Contacts of the strand formed by residues 172 - 185 (chain A) in PDB entry 5H9U
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 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A TYR* 5.7 2.4 - - - -
160A LEU* 4.2 15.0 - - + +
163A VAL* 3.6 31.9 - - + -
164A ARG* 3.5 26.6 - - + +
169A LEU* 3.4 30.1 - - + +
170A PRO 3.2 7.4 - - - +
171A TYR* 1.3 99.2 - - + +
173A ARG* 1.3 61.9 + - - +
199A ALA* 3.7 24.0 - - + -
200A GLN 3.6 14.6 - - - +
201A HIS* 4.4 4.3 - - + -
210A LEU* 4.4 4.9 - - + -
214A LEU* 4.3 3.1 - - + -
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Residues in contact with ARG 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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83A LYS* 3.2 34.6 + - - +
84A TYR* 3.6 29.1 - - + -
160A LEU* 6.2 0.3 - - - +
164A ARG* 3.5 11.1 + - - +
171A TYR 4.1 0.7 - - - +
172A LEU* 1.3 80.2 - - - +
174A PRO* 1.3 77.7 - - + +
175A ASP 3.3 6.5 + - - +
199A ALA* 5.9 0.2 - - - +
200A GLN* 2.7 41.4 + - - +
201A HIS 3.7 14.8 - - - -
202A SER* 3.5 34.9 + - - +
203A PRO* 3.8 6.1 - - - +
244A ILE* 3.1 33.1 + - - +
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Residues in contact with PRO 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 2.7 30.5 + - - +
15A GLY* 3.6 8.9 + - - -
77A VAL 3.3 26.0 - - - +
78A GLY* 3.6 24.9 - - - +
79A TYR* 3.7 27.6 - - + -
84A TYR* 4.5 9.9 - - + -
164A ARG* 3.4 21.3 + - - +
173A ARG* 1.3 90.3 - - + +
175A ASP* 1.3 51.3 + - - +
200A GLN* 3.6 7.6 - - - +
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Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 3.8 2.0 - - - -
15A GLY 4.1 7.4 - - - -
16A HIS* 3.5 27.6 - - - +
17A PRO* 4.1 5.2 - - - +
79A TYR* 3.7 8.9 + - - +
160A LEU* 5.0 1.4 - - - +
173A ARG 3.6 2.8 - - - +
174A PRO* 1.3 81.0 - - - +
176A GLY* 1.3 67.5 + - - +
177A LYS* 5.3 2.0 + - - +
199A ALA* 4.0 1.0 - - - +
200A GLN* 3.0 43.1 + - - +
243A PHE* 3.6 21.3 - - + -
246A GLY* 3.5 4.9 - - - -
247A GLY* 2.7 26.4 + - - +
250A ALA* 5.7 0.5 - - - +
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Residues in contact with GLY 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.4 6.6 - - - +
13A THR* 2.9 42.6 + - - -
16A HIS* 4.5 0.3 - - - +
160A LEU* 4.2 3.4 - - - -
175A ASP* 1.3 85.2 + - - +
177A LYS* 1.3 66.8 + - - +
198A SER 3.1 13.0 - - - -
243A PHE* 4.5 2.9 - - - -
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Residues in contact with LYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER 3.5 5.4 - - - -
12A VAL* 4.0 11.9 - - + +
13A THR* 4.5 0.6 - - - +
16A HIS* 4.5 14.2 + - + +
157A THR* 4.2 3.1 - - - -
160A LEU* 4.6 1.4 - - - +
175A ASP* 5.3 2.1 + - - +
176A GLY* 1.3 79.5 - - - +
178A ALA* 1.3 62.7 + - - +
196A VAL 4.4 0.2 - - - -
197A VAL* 3.5 5.0 - - - +
198A SER* 2.9 50.1 + - - +
243A PHE* 4.9 14.3 - - - -
251A ASP* 5.8 2.0 + - - -
130C ASP* 3.6 29.9 + - - +
131C GLN* 3.6 27.4 - - - +
315C ILE* 4.1 23.6 - - + +
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Residues in contact with ALA 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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10A GLU* 3.3 4.3 - - - +
11A SER 2.9 34.6 + - - +
153A ALA* 4.1 6.0 - - - +
156A LEU* 3.6 31.4 - - + -
157A THR* 3.6 19.9 - - + +
160A LEU* 6.2 0.9 - - + -
177A LYS* 1.3 76.6 - - - +
179A GLN* 1.3 60.8 + - - +
196A VAL 3.2 9.4 - - - +
197A VAL* 4.6 4.9 - - + -
131C GLN* 3.7 2.5 - - - -
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Residues in contact with GLN 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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8A THR* 3.5 24.7 - - + +
9A SER 3.6 12.1 - - - +
10A GLU* 3.4 22.4 + - + -
178A ALA* 1.3 75.3 - - - +
180A VAL* 1.3 67.9 + - - +
181A THR* 5.1 0.8 + - - -
194A THR 3.8 0.9 - - - +
195A VAL* 3.5 5.7 - - - +
196A VAL* 2.9 47.0 + - + +
131C GLN* 3.5 15.1 - - + +
132C GLY 3.7 7.3 + - - +
313C TYR 2.9 24.9 + - - +
314C ALA* 3.6 25.5 + - - +
321C VAL* 4.3 6.5 - - - +
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Residues in contact with VAL 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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7A VAL 3.6 1.6 - - - +
8A THR* 3.2 3.7 - - - -
9A SER 2.9 36.6 + - - +
149A PRO* 4.4 10.0 - - + +
152A LEU* 4.0 12.3 - - + -
153A ALA* 3.9 18.4 - - - +
156A LEU* 3.6 27.1 - - + -
179A GLN* 1.3 80.5 - - - +
181A THR* 1.3 65.1 + - - +
182A VAL* 3.5 25.4 - - + -
192A VAL* 3.9 22.0 - - + -
194A THR 3.5 3.1 - - - +
195A VAL* 5.0 1.3 - - + -
223A ILE* 4.8 3.6 - - + -
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Residues in contact with THR 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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6A LEU* 4.0 36.8 - - + -
7A VAL 3.4 4.3 - - - +
8A THR* 2.6 31.2 + - - +
179A GLN* 4.3 2.1 + - - -
180A VAL* 1.3 72.0 - - - +
182A VAL* 1.3 58.1 - - - +
192A VAL* 3.6 4.0 - - - +
193A LYS* 2.8 35.5 + - + -
194A THR* 2.9 27.5 + - - +
321C VAL* 3.8 19.9 - - - +
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Residues in contact with VAL 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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5A ARG 3.7 0.3 - - - +
6A LEU* 3.5 4.4 - - - -
7A VAL* 2.8 34.8 + - - +
148A LEU* 4.3 7.4 - - + -
149A PRO* 4.2 16.4 - - + -
152A LEU* 4.4 8.5 - - + -
180A VAL* 3.5 26.0 - - + -
181A THR* 1.3 73.2 - - - +
183A VAL* 1.3 76.6 + - - +
184A TYR* 3.6 23.8 + - + -
189A PRO* 3.9 14.4 - - + -
191A TYR 3.6 11.7 - - - +
192A VAL* 4.2 10.5 - - + -
227A TYR* 6.1 0.2 - - + -
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Residues in contact with VAL 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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4A LEU* 3.9 32.1 - - + -
5A ARG 3.6 6.5 - - - +
6A LEU* 3.5 22.2 - - + -
182A VAL* 1.3 72.7 - - - +
184A TYR* 1.3 62.6 + - - +
189A PRO* 3.6 2.6 - - - +
190A LEU* 2.8 32.3 + - + -
191A TYR* 2.9 59.1 + - + +
193A LYS* 3.9 11.7 - - + -
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Residues in contact with TYR 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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3A ALA 3.3 3.5 - - - +
4A LEU* 3.3 3.2 - - - -
5A ARG* 2.9 55.1 + - + +
7A VAL* 3.6 35.4 - - + -
141A GLU* 2.7 30.5 + - - -
147A PRO* 5.3 0.3 - - - +
148A LEU* 3.9 3.6 - - - +
149A PRO* 3.3 20.6 - - + +
182A VAL* 3.6 25.1 - - + -
183A VAL* 1.3 75.0 - - - +
185A GLU* 1.3 59.2 + - - +
186A GLY 3.6 16.6 + - - +
187A ASP* 3.5 25.6 - - - -
188A LYS 3.5 2.9 - - - -
189A PRO* 3.6 21.1 - - + -
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Residues in contact with GLU 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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1A MET 4.1 3.8 - - - +
2A ARG* 2.4 70.4 + - - +
3A ALA 3.3 3.6 - - - -
4A LEU* 3.6 11.7 - - + +
184A TYR* 1.3 71.2 - - - +
186A GLY* 1.3 59.7 + - - +
187A ASP* 3.4 0.5 + - - +
188A LYS* 2.8 32.4 + - - +
190A LEU* 3.6 36.1 - - + +
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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