Contacts of the strand formed by residues 160 - 166 (chain A) in PDB entry 2CUY
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 GLN 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ALA* 6.1 0.7 - - + -
132A VAL 3.6 4.0 - - - -
133A LEU* 3.5 18.8 - - + -
156A ASN* 3.2 31.1 + - + +
157A ALA* 2.8 24.7 + - + +
158A PRO 4.4 0.7 - - - +
159A GLU* 1.3 79.5 - - - +
161A THR* 1.3 62.0 + - - +
162A VAL* 5.6 1.1 - - + -
273A VAL* 6.2 0.4 - - - +
277A LEU* 3.2 26.6 - - - +
280A ARG* 2.7 38.2 + - - +
49B PRO* 3.6 22.0 - - + +
50B GLU* 4.8 2.6 - - - +
51B GLU* 3.8 12.7 + - - +
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Residues in contact with THR 161 (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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131A ALA* 3.5 1.0 - - - -
132A VAL* 2.6 42.5 + - + +
133A LEU* 4.9 0.4 - - - +
135A LEU 5.2 0.2 + - - -
137A LEU* 4.3 9.1 + - + +
140A ILE* 3.6 29.1 - - + +
152A ILE* 3.8 32.3 - - + -
154A ASN 3.6 12.3 - - - +
155A LEU* 4.1 13.2 - - + +
157A ALA 4.7 1.9 + - - -
159A GLU 5.1 1.9 + - - -
160A GLN* 1.3 79.0 + - - +
162A VAL* 1.3 67.9 + - - +
163A ILE* 4.5 2.9 - - + -
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Residues in contact with VAL 162 (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 MET* 3.9 16.6 - - + -
130A ALA 3.3 10.8 - - - +
131A ALA* 4.4 14.4 - - + -
152A ILE* 3.7 3.6 - - - -
153A ALA* 2.8 28.5 + - + -
154A ASN* 3.1 29.4 + - + +
156A ASN* 3.5 27.6 - - - +
160A GLN* 5.6 0.9 - - + -
161A THR* 1.3 78.1 - - - +
163A ILE* 1.3 67.2 + - - +
187A LEU* 3.6 27.1 - - + -
51B GLU* 5.7 3.6 - - - +
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Residues in contact with ILE 163 (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 MET* 3.2 0.9 - - - -
130A ALA* 2.8 47.6 + - + +
132A VAL* 4.3 14.1 - - + -
140A ILE* 4.5 2.7 - - + -
144A LEU* 3.9 13.7 - - + -
150A VAL* 4.2 8.1 - - + -
151A GLU 3.3 9.6 - - - +
152A ILE* 3.9 24.0 - - + -
153A ALA* 4.3 1.1 - - - -
161A THR* 4.5 1.1 - - + -
162A VAL* 1.3 79.3 - - - +
164A SER* 1.3 67.9 + - - +
170A VAL* 4.1 16.6 - - + +
173A ALA* 3.8 28.7 - - + -
174A ALA* 4.9 2.2 - - - +
177A LEU* 4.1 15.3 - - + -
184A VAL* 5.8 0.4 - - + -
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Residues in contact with SER 164 (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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128A ALA 3.2 6.3 - - - -
129A MET* 3.2 32.1 - - - -
149A GLY 4.5 0.2 - - - -
150A VAL* 4.6 0.6 - - - +
151A GLU* 2.9 38.6 + - - +
153A ALA* 3.7 3.9 - - - +
163A ILE* 1.3 79.6 - - - +
165A GLY* 1.3 59.7 + - - +
170A VAL* 3.9 9.0 - - - -
192A PRO* 3.6 2.8 - - - -
193A PHE 2.9 22.3 + - - -
195A SER* 3.6 10.3 - - - -
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Residues in contact with GLY 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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127A GLY* 3.3 6.1 - - - -
128A ALA 3.1 23.3 + - - -
149A GLY 3.2 8.5 - - - -
151A GLU* 5.7 0.2 - - - -
164A SER* 1.3 79.9 + - - +
166A ARG* 1.3 66.7 + - - -
170A VAL* 3.6 1.2 - - - +
192A PRO* 3.5 12.2 - - - +
195A SER* 4.2 5.2 - - - -
197A LEU* 3.8 16.4 - - - -
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Residues in contact with ARG 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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126A GLU* 3.5 15.5 - - - +
148A GLU 5.1 0.4 - - - +
149A GLY* 2.8 29.8 + - - +
165A GLY* 1.3 70.6 - - - -
167A ARG* 1.3 65.9 + - - +
168A GLN* 3.3 6.5 - - - +
169A ALA* 2.9 15.5 + - + +
170A VAL* 2.9 22.1 + - - +
197A LEU* 3.5 30.8 - - + +
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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