Contacts of the strand formed by residues 179 - 189 (chain C) in PDB entry 1XHU
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 ASP 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C LYS* 3.4 23.3 - - + +
20C VAL* 3.2 13.2 - - - +
21C LYS* 3.1 39.5 + - - +
175C LEU* 5.5 1.6 - - - -
176C ASN 2.6 26.0 + - - +
178C GLU* 1.3 92.4 - - - +
180C LEU* 1.3 63.1 + - - +
181C VAL* 3.1 8.0 + - - +
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Residues in contact with LEU 180 (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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19C LYS* 3.1 3.6 - - - -
20C VAL* 2.8 46.9 + - + +
21C LYS 3.9 0.2 - - - +
22C ARG* 3.3 34.8 - - + +
23C PRO* 4.7 2.0 - - + -
28C LEU* 4.4 8.3 - - + -
33C ALA* 3.7 24.5 - - - +
37C PHE* 3.2 18.7 - - + -
173C TRP* 3.4 46.2 - - + -
174C GLU 4.0 6.3 - - - -
175C LEU* 4.7 7.2 - - + +
176C ASN 4.9 0.9 - - - +
178C GLU 4.7 0.2 - - - +
179C ASP* 1.3 70.2 - - - +
181C VAL* 1.3 59.2 + - - +
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Residues in contact with VAL 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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17C GLY* 3.3 37.5 - - - +
18C GLN 3.3 1.1 - - - +
19C LYS* 3.3 35.0 - - + -
173C TRP* 3.1 21.5 - - - +
174C GLU 3.2 12.2 + - - +
176C ASN* 3.8 23.1 - - + +
179C ASP 3.1 18.8 - - - +
180C LEU* 1.3 74.3 - - - +
182C CYS* 1.3 70.3 + - - +
183C VAL* 3.3 6.3 - - + +
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Residues in contact with CYS 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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15C LEU* 3.5 23.1 - - + +
16C ILE* 4.0 14.8 - - - +
17C GLY* 3.4 15.2 + - - -
18C GLN* 3.2 12.1 + - + +
37C PHE* 3.7 7.1 - - + -
171C VAL* 4.1 20.0 - - + -
172C ASP 3.0 10.3 - - - +
173C TRP* 4.1 2.7 - - - +
181C VAL* 1.3 79.7 - - - +
183C VAL* 1.3 76.4 + - - +
184C SER 3.3 25.1 - - - -
185C THR* 3.9 9.9 - - - -
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Residues in contact with VAL 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 4.1 23.7 - - - +
133C ILE* 4.3 18.4 - - + -
172C ASP* 2.6 23.6 + - + +
174C GLU* 3.9 29.8 - - + +
181C VAL* 3.3 14.1 - - + +
182C CYS* 1.3 83.2 - - - +
184C SER* 1.3 74.6 + - - +
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Residues in contact with SER 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASN* 4.6 0.4 - - - -
16C ILE* 4.2 6.9 - - - +
171C VAL 3.9 0.3 - - - -
172C ASP* 2.9 45.5 + - - +
182C CYS* 3.3 6.4 - - - -
183C VAL* 1.3 97.0 + - - +
185C THR* 1.3 69.2 + - - +
213C ARG* 5.5 12.9 + - - -
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Residues in contact with THR 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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8C TYR* 3.1 18.3 + - + +
11C ILE* 5.6 0.4 - - + -
12C ASN* 2.9 34.2 + - - +
15C LEU* 4.8 10.4 - - + +
16C ILE* 4.2 4.3 - - - +
169C LEU* 3.3 27.6 - - + -
170C GLU 3.2 16.3 + - - +
171C VAL* 5.1 1.0 - - + +
172C ASP* 3.8 2.4 + - - -
182C CYS* 3.9 11.3 - - - -
184C SER* 1.3 81.4 + - - +
186C SER* 1.3 70.5 + - - +
213C ARG* 5.8 0.3 + - - -
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Residues in contact with SER 186 (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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8C TYR* 3.3 3.4 - - - -
169C LEU* 3.3 2.0 - - - -
170C GLU* 2.7 37.6 + - - +
172C ASP* 5.0 1.1 + - - -
185C THR* 1.3 84.4 + - - +
187C PHE* 1.3 61.3 + - - +
212C VAL* 2.8 12.1 - - - +
213C ARG* 3.0 56.2 + - - +
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Residues in contact with PHE 187 (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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2C SER* 3.1 31.0 - - - -
4C ILE* 3.4 27.6 - - + -
5C LYS* 3.5 26.2 - - + -
8C TYR* 3.5 33.4 + + + -
124C GLU* 4.5 0.2 - - - -
126C LEU* 5.1 1.6 - - + -
167C ASN* 3.5 34.1 - - + -
168C TYR 3.7 9.9 - - - -
169C LEU* 3.9 5.2 - - + -
186C SER* 1.3 71.6 - - - +
188C ALA* 1.3 62.0 + - - +
189C GLU* 3.5 25.0 - - + +
212C VAL* 4.3 0.2 - - - -
217C GLN* 5.6 0.3 - - - +
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Residues in contact with ALA 188 (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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167C ASN* 3.7 5.5 - - - +
168C TYR* 3.2 31.6 + - + +
187C PHE* 1.3 77.9 - - - +
189C GLU* 1.3 67.1 + - - +
190C LEU 4.1 0.9 - - - -
210C PHE* 5.8 0.4 - - + -
212C VAL* 3.6 30.0 - - + +
215C LEU* 4.2 16.6 - - + -
217C GLN* 3.4 17.5 - - - +
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Residues in contact with GLU 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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2C SER* 3.5 18.6 + - - -
5C LYS* 4.3 7.3 - - - +
165C ASP* 4.7 9.6 - - - +
167C ASN* 3.4 19.7 + - - +
187C PHE* 3.5 25.8 - - + +
188C ALA* 1.3 77.9 - - - +
190C LEU* 1.3 68.0 + - - +
191C PHE* 3.3 2.2 - - + +
192C LYS* 2.8 64.3 + - + +
193C SER* 3.1 2.9 + - - -
215C LEU* 4.9 0.4 - - - -
217C GLN* 2.7 23.9 + - - +
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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