Contacts of the strand formed by residues 179 - 192 (chain C) in PDB entry 5J0Z
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 ARG 179 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL* 5.3 0.4 - - - +
91B ASP* 3.9 16.2 + - - -
93B SER* 4.1 14.5 + - - -
101B GLN* 6.3 0.4 - - - +
133C ARG* 3.7 32.3 - - - +
134C SER* 3.8 18.9 + - - +
135C VAL* 3.6 8.7 - - - +
136C ASP* 3.0 53.9 + - - +
175C ALA* 3.5 4.6 - - - -
176C LEU* 2.9 28.8 + - - +
177C GLU 2.9 9.5 + - - +
178C ASP* 1.3 79.5 - - + +
180C LEU* 1.3 64.3 + - - +
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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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133C ARG* 4.0 4.5 - - - +
134C SER* 3.0 53.9 + - - +
139C ASN* 4.0 29.1 + - + +
140C ILE 3.6 15.3 - - - +
141C VAL* 5.0 3.8 - - + -
173C ASN* 4.2 20.9 - - + +
174C PHE* 3.4 15.5 - - - +
175C ALA* 4.5 1.1 - - - +
179C ARG* 1.3 77.5 - - - +
181C GLU* 1.3 74.2 - - - +
182C SER* 4.1 1.1 - - - +
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Residues in contact with GLU 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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42B PHE* 3.6 10.5 - - - -
77C ARG* 3.6 18.0 + - - -
131C ILE* 3.5 30.9 - - + +
132C VAL 3.5 18.4 - - - +
133C ARG* 3.3 34.9 + - - -
173C ASN* 3.4 3.8 - - - +
174C PHE* 2.8 47.9 + - + +
176C LEU* 3.6 27.9 - - + +
180C LEU* 1.3 76.4 - - - +
182C SER* 1.3 57.9 + - - +
183C LYS 4.2 0.4 - - - -
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Residues in contact with SER 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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131C ILE* 3.4 1.3 - - - -
132C VAL* 3.1 34.4 + - - -
140C ILE 3.6 21.3 - - - -
141C VAL* 3.7 6.1 - - - -
142C LEU* 3.1 29.8 + - - +
171C PRO* 3.7 6.8 - - - +
173C ASN* 2.9 26.5 + - - -
180C LEU* 4.1 1.0 - - - +
181C GLU* 1.3 72.1 - - - +
183C LYS* 1.3 58.7 + - - +
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Residues in contact with LYS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ASN* 4.6 6.7 - - - +
154B ASP* 3.4 29.1 + - - -
79C VAL* 4.5 9.2 - - - -
129C TYR* 3.6 33.5 - - + -
130C LEU 3.3 8.1 - - - +
131C ILE* 3.8 16.6 - - + -
171C PRO* 3.4 21.2 - - - +
172C ALA* 3.4 20.7 + - - +
173C ASN* 3.6 0.2 + - - -
174C PHE* 4.1 21.1 - - + -
182C SER* 1.3 74.1 + - - +
184C LEU* 1.3 69.7 + - - +
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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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20C THR* 3.0 31.0 - - + +
129C TYR* 3.6 6.4 - - - +
130C LEU* 2.7 37.8 + - + +
142C LEU* 3.7 28.3 - - + +
143C ALA* 4.0 9.6 - - - +
144C VAL* 3.7 14.4 - - + -
168C VAL 3.2 26.7 - - - +
169C VAL 4.0 8.3 - - - +
171C PRO* 4.1 13.9 - - + -
183C LYS* 1.3 82.2 - - - +
185C ASP* 1.3 62.5 + - - +
186C TYR* 4.1 13.5 - - + -
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Residues in contact with ASP 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C HIS* 3.2 14.0 + - - -
129C TYR* 3.4 26.6 + - + -
167C ALA* 3.5 1.4 - - - +
168C VAL* 3.0 40.8 + - + +
184C LEU* 1.3 82.2 - - - +
186C TYR* 1.3 65.6 + - - +
187C GLN* 3.1 38.2 + - - +
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Residues in contact with TYR 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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20C THR* 2.8 40.0 + - - -
21C GLY 3.5 0.2 + - - -
22C ILE* 3.6 39.0 - - + -
127C HIS* 3.4 3.3 - - - -
128C ILE* 2.9 46.4 + - + +
130C LEU* 3.6 20.0 - - + -
144C VAL* 4.5 3.0 - - + +
149C VAL* 3.9 13.7 - - + +
165C PHE* 3.7 29.5 - + + -
166C THR 3.7 4.0 - - - -
167C ALA* 3.8 23.1 - - + +
184C LEU* 4.1 18.5 - - + +
185C ASP* 1.3 84.3 - - - +
187C GLN* 1.3 58.7 + - - +
188C LEU 4.2 0.5 + - - -
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Residues in contact with GLN 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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125C THR* 4.3 4.4 - - + +
126C LEU 3.4 5.6 - - - +
127C HIS* 3.7 18.2 - - + +
164C SER 3.5 2.3 - - - +
165C PHE* 3.5 7.6 - - - -
166C THR* 2.9 38.1 + - - +
168C VAL* 3.3 24.2 - - + +
185C ASP* 3.1 38.6 + - - +
186C TYR* 1.3 71.8 - - - +
188C LEU* 1.3 60.9 + - - +
189C ARG* 3.1 39.2 + - - +
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Residues in contact with LEU 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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24C LEU* 4.2 19.5 - - + -
27C CYS* 3.8 28.5 - - + -
37C PHE* 4.4 12.1 - - + -
125C THR* 4.5 0.2 - - - -
126C LEU* 2.6 69.5 + - + +
128C ILE* 5.8 4.0 - - + +
151C LYS* 5.1 0.2 - - + -
157C LEU* 5.6 1.3 - - + -
162C ILE* 3.5 31.6 - - + -
164C SER 3.5 11.2 - - - +
165C PHE* 3.7 16.0 - - + -
186C TYR 4.2 0.4 + - - -
187C GLN* 1.3 70.9 - - - +
189C ARG* 1.3 58.2 + - - +
190C ILE* 4.5 7.6 - - + -
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Residues in contact with ARG 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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123C SER* 6.5 0.4 - - - -
124C GLN 3.2 6.7 - - - +
125C THR* 3.4 33.3 + - - +
162C ILE* 3.8 2.1 - - - +
163C GLU* 2.9 37.2 + - + +
164C SER* 3.0 27.6 + - - +
166C THR* 3.0 27.3 + - - +
187C GLN* 3.1 38.5 + - - +
188C LEU* 1.3 73.4 - - - +
190C ILE* 1.3 63.7 + - - +
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Residues in contact with ILE 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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30C LEU* 3.3 34.3 - - + -
123C SER* 3.2 5.5 - - - -
124C GLN* 2.7 55.3 + - + +
126C LEU* 3.8 19.1 - - + -
157C LEU* 3.9 12.6 - - + -
160C TRP* 3.6 21.1 - - + -
161C ASP 3.2 15.0 - - - +
162C ILE* 3.9 20.2 - - + -
163C GLU* 3.8 4.7 - - - -
188C LEU* 4.5 9.2 - - + -
189C ARG* 1.3 82.0 - - - +
191C SER* 1.3 60.3 + - - +
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Residues in contact with SER 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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122C ASP 3.8 0.7 - - - -
123C SER* 3.0 21.1 - - - +
160C TRP* 3.4 5.2 - - - -
161C ASP* 2.7 51.4 + - - +
163C GLU* 3.4 16.0 + - - -
190C ILE* 1.3 73.5 - - - +
192C ARG* 1.3 64.5 + - - +
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Residues in contact with ARG 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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32C ASP* 2.6 36.3 + - - -
116C PHE* 3.5 12.5 - - - -
119C TYR* 3.5 17.4 - - - -
120C PRO* 3.7 19.9 - - - +
121C PHE* 5.5 1.6 - - - -
122C ASP* 2.8 55.8 + - - +
159C GLY 3.6 9.3 + - - +
160C TRP* 3.2 44.3 - - + +
161C ASP* 4.8 1.7 - - - +
191C SER* 1.3 76.2 + - - +
193C GLN* 1.3 67.6 + - - +
194C TYR* 3.1 18.5 + - - +
197C TYR* 4.0 24.3 + - + -
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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