Contacts of the strand formed by residues 166 - 172 (chain A) in PDB entry 2A1I
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 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A SER 2.9 5.0 + - - +
136A THR* 3.2 31.1 - - + +
137A CYS 3.0 25.5 + - - +
164A PHE* 4.1 2.5 - - - +
165A ALA* 1.3 76.4 - - + +
167A ARG* 1.3 64.0 + - - +
168A VAL* 4.0 11.9 - - + -
195A THR* 4.0 20.6 - - - +
212A TYR* 3.9 22.0 - - + -
217A GLN* 3.5 36.3 - - + +
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Residues in contact with ARG 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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137A CYS* 3.5 11.7 - - - -
157A LEU* 5.5 3.1 - - + -
160A LEU* 4.1 24.5 - - + -
161A GLY 3.4 21.3 + - - -
162A LYS* 3.4 35.7 - - - +
164A PHE* 3.0 24.0 + - + +
165A ALA* 3.5 21.8 + - - +
166A LEU* 1.3 75.4 - - - +
168A VAL* 1.3 55.5 + - - +
192A ALA 2.9 17.8 + - - -
193A ASP* 2.7 41.1 + - - +
194A CYS* 3.6 16.5 - - + -
195A THR* 2.8 34.1 + - - -
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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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132A LEU* 5.5 1.1 - - + -
136A THR* 4.9 3.1 - - + -
137A CYS* 3.0 14.4 + - - +
138A ALA* 3.0 13.7 - - + +
139A LEU* 2.8 27.5 + - - +
166A LEU* 4.0 14.1 - - + +
167A ARG* 1.3 79.4 - - - +
169A LEU* 1.3 65.9 + - - +
170A LEU* 4.5 7.0 - - + +
194A CYS* 5.3 0.9 - - - -
195A THR* 3.5 8.5 - - + +
197A ILE* 4.0 28.0 - - + -
209A LEU* 6.4 0.2 - - + -
212A TYR* 3.9 41.1 - - + -
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Residues in contact with LEU 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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139A LEU* 3.6 29.4 - - + +
141A LEU* 4.0 16.2 - - + -
153A ILE* 3.9 22.9 - - + -
157A LEU* 5.5 7.0 - - + -
168A VAL* 1.3 73.0 - - - +
170A LEU* 1.3 62.9 + - - +
171A VAL* 3.6 22.4 + - + +
185A LEU* 4.2 22.9 - - + -
188A MET* 5.7 0.7 - - - -
189A CYS* 3.7 29.6 - - - -
194A CYS* 4.8 6.6 - - - +
195A THR 2.7 14.7 + - - +
196A LEU* 3.6 2.5 - - + -
197A ILE 2.9 26.9 + - - +
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Residues in contact with LEU 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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130A TYR* 5.8 1.1 - - + -
138A ALA* 5.0 3.4 - - + -
139A LEU 2.8 15.3 + - - +
140A PHE* 3.4 15.7 - - + -
141A LEU 2.8 26.6 + - - +
168A VAL* 3.8 8.5 + - + +
169A LEU* 1.3 72.7 - - - +
171A VAL* 1.3 59.2 + - - +
197A ILE* 3.6 31.0 - - + +
199A ALA* 4.1 13.0 - - + -
205A ALA* 3.7 27.1 - - + +
208A TYR* 3.8 20.4 - - + -
209A LEU* 3.4 36.1 - - + -
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Residues in contact with VAL 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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140A PHE* 5.4 0.2 - - - -
141A LEU* 3.2 9.2 - - + +
143A LEU* 3.5 37.2 - - + -
169A LEU* 3.7 33.0 - - + +
170A LEU* 1.3 72.7 - - - +
172A GLN* 1.3 63.4 + - - +
173A VAL* 3.5 2.9 + - + +
182A LEU* 4.0 15.7 - - + -
185A LEU* 4.3 9.6 - - + -
196A LEU* 4.3 14.6 - - + -
197A ILE 2.9 16.2 + - - +
198A LEU* 3.6 3.1 - - - -
199A ALA* 2.8 30.6 + - - +
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Residues in contact with GLN 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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110A ASN* 5.1 0.7 - - - +
111A PRO* 5.4 2.6 - - - +
112A VAL* 4.4 1.0 - - - +
140A PHE* 3.5 37.0 - - + -
141A LEU 2.9 9.9 + - - +
142A SER* 4.1 5.0 - - - -
143A LEU* 3.1 24.9 + - - +
170A LEU 3.9 1.6 + - - -
171A VAL* 1.3 72.3 - - - +
173A VAL* 1.3 60.0 + - - +
174A ASP* 3.0 36.0 + - + +
199A ALA* 3.2 11.4 - - + +
200A TRP 5.0 0.4 - - - -
201A SER* 4.0 11.6 - - - +
202A PRO* 3.6 37.3 - - - +
205A ALA* 5.2 0.2 - - - +
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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