Contacts of the helix formed by residues 117 - 130 (chain D) in PDB entry 2X1W
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 117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D ILE* 1.3 77.5 + - - +
119D LEU 3.7 1.3 - - - -
120D LYS* 4.0 30.7 + - + +
121D SER* 3.9 11.1 + - - -
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Residues in contact with ILE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C THR* 4.2 23.8 - - + +
117D GLU* 1.3 78.6 - - - +
119D LEU* 1.3 81.3 + - + +
121D SER* 2.9 31.2 + - - -
122D ILE* 3.2 21.9 - - + +
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C PHE* 5.4 5.8 - - + -
117D GLU 3.7 0.2 - - - -
118D ILE* 1.3 102.9 - - + +
120D LYS* 1.3 61.1 + - - +
121D SER 3.2 0.2 - - - -
122D ILE* 3.7 21.3 - - + -
123D ASP* 2.9 30.1 + - - +
132O GLN 4.5 12.1 - - - +
133O HIS* 4.1 15.7 - - + -
213O MET* 3.8 42.9 - - + +
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Residues in contact with LYS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D GLU* 4.0 29.1 + - + +
118D ILE 3.1 1.4 + - - -
119D LEU* 1.3 78.9 - - - +
121D SER* 1.3 57.8 + - - +
123D ASP* 3.7 6.5 - - - +
124D ASN* 3.1 23.4 + - - +
210O GLN* 6.0 1.8 - - - +
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Residues in contact with SER 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C THR* 6.0 1.2 + - - -
117D GLU 3.9 8.3 + - - -
118D ILE* 2.9 17.5 + - - +
120D LYS* 1.3 78.0 - - - +
122D ILE* 1.3 61.5 + - - +
124D ASN* 3.5 10.7 - - - +
125D GLU* 3.2 31.1 + - - +
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Residues in contact with ILE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C PRO* 4.4 10.1 - - + -
184C THR* 3.8 33.9 - - + +
186C PHE* 4.0 26.0 - - + -
118D ILE* 3.2 31.1 + - + +
119D LEU* 3.8 28.0 - - + +
120D LYS 3.4 0.2 - - - -
121D SER* 1.3 76.7 - - - +
123D ASP* 1.3 66.6 + - - +
125D GLU* 3.0 15.6 + - + +
126D TRP* 3.2 38.4 + - + -
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Residues in contact with ASP 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LEU 2.9 18.8 + - - +
120D LYS* 3.7 7.2 - - + +
122D ILE* 1.3 77.8 - - - +
124D ASN* 1.3 65.6 + - - +
126D TRP* 3.2 2.5 + - - +
127D ARG* 2.9 22.0 + - - +
164O ARG* 2.8 29.2 + - - -
165O TYR* 2.7 24.1 + - - -
197O MET* 2.8 33.0 - - + +
213O MET* 6.2 0.2 - - - -
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Residues in contact with ASN 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LYS 3.1 16.2 + - - +
121D SER* 3.5 14.1 - - - +
122D ILE 3.1 0.2 - - - -
123D ASP* 1.3 81.2 + - - +
125D GLU* 1.3 58.6 + - - +
127D ARG* 2.8 32.9 + - - +
128D LYS* 2.9 62.0 + - - +
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C PRO* 4.4 11.4 - - + -
156C CYS 4.1 3.1 - - - +
157C VAL* 3.8 24.5 - - + -
158C SER* 2.8 30.3 + - - +
183C LYS* 3.3 38.9 + - + +
184C THR 5.9 1.8 - - - +
185C LEU* 5.1 2.7 - - + -
121D SER* 3.2 20.2 + - - +
122D ILE* 3.0 14.2 + - + +
124D ASN* 1.3 76.0 + - - +
126D TRP* 1.3 57.2 + - - +
128D LYS* 4.1 2.5 - - - +
129D THR* 2.7 39.0 + - - +
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Residues in contact with TRP 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C LYS* 3.7 18.6 - - + +
154C PRO* 3.4 44.3 - - + +
155C PRO* 5.1 0.4 - - + -
186C PHE* 4.8 4.0 - + - -
122D ILE* 3.2 43.4 + - + -
123D ASP 3.2 5.6 + - - +
125D GLU* 1.3 75.9 - - - +
127D ARG* 1.3 65.0 + - - +
129D THR* 3.3 5.3 + - - -
130D GLN* 3.2 25.6 + - - +
167D ASN* 3.5 25.4 + - - -
164O ARG 5.5 0.7 - - - -
165O TYR* 3.8 17.7 - - + +
196O GLY* 3.6 33.5 - - - -
197O MET* 3.9 27.6 - - + -
213O MET* 4.7 7.0 - - - -
215O ILE* 4.5 17.0 - - + -
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Residues in contact with ARG 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ASP* 2.9 15.0 + - - +
124D ASN* 2.8 38.4 + - - +
126D TRP* 1.3 77.6 - - - +
128D LYS* 1.3 84.9 + - - +
129D THR 3.6 0.3 + - - -
130D GLN* 2.7 29.0 + - - +
132D MET* 4.4 4.7 - - - +
165O TYR* 3.4 47.8 - - + +
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C GLU* 3.5 29.0 + - - +
136C VAL 6.1 0.3 - - - -
137C ALA* 5.3 0.2 - - - +
158C SER* 3.6 33.7 + - - +
124D ASN* 2.9 39.1 + - - +
125D GLU* 4.3 2.7 - - - +
126D TRP 3.2 0.2 - - - -
127D ARG* 1.3 100.2 - - - +
129D THR* 1.3 54.6 + - - +
130D GLN 3.5 0.7 - - - -
132D MET* 4.0 7.2 - - - +
134D ARG* 2.7 27.9 + - - -
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Residues in contact with THR 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ALA* 4.1 10.3 - - + -
154C PRO* 4.9 2.9 - - - +
155C PRO* 5.9 0.5 - - - +
156C CYS* 3.9 20.2 + - - +
157C VAL* 3.4 38.1 - - - +
158C SER* 3.5 7.9 - - - +
125D GLU 2.7 23.7 + - - +
126D TRP* 3.3 8.9 + - - -
128D LYS* 1.3 80.2 - - - +
130D GLN* 1.3 63.0 + - - +
134D ARG* 3.4 5.6 - - - +
164D GLY* 3.4 1.7 - - - -
165D CYS* 2.9 30.7 + - - +
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Residues in contact with GLN 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D TRP 3.2 11.2 + - - +
127D ARG* 2.7 27.0 + - - +
128D LYS 3.5 0.6 - - - -
129D THR* 1.3 79.3 - - - +
131D CYS* 1.3 70.9 + - - +
132D MET* 3.2 23.9 + - - +
134D ARG* 3.1 18.7 + - - -
163D GLY 3.5 2.3 - - - +
164D GLY* 4.1 0.4 - - - -
165D CYS 4.6 4.3 - - - -
165O TYR* 3.4 41.1 - - + +
166O PRO* 3.2 31.7 - - - +
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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