5.5 3.1 - - + -
146C ASP 3.7 20.9 + - - -
147C GLY 3.5 11.2 - - - -
148C LEU* 3.7 22.0 - - + -
181C ALA* 1.3 75.1 - - - +
183C GLU* 1.3 83.5 + - - +
184C LEU* 3.7 30.5 + - + +
189C THR* 3.3 3.1 - - - -
190C LEU* 2.8 36.8 + - + +
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Residues in contact with GLU 183 (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 ASP 5.1 0.5 - - - +
147C GLY* 3.1 29.2 + - - +
181C ALA 6.0 0.2 - - - -
182C TYR* 1.3 92.1 + - - +
184C LEU* 1.3 62.6 + - - +
185C GLY* 3.7 5.3 + - - +
188C VAL 3.4 10.8 - - - +
189C THR* 3.9 16.6 + - + +
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Residues in contact with LEU 184 (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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182C TYR* 3.7 33.6 + - + +
183C GLU* 1.3 74.0 - - - +
185C GLY* 1.3 60.6 + - - +
186C TRP* 3.7 20.4 - - + -
188C VAL* 3.0 34.2 + - + +
190C LEU* 3.7 34.1 - - + -
418C LDA 5.9 2.5 - - + -
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Residues in contact with GLY 185 (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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183C GLU* 3.4 6.1 - - - +
184C LEU* 1.3 79.5 - - - +
186C TRP* 1.3 74.0 + - - +
187C GLY 3.0 6.1 - - - -
188C VAL* 2.9 26.9 + - - +
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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