Contacts of the strand formed by residues 172 - 181 (chain C) in PDB entry 2XTJ
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 TYR 172 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LYS* 5.2 0.2 - - - -
104B GLU* 2.6 40.5 + - - +
137C ASN* 3.2 1.2 - - - -
138C PHE* 2.8 51.4 + - + +
139C TYR* 3.9 20.9 - + - -
140C PRO 4.2 0.7 - - - -
141C ARG* 3.7 46.2 - - + +
162C VAL* 3.8 19.3 - - + -
163C THR* 3.3 22.7 - - - -
164C GLU* 4.8 0.4 - - - -
165C GLN* 3.5 40.9 + - + -
171C THR* 1.3 72.8 - - - +
173C SER* 1.3 67.9 + - - +
182E HIS* 6.1 0.2 - - - -
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Residues in contact with SER 173 (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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135C LEU 3.2 12.3 - - - -
136C ASN* 3.7 2.6 - - - -
137C ASN* 2.8 24.7 + - - -
138C PHE* 3.7 3.6 - - - -
162C VAL* 3.4 2.6 - - - -
163C THR* 2.9 36.0 + - - -
171C THR* 5.1 0.2 + - - -
172C TYR* 1.3 73.5 + - - +
174C LEU* 1.3 59.7 + - - +
182E HIS* 3.2 35.4 + - - -
184E PHE* 3.1 15.2 - - - -
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Residues in contact with LEU 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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134C LEU* 3.5 4.0 - - - +
135C LEU* 2.7 46.5 + - + +
138C PHE* 3.5 22.6 - - + -
141C ARG 5.7 1.1 - - - +
143C ALA* 4.7 15.5 - - + +
145C VAL* 4.1 20.6 - - + -
160C GLU* 3.7 24.9 - - + +
161C SER 3.3 12.1 - - - +
162C VAL* 3.9 17.7 - - + -
173C SER* 1.3 74.9 - - - +
175C SER* 1.3 78.4 + - - +
176C SER* 3.7 14.6 - - - +
184E PHE* 3.6 2.5 - - - -
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Residues in contact with SER 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 4.8 8.7 - - - -
133C CYS 3.4 7.6 - - - -
134C LEU* 4.9 3.6 - - - -
159C GLN 3.9 0.3 - - - +
160C GLU* 3.3 4.2 - - - -
161C SER* 3.0 33.7 + - - -
174C LEU* 1.3 77.6 - - - +
176C SER* 1.3 59.5 + - - +
177C THR* 5.0 3.3 + - - -
184E PHE* 3.4 28.1 - - - +
197E SER* 3.1 25.8 + - - -
199E VAL* 6.2 1.1 - - - -
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Residues in contact with SER 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 3.3 4.9 - - - +
133C CYS* 2.7 42.2 + - - +
145C VAL* 4.0 24.4 - - - +
147C TRP* 3.1 23.1 + - - -
158C SER* 4.1 4.3 - - - -
159C GLN 3.3 11.5 + - - -
160C GLU* 4.1 9.2 + - - +
174C LEU* 3.7 10.2 - - - +
175C SER* 1.3 73.1 - - - +
177C THR* 1.3 64.3 + - - +
178C LEU 4.2 0.7 - - - -
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Residues in contact with THR 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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130C SER* 4.0 22.2 - - - +
131C VAL 3.3 6.3 - - - +
132C VAL* 3.9 14.1 - - + +
147C TRP* 4.3 0.2 - - - -
158C SER* 3.3 6.4 - - - -
159C GLN* 3.0 38.4 + - - +
175C SER* 5.0 5.4 + - - -
176C SER* 1.3 75.0 + - - +
178C LEU* 1.3 69.2 + - - +
179C THR* 3.9 8.4 + - - +
159E LEU* 4.9 9.3 - - + +
161E LYS* 6.3 0.7 - - - -
187E VAL* 6.2 3.4 - - - -
189E GLN* 6.1 1.6 - - - +
195E SER* 5.7 3.6 - - - +
197E SER* 5.1 3.3 + - - -
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Residues in contact with LEU 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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129C ALA 3.8 0.5 - - - +
130C SER* 3.4 5.9 - - - -
131C VAL* 2.8 44.5 + - + +
147C TRP* 3.6 47.1 - - + +
149C VAL* 3.8 26.7 - - + -
154C GLN* 3.8 13.0 - - + -
157C ASN* 3.4 38.1 - - - +
158C SER* 4.4 1.1 - - - +
177C THR* 1.3 72.2 - - - +
179C THR* 1.3 68.5 + - - +
180C LEU* 4.2 15.9 + - + -
191C TYR* 4.7 2.7 - - + -
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Residues in contact with THR 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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128C THR* 6.0 5.2 - - + -
129C ALA 3.7 3.8 - - - +
130C SER* 4.1 12.0 + - - -
157C ASN* 3.5 30.9 + - - +
159C GLN* 5.9 1.2 + - - -
177C THR* 3.9 8.6 + - - +
178C LEU* 1.3 74.9 + - - +
180C LEU* 1.3 77.2 + - - +
161E LYS* 5.0 6.2 + - - +
189E GLN* 4.9 9.0 + - - -
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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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128C THR* 4.2 5.6 - - - +
129C ALA* 3.1 32.4 + - + +
131C VAL* 4.8 5.4 - - + -
149C VAL* 4.9 4.7 - - + -
154C GLN* 4.2 21.5 - - - +
157C ASN* 4.5 4.3 - - - +
178C LEU* 4.2 15.5 + - + -
179C THR* 1.3 87.9 - - - +
181C SER* 1.3 67.1 + - - +
184C ASP* 4.4 18.4 - - + +
185C TYR* 4.3 14.1 - - + +
188C HIS* 6.2 2.2 - - + +
191C TYR* 3.5 38.4 - - + +
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Residues in contact with SER 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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127C GLY 4.7 4.0 - - - -
128C THR* 4.9 6.1 - - - +
129C ALA 4.7 0.7 - - - -
180C LEU* 1.3 75.8 - - - +
182C LYS* 1.3 55.7 + - - +
183C ALA* 4.2 8.0 - - - +
184C ASP* 2.9 27.7 + - - +
185C TYR* 2.7 33.8 + - - +
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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