Contacts of the strand formed by residues 155 - 161 (chain A) in PDB entry 3C6Q
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 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLY 2.7 13.9 + - - +
125A LYS* 3.2 20.3 - - + +
126A VAL 2.8 30.5 + - - -
153A GLU 4.1 5.2 - - - +
154A ILE* 1.3 79.4 - - - +
156A ILE* 1.3 63.2 + - - +
157A VAL* 3.5 23.1 + - + +
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Residues in contact with ILE 156 (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 VAL* 3.4 14.6 - - + +
128A ILE* 4.0 18.4 - - + -
145A PHE* 4.1 13.7 - - + -
146A LYS* 3.8 32.8 - - + -
149A ILE* 4.1 23.8 - - + +
155A GLU* 1.3 76.5 - - - +
157A VAL* 1.3 63.5 + - - +
158A ASP 3.6 22.2 - - - +
159A ILE* 3.9 17.3 - - + -
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS* 3.6 39.9 - - + -
126A VAL 2.8 25.7 + - - +
127A VAL* 3.6 18.8 - - + -
155A GLU* 4.1 16.4 - - + +
156A ILE* 1.3 74.6 - - - +
158A ASP* 1.3 75.7 + - - +
180A HIS* 4.1 23.7 - - + +
183A LEU* 4.4 4.7 - - + -
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Residues in contact with ASP 158 (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 VAL 3.9 0.4 + - - -
127A VAL* 4.2 14.1 - - + -
128A ILE 3.1 20.5 + - - -
156A ILE* 3.5 7.2 - - - +
157A VAL* 1.3 85.7 - - - +
159A ILE* 1.3 71.6 + - - +
160A LEU* 4.1 21.1 - - + +
176A ALA* 5.7 1.7 - - + -
180A HIS* 2.7 32.3 + - - -
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Residues in contact with ILE 159 (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 ILE* 3.6 23.1 - - + -
130A THR* 4.1 22.2 - - + -
133A LEU* 4.2 22.6 - - + +
142A ILE* 4.4 7.6 - - + -
146A LYS* 4.4 25.1 - - - +
156A ILE* 3.9 17.3 - - + -
158A ASP* 1.3 83.5 + - - +
160A LEU* 1.3 63.8 + - - +
161A ASN* 3.4 5.4 + - - +
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Residues in contact with LEU 160 (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 VAL* 3.7 27.6 - - + -
128A ILE 2.9 10.9 + - - +
129A GLY* 3.9 4.8 - - - -
130A THR* 3.1 29.2 + - - +
158A ASP* 4.1 20.6 - - + +
159A ILE* 1.3 73.0 - - - +
161A ASN* 1.3 60.7 + - - +
162A ASP* 3.7 3.4 + - - +
172A LEU* 3.3 54.7 - - + +
173A ALA* 4.2 2.7 - - - +
175A ALA* 6.3 0.9 - - + -
176A ALA* 3.9 10.1 - - + +
186A PHE* 5.1 0.4 - - + -
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Residues in contact with ASN 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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130A THR* 3.7 3.4 - - - -
131A GLY 3.3 18.8 - - - +
132A SER* 4.5 1.6 - - - +
133A LEU* 3.4 48.8 - - + +
159A ILE 3.4 3.2 + - - +
160A LEU* 1.3 70.8 - - - +
162A ASP* 1.3 57.3 + - - +
163A CYS* 2.9 36.4 + - - +
168A ARG* 4.0 6.9 + - - -
172A LEU* 3.7 8.8 - - - +
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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