Contacts of the strand formed by residues 170 - 179 (chain A) in PDB entry 4X5O
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 GLU 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLY 3.7 3.7 + - - +
62A THR* 4.0 18.1 - - + +
63A ARG* 4.1 19.8 + - - +
65A TYR* 4.8 9.0 + - - -
154A LYS* 3.8 28.9 + - + +
155A VAL 3.8 3.6 - - - -
156A TYR* 3.4 31.9 + - + -
168A TYR* 4.0 9.9 - - - +
169A ARG* 1.3 77.4 - - - +
171A PHE* 1.3 62.1 + - - +
387A GLU* 4.7 1.7 - - - +
94B THR 4.1 2.1 - - - +
95B PRO* 3.3 23.0 - - - +
96B VAL* 2.9 27.6 + - - +
97B PHE* 6.1 0.2 - - - -
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Residues in contact with PHE 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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65A TYR* 5.2 0.2 - - - -
154A LYS* 4.3 5.8 - - - -
155A VAL* 3.1 56.0 + - + +
157A ARG* 3.5 39.7 - - + -
168A TYR* 3.4 32.8 - - + +
169A ARG 4.2 3.1 - - - -
170A GLU* 1.3 76.5 - - - +
172A TYR* 1.3 74.5 + - - +
173A GLN* 3.6 8.5 + - + -
387A GLU* 3.6 22.9 - - + +
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Residues in contact with TYR 172 (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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65A TYR* 3.9 16.4 + - - -
73A ARG* 2.6 53.4 + - - -
77A PHE* 3.9 22.2 - + - -
152A ILE* 4.1 14.6 - - + -
153A ALA* 3.6 30.5 - - - -
154A LYS* 3.5 28.7 - - + +
171A PHE* 1.3 83.8 - - - +
173A GLN* 1.3 59.0 + - - +
174A CYS 4.3 0.2 - - - -
384A ILE 5.5 0.3 - - - +
386A VAL* 3.7 25.2 + - + +
387A GLU* 3.0 19.8 + - - +
390A PHE* 4.2 8.5 - + - -
93B ASP* 4.3 0.3 + - - -
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Residues in contact with GLN 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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129A TYR 4.7 1.4 - - - +
130A ASP* 3.0 27.8 + - - +
131A LEU* 3.4 16.7 - - + +
132A THR* 5.8 0.6 - - - +
152A ILE* 3.5 2.3 - - - +
153A ALA 2.8 31.5 + - - +
155A VAL* 3.5 34.9 - - + +
157A ARG* 5.8 0.3 - - - -
171A PHE* 3.6 9.1 + - + -
172A TYR* 1.3 75.2 - - - +
174A CYS* 1.3 63.7 + - - +
175A ASP* 3.1 29.6 + - - +
383A SER* 5.4 4.4 - - - -
384A ILE 5.6 0.4 - - - -
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Residues in contact with CYS 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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77A PHE* 5.2 0.4 - - - -
80A ILE* 3.9 27.4 - - - -
84A PHE* 4.0 10.5 - - - -
151A HIS 3.7 3.6 - - - -
152A ILE* 3.7 27.6 - - + -
172A TYR 4.3 0.2 - - - -
173A GLN* 1.3 76.2 - - - +
175A ASP* 1.3 62.0 + - - +
382A LEU* 4.0 1.6 - - - +
383A SER* 3.4 1.8 - - - -
384A ILE* 3.1 36.3 + - - +
386A VAL* 3.7 30.0 - - + +
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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
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84A PHE* 4.7 2.7 - - - -
130A ASP* 4.8 0.3 - - - +
131A LEU* 3.2 26.6 - - + +
132A THR* 4.8 9.0 - - + +
149A ARG* 4.6 6.7 + - - +
150A TYR* 3.1 6.5 - - - +
151A HIS 2.9 33.6 + - - +
173A GLN* 3.1 30.5 + - - +
174A CYS* 1.3 81.1 - - - +
176A PHE* 1.3 61.2 + - - +
177A ASP* 3.9 13.7 - - - +
382A LEU 3.5 4.9 - - - +
383A SER* 3.2 22.0 - - - -
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Residues in contact with PHE 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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84A PHE* 3.6 44.2 - + + -
87A HIS* 5.0 3.8 - - + -
89A ALA* 3.7 24.7 - - + -
148A LYS* 3.9 23.3 - - + -
149A ARG 3.4 11.4 - - - -
150A TYR* 4.2 3.8 - - + -
175A ASP* 1.3 74.6 - - - +
177A ASP* 1.3 64.1 + - - +
178A ILE* 3.8 25.1 - - + -
190A GLU* 5.3 0.9 - - - -
191A CYS* 4.0 8.7 - - - -
194A ILE* 3.5 26.7 - - + -
381A GLY* 3.1 4.2 - - - -
382A LEU* 2.9 53.2 + - + +
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Residues in contact with ASP 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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132A THR* 5.0 3.0 - - - +
135A PHE* 3.9 18.2 - - + -
147A ILE 4.4 0.7 - - - -
148A LYS* 3.3 7.3 - - - +
149A ARG* 2.7 65.2 + - - +
175A ASP* 3.9 8.4 - - - +
176A PHE* 1.3 86.5 + - - +
178A ILE* 1.3 68.2 + - - +
179A ALA 4.0 0.4 - - - -
363A TYR* 2.3 34.9 + - - -
379A CYS* 4.1 2.5 - - - -
380A VAL 3.4 8.6 - - - +
381A GLY* 3.8 2.9 - - - -
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Residues in contact with ILE 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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147A ILE 3.6 4.3 - - - +
148A LYS* 4.0 13.5 - - + +
176A PHE* 3.8 26.7 - - + -
177A ASP* 1.3 77.9 - - - +
179A ALA* 1.3 59.6 + - - +
182A PHE* 4.0 18.9 - - + -
187A PRO* 3.8 40.4 - - + +
190A GLU* 4.1 8.7 - - + +
191A CYS* 4.2 3.6 - - - -
362A ARG* 5.3 1.4 + - - -
378A PRO 3.8 1.9 - - - +
379A CYS* 3.6 4.0 - - - -
380A VAL* 2.9 35.9 + - + +
442B TYR* 3.9 27.1 - - + +
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Residues in contact with ALA 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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135A PHE* 4.5 2.2 - - + -
139A LEU* 4.0 26.7 - - + -
146A ASN* 3.0 24.6 - - - +
147A ILE* 2.7 26.2 + - + +
177A ASP 4.0 0.4 - - - -
178A ILE* 1.3 74.6 - - - +
180A GLY* 1.3 58.8 + - - +
182A PHE* 3.2 8.0 - - - -
367A VAL* 5.5 0.4 - - + -
377A VAL* 4.0 10.5 - - + -
378A PRO 3.7 4.3 - - - -
379A CYS* 3.9 15.9 - - + -
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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