Contacts of the strand formed by residues 169 - 179 (chain C) in PDB entry 1QD6
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 TRP 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C TRP* 3.6 27.4 - + + -
165C GLU* 3.3 8.1 - - - +
166C ASN* 3.0 39.6 + - + +
167C GLY 4.3 1.2 - - - +
168C ASN* 1.3 82.4 - - + +
170C LEU* 1.3 61.6 + - - +
171C VAL* 5.4 0.9 - - + -
199C ILE* 3.6 26.7 - - + -
200C GLY 3.5 15.3 - - - -
201C TYR* 3.3 41.4 - + + -
269C PHE* 4.0 3.2 - - - -
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Residues in contact with LEU 170 (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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15A ARG 4.2 2.5 - - - +
16A GLY* 4.0 15.9 - - - +
131C TRP* 4.6 0.4 - - - -
163C MET* 3.9 34.8 - - + -
164C ALA 3.5 4.5 - - - -
165C GLU* 4.8 2.0 - - + -
169C TRP* 1.3 75.8 - - - +
171C VAL* 1.3 77.8 + - - +
172C GLU* 4.2 9.9 - - + +
198C LYS* 4.8 2.7 - - + +
199C ILE* 3.4 2.8 - - - +
200C GLY* 2.8 37.1 + - - +
268C LEU* 4.4 17.5 - - + +
269C PHE* 3.7 44.9 - - + -
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Residues in contact with VAL 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TRP* 3.7 29.8 - - + -
162C LEU 3.8 0.7 - - - +
163C MET* 3.5 2.1 - - - +
164C ALA* 2.8 36.7 + - + +
169C TRP* 5.4 1.8 - - + -
170C LEU* 1.3 81.3 - - - +
172C GLU* 1.3 66.2 + - - +
173C VAL* 4.7 5.6 - - + -
197C LEU* 3.9 23.6 - - + -
198C LYS 3.3 3.8 - - - +
199C ILE* 4.4 16.8 - - + -
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Residues in contact with GLU 172 (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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18A ILE* 4.9 4.5 - - - +
161C ARG* 3.0 52.1 + - + +
162C LEU 3.2 11.2 - - - +
163C MET* 4.6 4.8 - - + +
170C LEU* 4.4 10.9 - - + +
171C VAL* 1.3 75.0 - - - +
173C VAL* 1.3 66.1 + - - +
174C LYS* 4.9 5.4 - - + +
196C GLN* 3.7 6.1 + - - +
197C LEU* 3.5 5.5 - - - +
198C LYS* 2.8 83.6 + - + +
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Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ARG* 3.6 0.3 - - - -
162C LEU* 2.9 61.6 + - + +
171C VAL* 4.3 6.9 - - + -
172C GLU* 1.3 74.1 - - - +
174C LYS* 1.3 61.3 + - - +
175C PRO* 3.5 10.9 - - + +
195C TYR* 6.0 4.7 - - + -
196C GLN 3.6 3.8 - - - +
197C LEU* 3.6 25.6 - - + -
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Residues in contact with LYS 174 (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 TYR* 4.2 10.3 + - - -
115C GLU* 4.4 6.6 + - - -
117C GLN* 2.8 29.0 + - - +
141C ASN* 4.1 8.7 - - - +
157C ARG* 5.5 3.8 - - - +
159C TYR* 3.5 35.9 - - + -
160C THR 3.2 10.8 - - - +
161C ARG* 4.5 15.7 - - + +
172C GLU* 4.9 6.3 - - - +
173C VAL* 1.3 73.7 - - - +
175C PRO* 1.3 59.9 - - - +
176C TRP* 3.2 17.5 - - + -
195C TYR* 3.2 3.7 - - - +
196C GLN* 2.9 55.1 + - + +
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Residues in contact with PRO 175 (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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159C TYR* 3.2 5.5 - - - +
160C THR* 3.0 48.4 + - + +
162C LEU* 5.3 5.4 - - + -
173C VAL* 3.5 15.3 - - + +
174C LYS* 1.3 88.6 - - - +
176C TRP* 1.3 61.2 + - - +
194C TYR 3.4 9.0 - - - +
195C TYR* 3.8 9.4 - - + -
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Residues in contact with TRP 176 (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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155C TRP* 3.7 22.1 - + - -
157C ARG* 3.5 46.7 - - + -
158C LEU 3.2 12.3 - - - +
159C TYR* 3.8 8.5 - - + +
174C LYS* 3.2 30.5 - - + -
175C PRO* 1.3 76.0 - - - +
177C TYR* 1.3 62.2 + - - +
178C VAL* 4.4 8.2 - - + +
192C MET 3.7 10.8 - - - -
193C GLY 3.1 26.8 + - - -
194C TYR* 2.7 36.5 + + + +
195C TYR* 3.5 17.5 - - - -
196C GLN* 3.5 29.2 - - + -
213C GLN* 3.8 16.6 - - - -
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Residues in contact with TYR 177 (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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157C ARG* 3.4 2.2 - - - -
158C LEU* 2.8 49.1 + - + +
176C TRP* 1.3 75.0 - - - +
178C VAL* 1.3 76.1 + - - +
179C VAL* 3.5 28.5 + - + +
194C TYR* 5.7 4.0 - + - -
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Residues in contact with VAL 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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155C TRP* 3.6 26.2 - - + -
156C ASN 3.4 13.2 - - - +
157C ARG* 4.2 2.5 - - + -
176C TRP* 4.2 5.1 - - + -
177C TYR* 1.3 93.4 - - + +
179C VAL* 1.3 68.9 + - - +
180C GLY 5.3 0.4 - - - +
182C THR* 3.6 31.0 - - + -
188C ILE* 5.5 0.7 - - + -
189C THR* 3.3 33.9 - - + -
194C TYR* 5.3 4.3 - - + -
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Residues in contact with VAL 179 (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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140C TYR* 4.8 7.2 - - + -
156C ASN* 3.0 41.9 + - + +
157C ARG 4.4 2.7 - - - +
158C LEU* 3.8 29.4 - - + -
177C TYR* 3.6 31.4 - - + +
178C VAL* 1.3 84.8 - - - +
180C GLY* 1.3 67.3 + - - +
181C ASN 4.6 1.0 - - - +
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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