Contacts of the strand formed by residues 175 - 187 (chain A) in PDB entry 3PIJ
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 VAL 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A CYS* 4.0 18.4 - - - -
171A PRO* 3.9 13.2 - - + +
172A THR 2.9 17.5 + - - +
173A ASP 3.4 1.7 - - - -
174A LYS* 1.3 87.0 - - - +
176A ASP* 1.3 61.8 + - - +
177A HIS 3.5 17.3 + - - +
178A HIS 3.4 25.8 - - - +
179A TYR* 3.8 12.6 - - + -
197A VAL* 3.6 18.2 - - + -
198A SER 3.4 5.6 - - - +
200A ALA* 4.1 5.3 - - - +
207A TRP* 3.7 16.4 - - + -
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Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A VAL* 1.3 70.7 - - - +
177A HIS* 1.3 77.7 + - - +
178A HIS* 2.9 25.8 + - - -
198A SER* 2.8 20.2 + - - +
199A SER 3.4 18.2 + - - +
200A ALA* 4.8 4.7 - - - +
202A LYS* 3.1 36.5 + - + +
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Residues in contact with HIS 177 (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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135A ALA* 4.0 9.8 - - + +
142A GLY 3.6 21.6 + - - -
143A GLY* 4.8 3.8 - - - -
144A ASP* 3.0 47.5 + - + +
145A TRP* 4.8 0.3 - - - -
146A GLN* 4.0 8.8 + - - +
170A CYS* 5.1 3.1 - - - -
175A VAL* 3.4 11.1 + - - +
176A ASP* 1.3 95.9 + - - +
178A HIS* 1.3 70.0 + - + +
179A TYR* 3.3 9.7 + - - +
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Residues in contact with HIS 178 (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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144A ASP* 3.6 15.3 + - - -
146A GLN* 4.0 0.2 - - - -
175A VAL* 3.4 7.8 - - - +
176A ASP* 2.9 24.2 + - - -
177A HIS* 1.3 70.7 - - + +
179A TYR* 1.3 64.4 + - - +
180A ARG* 3.0 35.2 + - - +
197A VAL* 3.4 5.3 - - - -
198A SER* 3.2 33.2 + - - -
232A PHE* 3.8 28.7 - + - -
233A MET* 3.5 25.6 - - + -
258A MET* 5.0 4.5 - - + -
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Residues in contact with TYR 179 (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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4A PHE* 3.4 19.4 - - - -
130A THR* 4.0 0.2 - - - +
146A GLN* 3.1 44.1 + - + +
148A GLN* 2.8 26.4 + - - -
168A ILE* 3.5 7.6 - - + +
169A ASP 2.9 31.2 + - - -
170A CYS* 3.7 11.7 - - + -
171A PRO* 3.8 9.6 - - + -
175A VAL* 3.8 18.8 - - + -
177A HIS 3.8 8.1 - - - +
178A HIS* 1.3 74.7 - - - +
180A ARG* 1.3 64.6 + - - +
195A PHE* 3.4 35.9 - + - -
196A GLY 3.4 7.2 + - - -
197A VAL* 3.8 7.0 - - + -
207A TRP* 3.8 19.6 - + - -
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Residues in contact with ARG 180 (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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113A PHE* 4.2 3.5 - - - -
130A THR* 3.3 19.7 - - + +
144A ASP* 3.4 12.2 + - - -
146A GLN* 2.9 32.3 + - - +
148A GLN* 3.8 3.3 - - - +
178A HIS* 3.0 41.0 + - - +
179A TYR* 1.3 74.8 - - - +
181A ASP* 1.3 77.5 + - - +
195A PHE* 3.7 6.0 - - - -
196A GLY* 2.9 32.5 + - - +
233A MET* 3.6 14.8 - - + +
235A GLU* 2.8 27.1 + - - +
237A PRO* 4.3 0.2 - - - +
258A MET* 3.8 10.3 - - - +
527A FRU 2.9 34.0 + - - -
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Residues in contact with ASP 181 (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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114A SER* 3.5 17.6 + - - -
115A GLY* 5.4 0.4 - - - -
130A THR* 2.8 13.3 + - - -
180A ARG* 1.3 82.2 - - - +
182A PRO* 1.3 69.7 - - - +
183A LYS 3.7 0.2 + - - -
195A PHE* 3.6 5.0 - - - +
235A GLU* 3.6 4.0 - - - -
236A CYS* 2.9 37.6 + - - +
237A PRO* 3.3 19.1 - - + +
527A FRU 2.5 51.5 + - - -
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Residues in contact with PRO 182 (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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114A SER 3.7 12.3 - - - +
115A GLY* 4.2 2.5 - - - -
116A SER* 2.9 24.4 + - - -
128A TYR* 3.7 13.5 - - + -
129A TYR* 3.7 25.1 - - - +
130A THR* 3.4 12.8 - - - +
148A GLN* 3.6 12.8 - - + +
181A ASP* 1.3 91.2 - - - +
183A LYS* 1.3 59.8 + - - +
193A MET* 4.0 26.2 - - + -
194A THR 3.3 7.0 - - - +
195A PHE* 3.9 3.4 - - + -
305A GLN* 5.5 0.5 + - - -
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Residues in contact with LYS 183 (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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116A SER* 3.9 10.1 - - - +
181A ASP 3.7 0.4 + - - +
182A PRO* 1.3 75.0 - - - +
184A VAL* 1.3 67.2 + - - +
185A TRP* 3.6 24.4 - - + -
193A MET* 3.2 3.3 - - - -
194A THR* 2.8 40.2 + - + +
237A PRO 4.1 13.9 - - - +
238A ASP* 2.9 32.0 + - - +
239A PHE* 3.4 28.5 - - + +
240A SER* 5.0 1.6 - - - -
305A GLN* 5.8 0.6 - - - +
306A SER* 3.3 27.1 + - - +
307A PHE* 4.9 1.4 - - - +
313A GLN* 4.1 6.1 + - - -
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Residues in contact with VAL 184 (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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116A SER* 4.3 4.8 + - - -
118A VAL* 4.0 20.7 - - + +
128A TYR* 3.5 46.0 - - + +
183A LYS* 1.3 83.6 - - - +
185A TRP* 1.3 67.5 + - - +
191A TRP* 3.8 20.2 - - + -
192A TYR 3.2 10.8 - - - +
193A MET* 3.7 32.1 - - + -
214A MET* 4.3 0.2 - - + -
217A TRP* 3.8 11.9 - - + -
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Residues in contact with TRP 185 (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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118A VAL* 4.9 2.2 - - - -
183A LYS* 3.6 40.2 - - + -
184A VAL* 1.3 77.9 - - - +
186A LYS* 1.4 61.5 + - - +
187A THR* 3.1 28.3 + - - -
191A TRP* 3.5 12.8 - - - -
192A TYR* 2.8 55.6 + - + +
193A MET 4.0 1.8 - - - -
194A THR* 3.7 25.1 - - + -
208A LEU* 3.8 15.5 - - + -
223A LEU* 4.8 0.9 - - + -
239A PHE* 3.4 39.7 - + + +
241A PRO* 6.2 0.9 - - + -
251A TRP* 3.9 11.0 - + - -
280A TRP* 3.7 19.6 - + - -
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Residues in contact with LYS 186 (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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121A ASP* 3.6 28.2 + - - +
185A TRP* 1.4 79.1 - - - +
187A THR* 1.3 65.4 + - - +
188A GLY 3.4 21.3 - - - +
189A ASP* 3.5 29.1 + - - +
190A THR 3.5 10.8 - - - +
191A TRP* 3.4 44.0 - - + +
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Residues in contact with THR 187 (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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185A TRP* 3.1 26.8 + - - -
186A LYS* 1.3 71.5 + - - +
188A GLY* 1.3 69.4 + - - +
189A ASP 3.3 0.3 + - - -
190A THR* 3.1 25.4 + - - +
192A TYR* 3.9 15.7 + - - -
249A GLU* 6.1 0.4 - - - +
251A TRP* 3.7 14.9 - - + -
280A TRP* 3.6 8.1 - - + -
282A PRO* 3.4 32.2 - - + +
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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