Contacts of the strand formed by residues 163 - 176 (chain A) in PDB entry 5TJC
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 LEU 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ALA 4.8 0.2 - - - +
133A VAL* 4.1 20.9 - - + -
136A TYR* 3.7 46.0 + - + -
162A GLY* 1.3 74.9 - - - +
164A ALA* 1.3 64.6 + - - +
165A LEU* 3.7 22.4 - - + +
193A ILE 3.5 0.2 - - - +
194A GLN* 3.5 7.3 - - - +
195A VAL* 2.7 59.6 + - + +
233A ILE* 3.6 26.9 - - + -
234A HIS 3.4 6.5 - - - +
235A PHE* 3.8 7.9 - - + -
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLY 4.2 0.2 + - - -
163A LEU* 1.3 74.2 - - - +
165A LEU* 1.3 60.2 + - - +
166A CYS* 3.7 12.8 - - - -
192A CYS* 5.0 0.2 - - - -
193A ILE 3.8 4.0 - - - -
194A GLN* 4.1 19.7 - - - +
233A ILE* 3.3 2.8 - - - -
234A HIS* 2.9 56.1 + - + +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE* 3.6 33.0 - - + -
130A PHE* 5.3 0.2 - - + -
133A VAL* 4.4 5.6 - - + -
163A LEU* 3.7 13.4 - - + +
164A ALA* 1.3 71.8 - - - +
166A CYS* 1.3 60.7 + - - +
167A GLN 4.3 0.2 + - - -
191A ASP 3.9 1.4 - - - +
192A CYS* 3.4 1.0 - - - -
193A ILE* 2.9 45.2 + - + +
195A VAL* 5.2 1.6 - - + -
218A TYR* 4.4 29.6 - - + +
221A LEU* 4.1 26.0 - - + -
231A VAL* 3.9 14.1 - - + -
232A THR 3.6 1.1 - - - -
233A ILE* 3.8 17.0 - - + +
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Residues in contact with CYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 3.9 12.1 - - - -
165A LEU* 1.3 76.1 - - - +
167A GLN* 1.3 60.8 + - - +
168A ARG* 3.9 12.9 + - - +
190A THR* 4.1 3.6 - - + -
191A ASP 3.4 3.6 - - - +
192A CYS* 2.1 47.6 - - - -
231A VAL* 3.2 6.3 - - - +
232A THR* 2.7 51.4 + - - +
234A HIS* 3.6 19.7 - - - -
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Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU 4.3 0.2 + - - -
166A CYS* 1.3 75.0 - - - +
168A ARG* 1.3 62.0 + - - +
169A TYR* 3.6 28.3 - - + -
189A VAL 3.9 0.7 - - - +
191A ASP* 2.9 48.6 + - + +
221A LEU* 3.8 17.2 - - + +
222A THR 3.1 22.8 + - - -
223A LEU* 3.5 22.7 - - + +
224A LYS* 3.1 27.2 + - - +
228A LEU* 4.0 6.0 - - + +
230A ASN 3.5 4.9 - - - +
231A VAL* 4.1 7.0 - - + +
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A CYS* 3.9 15.1 + - - +
167A GLN* 1.3 78.3 - - - +
169A TYR* 1.3 59.4 + - - +
188A VAL* 3.8 18.4 - - + -
189A VAL 3.2 5.8 - - - +
190A THR* 3.5 34.0 + - + +
228A LEU* 3.6 4.5 - - - +
229A VAL* 2.7 35.3 + - + -
230A ASN* 2.8 45.5 + - - +
232A THR* 2.8 35.2 + - - +
234A HIS* 3.7 16.4 + - - -
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Residues in contact with TYR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN* 3.6 37.5 - - + -
168A ARG* 1.3 78.5 - - - +
170A TYR* 1.3 76.2 + - - +
171A HIS* 5.5 1.1 - - - -
188A VAL* 4.4 0.6 - - - +
189A VAL* 2.8 54.6 + - + +
191A ASP* 3.7 23.8 + - + +
224A LYS* 3.5 39.0 - - + -
227A LYS* 3.1 37.2 - - + +
228A LEU* 4.3 2.2 - - - -
229A VAL* 3.9 8.0 - - - +
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Residues in contact with TYR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A TYR* 1.3 78.3 - - - +
171A HIS* 1.3 66.6 + - - +
172A ARG 3.0 13.9 + - - +
173A GLY* 5.5 1.3 - - - -
184A ILE* 4.4 20.2 - - + -
185A ASP 3.6 9.2 - - - +
186A PRO* 3.6 33.7 - - + -
187A MET 3.5 2.7 - - - -
188A VAL* 4.5 6.7 - - + -
227A LYS* 3.0 45.0 + - + +
229A VAL* 3.8 19.9 - - + +
265A LYS 5.2 0.3 + - - -
267A HIS* 2.8 41.7 + + - -
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Residues in contact with HIS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A TYR* 3.5 2.9 + - - -
170A TYR* 1.3 71.8 - - - +
172A ARG* 1.3 65.5 + - + +
185A ASP* 3.5 30.0 + - + +
187A MET* 2.8 34.0 + - + +
189A VAL* 3.6 23.4 - - + +
227A LYS* 3.5 9.6 + - - +
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TYR* 3.0 5.2 - - - +
171A HIS* 1.3 89.2 + - + +
173A GLY* 1.3 60.2 + - - +
174A HIS* 5.0 2.5 - - + +
183A ASP* 2.9 60.9 + - - +
184A ILE* 3.3 8.2 - - - +
185A ASP* 2.9 58.9 + - + +
227A LYS* 4.3 2.0 - - - +
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Residues in contact with GLY 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A TYR* 4.8 1.6 - - - -
172A ARG* 1.3 77.8 - - - +
174A HIS* 1.3 61.3 + - - +
175A VAL* 3.7 6.4 + - - +
183A ASP 3.8 1.6 - - - -
184A ILE* 4.4 8.1 - - - -
226A HIS* 3.2 29.3 + - - -
227A LYS* 3.7 26.8 - - - +
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Residues in contact with HIS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ARG* 5.0 2.4 - - + +
173A GLY* 1.3 70.9 - - - +
175A VAL* 1.3 61.7 + - - +
176A ASP* 3.8 29.2 + - + +
181A THR* 5.0 5.6 + - - -
182A PHE* 3.0 11.7 - - - +
183A ASP* 2.8 57.4 + - + +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A TYR* 6.4 1.3 - - + -
173A GLY* 3.7 11.4 + - - +
174A HIS* 1.3 77.3 + - - +
176A ASP* 1.3 62.6 + - - +
177A PRO* 3.6 19.0 - - + +
181A THR 5.2 0.2 - - - +
182A PHE* 4.2 8.1 - - + -
184A ILE* 4.4 19.1 - - + -
226A HIS* 3.8 28.6 - - + +
227A LYS* 5.5 1.1 - - + -
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Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A HIS* 3.8 24.8 + - + +
175A VAL* 1.3 75.5 - - - +
177A PRO* 1.3 64.0 - - - +
178A ALA* 3.7 15.8 + - - +
179A ASN* 2.9 38.2 + - - +
180A ASP 3.1 4.0 + - - -
181A THR* 3.0 40.6 + - - +
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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