Contacts of the helix formed by residues 128 - 143 (chain A) in PDB entry 3R2W
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 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN* 6.3 1.8 - - - -
117A SER* 3.4 27.8 + - - +
118A LEU* 5.1 9.0 - - + -
126A THR* 3.7 5.4 - - + -
127A PHE* 1.3 77.9 - - - +
129A ASP* 1.3 66.9 + - - +
131A THR* 2.6 31.1 + - - +
132A VAL* 3.3 16.3 + - + +
148A LEU* 5.2 0.2 - - + -
150A LEU* 4.0 33.9 - - + -
160A THR* 5.3 7.6 - - + -
163A ILE* 4.5 9.0 - - + +
164A LEU* 4.7 9.2 - - + -
167A TYR* 3.6 30.7 - - + +
174A ILE* 5.8 1.1 - - + -
241A ILE* 5.0 6.1 - - + -
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Residues in contact with ASP 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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125A ASN* 4.2 18.2 + - + +
126A THR* 2.7 43.0 + - - +
128A LEU* 1.3 78.4 - - - +
130A LEU* 1.3 57.1 + - - +
131A THR 3.1 0.2 - - - -
132A VAL* 3.4 10.0 - - - +
133A GLN* 2.8 34.1 + - - +
166A LYS* 3.6 18.9 + - - -
167A TYR* 3.1 29.0 + - - -
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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
----------------------------------------------------------
121A VAL* 3.9 31.4 - - + -
122A ARG* 5.4 4.0 - - + +
125A ASN* 3.6 26.2 - - + +
126A THR 3.2 17.0 + - - +
127A PHE* 4.0 6.5 - - - +
128A LEU 2.8 4.0 + - - -
129A ASP* 1.3 75.8 - - - +
131A THR* 1.3 60.5 + - + +
133A GLN* 4.3 0.4 - - - -
134A GLN* 3.2 9.9 - - - +
244A LEU* 4.3 18.8 - - + -
400A LEU* 3.8 22.4 - - + -
403A GLY* 3.1 46.4 - - - +
405A LEU* 4.9 9.6 - - + -
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Residues in contact with THR 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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99A VAL* 6.3 1.1 - - - -
101A LYS* 2.9 45.2 - - + +
127A PHE 3.8 7.5 + - - +
128A LEU* 2.6 32.9 + - - +
130A LEU* 1.3 79.0 - - + +
132A VAL* 1.3 57.5 + - - +
133A GLN 3.0 1.3 - - - -
134A GLN* 2.6 37.4 + - - +
135A ILE* 2.8 19.1 + - - +
148A LEU* 4.6 8.9 - - - +
150A LEU* 6.0 0.5 - - - +
241A ILE* 4.6 7.0 - - + +
244A LEU* 6.4 2.0 - - + -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.9 18.4 - - + +
129A ASP* 3.4 11.0 - - - +
131A THR* 1.3 75.1 - - - +
133A GLN* 1.3 58.1 + - + +
135A ILE* 3.7 9.7 - - - +
136A GLU* 2.7 43.8 + - - +
148A LEU* 3.7 22.8 - - + +
167A TYR* 3.7 34.1 - - + -
170A CYS* 5.2 4.5 - - + -
172A VAL* 3.9 9.8 - - + +
174A ILE* 4.1 18.6 - - + -
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Residues in contact with GLN 133 (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 ASN* 5.3 8.5 - - - +
129A ASP 2.8 20.9 + - - +
130A LEU* 4.3 0.9 - - - -
132A VAL* 1.3 79.0 - - + +
134A GLN* 1.3 61.7 + - - +
136A GLU* 3.6 10.6 + - - +
137A HIS* 3.0 24.3 + - - +
402A ALA* 3.7 8.6 - - + +
403A GLY* 3.7 21.3 - - - +
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Residues in contact with GLN 134 (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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101A LYS* 4.5 3.7 + - - +
130A LEU 3.2 19.0 + - - +
131A THR* 2.6 34.0 + - - +
133A GLN* 1.3 73.5 - - - +
135A ILE* 1.3 58.4 + - + +
137A HIS* 3.3 6.5 + - - +
138A LEU* 3.2 28.4 + - - +
244A LEU 4.4 11.7 + - - -
246A ALA 4.5 1.5 + - - +
247A THR* 3.6 30.4 + - - +
248A VAL* 4.8 6.8 + - + +
402A ALA 3.7 7.1 + - - -
403A GLY 3.9 3.0 + - - -
404A SER* 3.5 42.5 - - - +
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Residues in contact with ILE 135 (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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99A VAL* 4.2 33.7 - - + -
131A THR* 2.8 27.6 + - - +
132A VAL* 3.7 6.5 - - - +
134A GLN* 1.3 72.0 - - + +
136A GLU* 1.3 57.9 + - - +
137A HIS 3.1 1.1 - - - -
138A LEU* 2.8 29.7 + - + +
139A ASN* 2.9 17.2 + - - +
146A VAL* 3.6 37.0 - - + +
147A PRO 5.1 1.3 - - - +
148A LEU* 4.5 13.7 - - + -
172A VAL* 3.8 20.2 - - + -
248A VAL* 4.5 11.9 - - + -
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Residues in contact with GLU 136 (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 VAL* 2.7 22.1 + - - +
133A GLN* 3.8 10.2 - - - +
135A ILE* 1.3 70.8 - - - +
137A HIS* 1.3 62.8 + - - +
139A ASN* 4.2 0.5 - - - +
140A LYS* 3.0 30.3 + - + +
169A HIS 4.4 1.9 - - - +
170A CYS* 3.1 42.5 - - + -
171A ARG* 3.4 24.6 + - + +
172A VAL* 3.4 14.6 - - + +
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Residues in contact with HIS 137 (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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133A GLN 3.0 15.0 + - - +
134A GLN 3.4 10.8 - - - +
135A ILE 3.1 0.2 - - - -
136A GLU* 1.3 75.7 - - - +
138A LEU* 1.3 62.0 + - + +
140A LYS* 3.7 2.2 - - - -
141A THR* 2.7 61.9 + - + +
142A TYR* 6.1 0.4 - + - -
401A ASN 5.0 5.1 + - - -
402A ALA* 4.2 27.3 - - + +
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Residues in contact with LEU 138 (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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94A LEU* 4.3 19.3 - - + -
134A GLN 3.2 15.0 + - - +
135A ILE* 2.8 18.5 + - + +
137A HIS* 1.3 84.2 - - + +
139A ASN* 1.3 69.9 + - - +
141A THR* 3.2 2.0 + - - +
142A TYR* 3.2 54.8 + - + +
144A THR* 4.0 4.0 - - + -
146A VAL* 5.0 8.1 - - + -
248A VAL* 4.4 31.9 - - + +
250A LEU* 5.8 7.6 - - + -
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Residues in contact with ASN 139 (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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135A ILE* 2.9 13.9 + - - +
136A GLU 4.4 1.1 - - - +
138A LEU* 1.3 73.2 - - - +
140A LYS* 1.3 57.8 + - - +
141A THR 3.1 0.2 + - - -
143A ASN* 3.0 30.8 + - - -
144A THR* 2.9 40.1 + - - +
145A ASP* 3.5 11.3 + - - +
146A VAL* 3.2 41.8 + - - +
171A ARG* 2.9 42.4 + - - +
172A VAL* 4.5 0.6 - - - +
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Residues in contact with LYS 140 (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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136A GLU 3.0 19.6 + - - +
137A HIS* 3.7 3.4 - - - +
139A ASN* 1.3 74.5 - - - +
141A THR* 1.3 66.0 + - - +
143A ASN 5.1 0.2 - - - -
171A ARG* 4.4 19.5 - - + +
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Residues in contact with THR 141 (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 HIS* 2.7 51.4 + - + +
138A LEU* 3.2 0.4 + - - -
139A ASN 3.1 0.6 - - - -
140A LYS* 1.3 81.3 - - + +
142A TYR* 1.3 92.1 + - - +
143A ASN* 3.8 3.8 - - - -
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Residues in contact with TYR 142 (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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86A LEU* 6.0 1.0 - - - +
91A SER* 4.2 32.6 - - - +
94A LEU* 4.5 11.2 - - + -
137A HIS* 6.1 0.7 - + - -
138A LEU* 3.2 34.5 + - + +
141A THR* 1.3 110.3 - - - +
143A ASN* 1.3 66.7 + - - +
144A THR* 3.0 22.8 + - + -
250A LEU* 4.2 23.0 - - + +
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Residues in contact with ASN 143 (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 ASN 3.0 8.7 + - - -
140A LYS 5.1 0.2 - - - -
141A THR 3.8 2.2 - - - +
142A TYR* 1.3 81.3 - - - +
144A THR* 1.3 60.4 + - - +
145A ASP* 5.0 0.2 - - - +
171A ARG* 3.3 23.8 + - - +
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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