Contacts of the helix formed by residues 153 - 164 (chain A) in PDB entry 2W3C
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A SER 5.7 1.3 - - - +
114A THR* 4.0 13.0 - - + +
115A GLU* 3.7 55.4 - - + +
118A ILE* 3.7 19.3 - - + -
149A LEU 3.0 13.6 + - - +
152A GLN* 1.3 83.3 - - + +
154A GLY* 1.3 62.3 + - - +
155A PRO* 3.6 4.5 - - - -
156A GLN* 3.3 28.6 + - - +
157A VAL* 3.0 29.2 + - + +
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Residues in contact with GLY 154 (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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150A LEU* 3.0 23.7 + - - -
151A LYS 4.7 0.8 + - - -
152A GLN 3.7 2.2 - - - -
153A LEU* 1.3 73.7 - - - +
155A PRO* 1.3 65.6 - - - +
157A VAL* 4.0 0.3 - - - +
158A GLN* 2.8 50.5 + - - +
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Residues in contact with PRO 155 (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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153A LEU* 3.8 2.9 - - - -
154A GLY* 1.3 89.0 - - - +
156A GLN* 1.3 62.6 + - + +
158A GLN* 3.9 11.6 - - - +
159A GLN* 3.2 26.9 + - - +
197A ASN* 5.2 1.7 + - - +
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Residues in contact with GLN 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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115A GLU* 6.3 0.2 - - - +
118A ILE* 3.8 26.8 - - + +
153A LEU* 3.3 37.4 + - - +
154A GLY 3.2 0.4 - - - -
155A PRO* 1.3 84.4 - - + +
157A VAL* 1.3 66.8 + - - +
159A GLN* 3.2 7.3 + - - +
160A ILE* 3.1 28.6 + - + +
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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
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118A ILE* 3.8 32.8 - - + -
124A VAL* 4.3 13.0 - - + -
146A LEU* 4.2 14.6 - - + -
149A LEU* 3.7 19.3 - - + +
150A LEU* 3.4 25.6 - - + -
153A LEU* 3.0 19.7 + - + +
156A GLN* 1.3 77.0 - - - +
158A GLN* 1.3 60.2 + - - +
160A ILE* 3.5 7.1 + - + +
161A ILE* 3.2 31.5 + - + +
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Residues in contact with GLN 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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150A LEU* 4.6 4.7 - - + -
154A GLY* 2.8 32.6 + - - +
155A PRO* 3.9 8.2 - - - +
157A VAL* 1.3 73.2 - - - +
159A GLN* 1.3 59.6 + - - +
161A ILE* 3.5 6.3 + - - +
162A LEU* 2.9 29.9 + - - +
192A ALA 2.8 26.4 + - - +
193A LEU* 2.9 28.7 + - + +
195A ARG* 3.1 21.9 + - - +
196A SER 4.7 1.6 - - - +
197A ASN* 3.0 33.5 + - - +
200A ILE* 3.8 11.0 - - + +
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Residues in contact with GLN 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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155A PRO 3.2 13.6 + - - +
156A GLN* 3.2 11.9 + - - +
158A GLN* 1.3 76.4 - - - +
160A ILE* 1.3 65.0 + - + +
162A LEU* 3.3 22.2 + - - +
163A VAL* 3.0 51.7 + - + +
197A ASN* 5.0 5.1 - - - +
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Residues in contact with ILE 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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118A ILE* 4.2 19.3 - - + +
121A GLN* 3.7 50.7 - - + +
124A VAL* 3.7 42.2 - - + -
125A THR* 4.6 10.3 - - + -
128A LEU* 6.0 0.2 - - + -
156A GLN* 3.1 22.5 + - + +
157A VAL* 3.8 8.3 - - - +
159A GLN* 1.3 75.7 - - + +
161A ILE* 1.3 62.7 + - - +
163A VAL* 3.5 6.3 + - - +
164A SER* 3.2 22.2 + - - -
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Residues in contact with ILE 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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124A VAL* 4.2 14.8 - - + -
128A LEU* 4.4 12.1 - - + -
146A LEU* 4.5 11.9 - - + -
150A LEU* 3.9 15.5 - - + -
157A VAL* 3.2 23.0 + - + +
158A GLN 3.8 4.0 - - - +
159A GLN 3.2 0.6 - - - -
160A ILE* 1.3 75.2 - - - +
162A LEU* 1.3 65.2 + - - +
164A SER* 3.1 25.9 + - - +
167A GLY* 3.9 17.0 - - - -
168A VAL* 4.1 8.3 + - + -
171A LEU* 3.8 27.1 - - + -
193A LEU* 3.5 28.0 - - + -
200A ILE* 5.4 0.2 - - + -
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Residues in contact with LEU 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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158A GLN 2.9 21.2 + - - +
159A GLN* 3.3 28.5 + - - +
161A ILE* 1.3 74.9 - - - +
163A VAL* 1.3 61.2 + - + +
164A SER 3.5 5.0 + - - +
168A VAL* 4.8 7.0 - - + -
197A ASN* 5.0 4.5 - - - +
199A ALA* 4.4 18.4 - - + -
200A ILE* 4.2 16.8 - - + -
203A ILE* 3.4 32.8 - - + -
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Residues in contact with VAL 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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121A GLN* 6.0 1.6 - - - +
159A GLN* 3.0 40.1 + - + +
160A ILE* 4.0 5.4 - - - +
162A LEU* 1.3 77.7 - - + +
164A SER* 1.3 59.9 + - - +
165A PRO* 3.8 6.2 - - - +
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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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125A THR* 4.4 16.1 - - - +
128A LEU* 3.4 27.6 - - - +
160A ILE 3.2 17.6 + - - -
161A ILE 3.1 17.0 + - - +
162A LEU 3.8 5.3 - - - +
163A VAL* 1.3 78.2 - - - +
165A PRO* 1.4 70.1 - - - +
166A MET 3.6 0.3 + - - -
167A GLY* 3.1 7.4 + - - -
170A ARG* 3.4 12.0 + - - -
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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