Contacts of the strand formed by residues 164 - 170 (chain A) in PDB entry 4COO
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 ARG 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A GLY* 5.0 3.6 + - - +
140A ASP 3.4 6.4 + - - +
141A THR* 3.4 26.0 + - + +
142A ILE* 2.9 28.5 + - - +
162A GLY 4.2 0.4 + - - -
163A TYR* 1.3 73.2 - - - +
165A CYS* 1.3 60.7 + - - +
166A ILE* 3.9 17.0 - - + +
187A GLU* 2.7 43.7 + - - +
214A ILE* 4.0 26.5 - - - +
1554A EDO 4.0 8.3 - - - -
530B LEU* 5.5 1.6 - - - +
1542B ACT 4.4 11.1 + - - +
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Residues in contact with CYS 165 (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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142A ILE* 3.4 11.4 - - + -
154A LEU* 4.1 8.7 - - - -
155A ALA* 3.7 30.5 - - - -
158A ALA* 3.7 19.3 - - + -
163A TYR 3.6 0.8 + - - +
164A ARG* 1.3 76.7 - - - +
166A ILE* 1.3 56.7 + - - +
167A ILE* 3.6 29.2 - - - -
185A GLY 4.4 4.8 + - - +
186A ALA* 3.4 9.4 - - + -
187A GLU* 2.8 33.1 + - - +
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Residues in contact with ILE 166 (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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141A THR* 3.9 19.1 - - + -
142A ILE 2.8 10.8 + - - +
143A ILE* 3.1 15.9 - - + +
144A GLU 3.0 24.3 + - - -
164A ARG* 3.9 10.5 - - - +
165A CYS* 1.3 79.1 - - - +
167A ILE* 1.3 72.8 + - - +
187A GLU* 3.4 20.9 - - - +
189A VAL* 4.5 2.2 - - + -
210A LEU* 4.1 20.0 - - + -
214A ILE* 3.6 30.7 - - + -
1554A EDO 3.8 28.0 - - - -
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Residues in contact with ILE 167 (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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142A ILE* 6.1 0.2 - - + -
144A GLU* 3.6 16.4 - - + +
146A THR* 3.6 17.9 - - + -
151A GLY* 3.5 30.3 - - - +
154A LEU* 4.9 2.0 - - + -
165A CYS* 3.6 24.9 - - - -
166A ILE* 1.3 79.8 - - - +
168A VAL* 1.3 66.1 + - - +
169A MET* 4.1 13.2 - - + -
181A LEU* 3.8 37.0 - - + -
186A ALA* 4.3 4.5 - - + -
187A GLU 2.8 11.5 + - - +
188A ILE* 3.6 4.8 - - + -
189A VAL* 2.9 26.2 + - - +
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Residues in contact with VAL 168 (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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143A ILE* 4.4 7.0 - - + -
144A GLU 3.0 10.6 + - - +
145A PRO* 3.4 3.0 - - + +
146A THR 2.9 28.4 + - - +
166A ILE* 4.7 0.7 - - + -
167A ILE* 1.3 77.2 - - - +
169A MET* 1.3 62.2 + - - +
189A VAL* 3.3 9.4 - - + +
191A THR* 3.8 16.2 - - + -
203A HIS* 3.4 36.9 - - - +
206A VAL* 3.9 11.2 - - + -
207A ALA* 4.0 16.2 - - + -
210A LEU* 3.8 27.8 - - + -
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Residues in contact with MET 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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146A THR 3.3 11.4 - - - +
148A GLY* 3.6 27.6 - - - -
167A ILE* 4.1 9.9 - - + -
168A VAL* 1.3 75.9 - - - +
170A PRO* 1.3 71.8 - - - +
173A MET* 3.6 25.4 - - + -
174A SER 4.6 0.2 - - - +
177A LYS* 4.2 11.0 - - + -
178A VAL* 3.7 30.1 - - + -
181A LEU* 3.9 23.1 - - + -
188A ILE* 4.7 2.7 - - + -
189A VAL 2.9 7.9 + - - +
190A ARG* 3.0 44.5 + - - +
191A THR* 3.9 3.8 - - - -
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Residues in contact with PRO 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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146A THR 3.2 17.7 - - - +
147A SER* 5.2 0.7 - - - -
169A MET* 1.3 87.7 - - + +
171A GLU* 1.3 62.7 + - - +
172A LYS* 3.2 6.1 + - + +
173A MET* 3.2 33.1 + - + +
190A ARG* 2.9 18.4 + - - -
191A THR* 3.3 17.5 - - - +
192A PRO 5.0 0.7 - - - +
193A THR* 4.5 14.4 - - + +
203A HIS* 4.1 23.8 - - + +
1553A EDO 4.8 6.1 - - - +
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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