Contacts of the strand formed by residues 173 - 181 (chain A) in PDB entry 4F8Q
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 TYR 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A THR* 3.6 1.6 - - - -
141A GLY 3.0 20.3 + - - -
142A TRP* 2.8 42.1 + - - +
143A TYR* 3.5 32.8 - + - -
144A PRO* 4.3 0.4 - - + -
145A GLN* 3.6 45.9 + - + +
146A PRO* 3.8 16.4 - - + -
165A VAL* 3.4 24.5 - - + -
166A VAL 3.5 2.2 - - - -
167A ALA* 3.8 25.1 - - + +
171A GLY 3.9 7.0 - - - -
172A LEU* 1.3 74.0 - - - +
174A GLU* 1.3 58.4 + - - +
175A VAL* 5.0 0.9 - - - -
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Residues in contact with GLU 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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138A ARG* 3.9 21.2 + - + -
139A SER 3.2 19.7 - - - +
140A THR* 3.9 17.6 - - + +
141A GLY 5.3 0.2 - - - +
164A PRO 4.2 1.0 - - - +
165A VAL* 3.4 3.8 - - - +
166A VAL* 2.8 54.2 + - + +
173A TYR* 1.3 72.3 - - - +
175A VAL* 1.3 70.6 + - - +
176A ALA* 6.3 0.2 - - + -
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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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137A CYS 4.1 0.2 - - - +
138A ARG* 3.5 3.9 - - - +
139A SER* 3.2 28.3 + - - +
142A TRP* 4.8 1.8 - - + -
146A PRO* 3.5 42.2 - - + +
148A ILE* 4.3 18.5 - - + +
162A GLU* 4.8 4.0 - - + +
163A ALA 5.8 0.2 - - - -
164A PRO 5.1 3.6 - - - -
165A VAL* 3.7 27.8 - - + +
174A GLU* 1.3 85.5 - - - +
176A ALA* 1.3 61.4 + - - +
193A ILE* 4.2 21.5 - - + -
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Residues in contact with ALA 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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136A GLU* 3.5 20.9 - - - +
137A CYS 3.2 9.0 - - - +
138A ARG* 4.4 11.9 - - + -
148A ILE* 4.3 2.7 - - - -
162A GLU* 3.5 6.7 - - - +
163A ALA* 2.8 46.5 + - + +
174A GLU* 6.3 0.2 - - + -
175A VAL* 1.3 76.5 - - - +
177A ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 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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136A GLU* 3.5 3.7 - - - +
137A CYS 2.9 35.1 + - - -
148A ILE* 3.8 32.7 - - + +
150A TRP* 3.3 24.9 + - + +
160A ALA* 4.4 6.5 - - + -
161A VAL 3.2 10.1 - - - +
162A GLU* 4.7 2.5 - - + -
176A ALA* 1.3 74.8 - - - +
178A SER* 1.3 61.7 + - - +
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Residues in contact with SER 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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134A HIS* 3.0 24.2 + - - -
135A LEU 3.2 4.4 + - - -
136A GLU* 2.7 32.4 + - - -
160A ALA* 3.3 1.0 - - - -
161A VAL* 2.8 47.2 + - - +
177A ALA* 1.3 72.2 - - - +
179A VAL* 1.3 70.4 + - - +
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Residues in contact with VAL 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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133A ILE 3.5 0.9 - - - +
134A HIS* 3.4 3.3 - - - -
135A LEU* 2.8 44.8 + - + -
150A TRP* 3.3 58.1 - - + -
158A ILE* 4.5 10.5 - - + -
159A PRO 3.2 23.8 - - - +
160A ALA* 3.6 1.6 - - + -
161A VAL* 5.9 0.7 - - - -
178A SER* 1.3 81.0 - - - +
180A ILE* 1.3 70.1 + - - +
181A MET* 5.4 1.3 - - + -
189A VAL* 5.8 1.1 - - + -
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Residues in contact with ILE 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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129A GLU* 3.4 62.4 - - + +
130A ASP* 4.4 6.1 - - + +
132A GLY* 3.9 6.7 - - - -
133A ILE 3.3 15.5 - - - +
158A ILE* 5.2 7.3 - - - +
179A VAL* 1.3 81.4 - - - +
181A MET* 1.3 63.7 + - - +
182A ARG* 4.0 34.5 + - - +
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Residues in contact with MET 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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132A GLY* 3.3 3.8 - - - -
133A ILE* 2.8 38.5 + - + +
135A LEU* 4.0 20.0 - - + -
158A ILE* 6.4 0.4 - - + -
179A VAL* 4.0 2.4 + - + -
180A ILE* 1.3 73.5 - - - +
182A ARG* 1.3 69.2 + - - +
187A GLU* 3.5 36.1 - - + +
188A GLY* 4.7 0.4 - - - -
189A VAL* 4.0 30.1 - - + -
208A ILE* 4.0 24.9 - - + +
213A HIS* 3.4 36.0 - - + +
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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