Contacts of the helix formed by residues 121 - 131 (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 GLN 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ILE 3.5 14.8 - - - +
119A LYS 3.5 6.8 + - - +
120A GLN* 1.3 66.5 - - - +
122A GLU* 1.3 61.8 + - - +
123A ASN 2.9 6.1 - - - -
124A VAL* 2.9 25.5 + - - +
125A THR* 3.4 11.7 + - + +
160A ILE* 3.7 38.2 - - + +
163A VAL* 6.0 1.4 - - - +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A GLN* 2.9 43.1 + - - +
121A GLN* 1.3 78.2 + - - +
123A ASN* 1.3 62.6 + - - +
124A VAL 3.4 0.2 - - - -
125A THR* 3.1 26.9 + - + +
126A LEU* 3.1 17.2 + - - +
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Residues in contact with ASN 123 (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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66A ILE* 3.4 40.9 - - - +
70A GLN* 4.2 5.5 - - - +
116A ILE 5.0 0.6 + - - -
117A PHE* 3.0 44.6 + - + +
120A GLN* 3.0 31.3 + - - +
121A GLN 2.9 0.4 - - - -
122A GLU* 1.3 80.2 - - - +
124A VAL* 1.3 59.5 + - - +
126A LEU* 3.3 12.1 + - - +
127A LEU* 3.1 25.6 + - - +
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Residues in contact with VAL 124 (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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117A PHE* 4.3 11.7 - - + -
118A ILE* 4.2 25.4 - - + -
121A GLN 2.9 12.0 + - - +
123A ASN* 1.3 75.7 - - - +
125A THR* 1.3 56.7 + - - +
127A LEU* 3.2 8.0 + - - +
128A LEU* 3.0 31.1 + - + +
146A LEU* 4.6 9.2 - - + -
149A LEU* 4.8 2.0 - - + -
157A VAL* 4.3 15.3 - - + -
160A ILE* 3.7 37.7 - - + -
161A ILE* 4.2 20.4 - - + -
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Residues in contact with THR 125 (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* 3.4 11.8 + - + +
122A GLU* 3.1 24.1 + - + +
124A VAL* 1.3 75.3 - - - +
126A LEU* 1.3 55.7 + - - +
128A LEU* 3.7 13.2 - - + +
129A SER* 3.2 22.3 + - - -
160A ILE* 4.6 10.3 - - + -
164A SER* 4.4 22.4 - - - -
170A ARG* 5.0 3.1 + - - -
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Residues in contact with LEU 126 (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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66A ILE* 4.5 5.6 - - + +
69A LEU* 3.5 33.0 - - + +
70A GLN* 3.6 33.9 - - + +
73A ARG* 3.4 29.4 - - - +
122A GLU 3.1 16.6 + - - +
123A ASN* 3.4 13.7 - - + +
124A VAL 3.2 0.2 - - - -
125A THR* 1.3 76.5 - - - +
127A LEU* 1.3 60.3 + - - +
128A LEU 3.3 0.2 - - - -
129A SER* 3.2 6.4 + - - -
130A LEU* 2.8 40.6 + - + +
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Residues in contact with LEU 127 (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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69A LEU* 5.4 2.2 - - + -
83A LEU* 3.5 31.6 - - + -
117A PHE* 4.1 9.4 - - + -
123A ASN 3.1 11.0 + - - +
124A VAL* 3.4 9.9 - - - +
126A LEU* 1.3 72.4 - - - +
128A LEU* 1.3 66.3 + - - +
130A LEU* 3.0 18.8 + - + +
131A LEU* 3.1 20.5 + - + +
142A GLY* 4.4 14.4 - - - +
145A LEU* 3.8 22.0 - - + -
146A LEU* 3.9 24.7 - - + -
149A LEU* 3.6 30.1 - - + -
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Residues in contact with LEU 128 (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* 3.0 22.9 + - + +
125A THR* 3.7 13.2 - - + +
127A LEU* 1.3 76.0 - - - +
129A SER* 1.3 60.7 + - - +
131A LEU* 3.2 21.8 + - + +
132A GLU* 3.8 9.4 + - - +
146A LEU* 4.0 13.2 - - + -
161A ILE* 4.4 18.6 - - + -
164A SER* 3.4 31.2 - - - +
167A GLY* 4.5 9.0 - - - +
170A ARG* 3.6 25.1 + - + +
171A LEU* 3.9 37.5 - - + -
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Residues in contact with SER 129 (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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73A ARG* 2.8 34.1 + - - -
125A THR 3.2 12.0 + - - -
126A LEU* 3.2 10.9 + - - -
127A LEU 3.2 0.4 - - - -
128A LEU* 1.3 79.4 - - - +
130A LEU* 1.3 61.0 + - - +
132A GLU* 3.3 33.5 + - - +
133A GLU* 4.2 2.3 + - - +
170A ARG* 3.9 4.6 - - - +
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Residues in contact with LEU 130 (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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69A LEU* 4.0 35.0 - - + +
73A ARG* 3.5 33.9 - - + +
79A ILE* 3.8 22.0 - - + -
83A LEU* 4.2 13.5 - - + -
126A LEU* 2.8 32.0 + - + +
127A LEU* 3.0 15.5 + - + +
129A SER* 1.3 72.0 - - - +
131A LEU* 1.3 58.8 + - + +
132A GLU 3.2 2.0 - - - -
133A GLU* 3.1 32.8 - - + +
138A VAL* 3.5 16.0 - - + +
139A ARG* 4.9 0.5 - - - -
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Residues in contact with LEU 131 (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 LEU* 3.1 19.9 + - + +
128A LEU* 3.3 11.4 - - - +
129A SER 3.2 0.4 - - - -
130A LEU* 1.3 75.1 - - + +
132A GLU* 1.3 56.7 + - - +
133A GLU 3.2 5.6 - - - -
138A VAL 5.0 0.2 - - - +
139A ARG* 3.2 41.9 + - + +
142A GLY* 3.6 38.4 - - - +
143A VAL* 3.8 8.7 - - + +
146A LEU* 3.8 29.8 - - + -
171A LEU* 4.0 16.6 - - + -
174A LEU* 4.0 19.4 - - + +
189A LEU* 5.1 0.7 - - + -
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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