Contacts of the helix formed by residues 111 - 124 (chain D) in PDB entry 2QW4
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 ALA 111 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU 3.1 21.6 + - - +
108D LEU 3.1 2.7 + - - +
110D SER* 1.3 81.4 - - - +
112D PHE* 1.3 65.8 + - - +
113D LEU 3.4 1.1 - - - -
114D GLU* 3.2 13.4 + - - +
115D LEU* 2.9 42.7 + - + +
179D VAL 3.9 7.0 - - - +
180D LEU* 3.6 19.5 - - + +
184D ARG* 4.3 2.5 - - - +
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Residues in contact with PHE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LEU* 3.6 42.8 - - + -
82D SER* 4.2 6.1 - - - -
83D LEU* 3.7 40.8 - - + -
86D ILE* 5.1 8.7 - - + -
108D LEU* 2.9 15.9 + - + +
109D GLU 3.5 8.5 + - - +
110D SER 3.4 1.4 - - - -
111D ALA* 1.3 76.9 - - - +
113D LEU* 1.3 65.8 + - + +
115D LEU* 3.2 7.1 + - - +
116D PHE* 2.6 44.8 + + + +
257D ILE* 3.8 26.5 - - + -
260D ILE* 4.0 27.1 - - + -
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LEU* 4.6 10.1 - - + -
109D GLU 4.9 1.0 + - - -
110D SER 4.9 2.2 + - - +
111D ALA 3.4 0.6 - - - -
112D PHE* 1.3 97.1 - - + +
114D GLU* 1.3 63.0 + - + +
116D PHE* 3.5 6.3 - - + +
117D ILE* 3.1 31.9 + - + +
151D TRP* 4.3 22.7 - - + -
235D CYS* 4.2 28.9 - - + +
239D LEU* 4.2 26.2 - - + +
242D ILE* 4.5 17.5 - - + -
260D ILE* 5.5 12.1 - - + +
261D PHE* 6.3 1.3 - - - +
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Residues in contact with GLU 114 (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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110D SER 3.0 23.8 - - - +
111D ALA 3.2 4.5 + - - +
113D LEU* 1.3 75.5 - - + +
115D LEU* 1.3 54.0 + - - +
117D ILE* 3.1 5.2 + - - +
118D LEU* 2.8 37.5 + - - +
179D VAL* 3.7 25.2 - - + +
184D ARG* 3.3 10.9 + - - -
228D LEU* 5.7 2.3 - - - +
231D LEU* 3.8 15.8 - - + +
232D ARG* 3.1 47.4 + - - +
235D CYS* 3.5 26.0 - - - -
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ILE* 4.2 23.8 - - + -
89D TRP* 4.0 21.1 - - + -
108D LEU* 5.4 0.7 - - + -
111D ALA* 2.9 42.9 + - + +
112D PHE* 3.4 6.7 - - - +
114D GLU* 1.3 72.9 - - - +
116D PHE* 1.3 68.1 + - - +
118D LEU* 4.6 4.5 - - + -
119D ARG* 2.9 38.4 + - + +
176D SER* 3.6 31.2 - - - +
179D VAL* 3.9 13.0 - - + -
180D LEU* 3.9 16.8 - - + -
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Residues in contact with PHE 116 (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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78D LEU 4.0 9.6 - - - -
79D LEU* 4.2 26.0 - - + -
82D SER* 3.6 35.0 - - - -
86D ILE* 4.9 4.8 - - - +
112D PHE* 2.6 32.2 + + + +
113D LEU* 3.5 10.1 - - + +
115D LEU* 1.3 73.7 - - - +
117D ILE* 1.3 68.9 + - + +
119D ARG* 4.0 2.2 - - - +
120D LEU* 3.0 37.8 + - + +
133D PHE* 4.2 18.8 - + - -
134D CYS* 5.3 3.6 - - - -
148D PHE* 4.0 30.7 - + - -
151D TRP* 4.3 19.3 - + - -
155D ILE* 5.3 2.0 - - + -
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Residues in contact with ILE 117 (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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113D LEU* 3.1 18.3 + - + +
114D GLU* 3.1 3.2 + - - +
116D PHE* 1.3 78.4 - - + +
118D LEU* 1.3 55.8 - - - +
120D LEU* 3.3 3.4 + - - +
121D ALA* 2.7 38.5 + - - +
151D TRP* 4.1 22.2 - - + -
155D ILE* 4.2 21.3 - - + +
158D PHE* 4.8 6.1 - - + -
231D LEU* 3.4 19.7 - - + +
234D LEU* 3.9 26.2 - - + -
235D CYS* 3.6 41.7 - - - +
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Residues in contact with LEU 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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114D GLU 2.8 19.3 + - - +
115D LEU* 4.1 4.7 - - + +
117D ILE* 1.3 73.6 - - - +
119D ARG* 1.3 65.2 + - + +
121D ALA* 3.8 4.8 - - - +
122D TYR* 2.9 26.0 + - - +
158D PHE* 4.5 7.4 - - + -
162D LEU* 4.3 15.7 - - + -
172D PHE* 3.7 25.6 - - + -
175D LEU* 4.1 18.6 - - + -
176D SER* 4.0 23.1 - - - +
179D VAL* 3.7 32.3 - - + -
227D LYS* 6.5 0.2 - - + -
228D LEU* 5.3 0.7 - - + -
231D LEU* 3.8 19.3 - - + +
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Residues in contact with ARG 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D HIS* 4.7 10.3 + - - +
44D SER* 2.9 20.6 + - - -
45D GLY* 3.3 26.7 - - - +
85D VAL* 3.7 15.3 - - - +
86D ILE* 3.3 27.3 - - - +
89D TRP* 3.8 26.8 - - - +
115D LEU* 2.9 29.5 + - + +
116D PHE 4.0 1.3 - - - +
118D LEU* 1.3 79.4 - - + +
120D LEU* 1.3 63.1 + - - +
122D TYR* 3.2 3.5 + - - +
123D ARG* 3.0 52.6 + - - +
134D CYS* 3.2 17.0 - - - +
172D PHE* 4.3 16.8 - - + -
176D SER* 5.4 4.0 - - - -
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Residues in contact with LEU 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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116D PHE* 3.0 33.0 + - + +
117D ILE* 3.8 1.3 - - - +
119D ARG* 1.3 74.2 - - - +
121D ALA* 1.3 58.1 + - - +
123D ARG* 4.0 8.9 - - - +
124D SER* 2.5 46.5 + - - +
131D LEU* 3.6 23.1 - - + -
132D ILE 3.3 27.1 - - - +
133D PHE* 3.6 37.9 - - + -
134D CYS* 5.3 1.8 - - - +
152D ILE* 4.6 6.1 - - + -
155D ILE* 3.8 25.4 - - + -
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ILE 2.7 22.5 + - - +
118D LEU 3.8 3.1 - - - +
120D LEU* 1.3 76.3 - - - +
122D TYR* 1.3 63.2 + - - +
123D ARG 3.3 0.2 + - - -
124D SER* 3.6 3.8 + - - -
155D ILE* 4.4 9.6 - - + +
158D PHE* 3.6 33.0 - - + -
159D SER* 2.5 40.1 + - - +
162D LEU* 4.1 3.1 - - + -
163D HIS* 3.4 5.2 + - - -
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Residues in contact with TYR 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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41D HIS* 4.4 18.6 - + - -
118D LEU 2.9 11.5 + - - +
119D ARG 3.6 3.1 - - - +
120D LEU 3.2 0.2 - - - -
121D ALA* 1.3 78.1 - - - +
123D ARG* 1.3 61.0 + - + +
124D SER 4.0 0.2 - - - +
162D LEU* 4.2 15.9 - - + +
163D HIS* 3.1 33.3 - + - -
167D VAL* 2.5 36.7 + - + -
168D ASP* 3.6 12.5 - - - -
169D VAL* 3.6 9.4 + - + +
172D PHE* 3.4 59.7 - + + -
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Residues in contact with ARG 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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41D HIS* 6.3 1.4 - - - -
45D GLY* 4.2 4.8 - - - -
46D PRO* 3.7 22.4 - - - +
51D LEU* 5.7 0.2 - - - -
119D ARG* 3.0 57.4 + - - +
120D LEU* 3.9 12.1 - - - +
122D TYR* 1.3 77.9 - - + +
124D SER* 1.3 70.8 + - - +
125D LYS* 3.9 5.4 - - - +
132D ILE* 3.0 60.3 + - + +
133D PHE* 3.8 0.6 - - - +
134D CYS* 3.2 31.8 - - - +
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Residues in contact with SER 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D LEU* 2.5 42.5 + - - +
121D ALA* 3.6 4.0 + - - -
122D TYR 3.6 0.9 - - - +
123D ARG* 1.3 84.9 - - - +
125D LYS* 1.3 70.5 + - - +
126D PRO* 4.0 2.9 - - - -
130D LYS 3.2 14.1 - - - -
131D LEU* 3.7 12.1 - - - +
132D ILE* 3.4 17.2 + - - +
156D LEU* 4.8 5.2 - - - -
159D SER* 4.7 4.3 - - - -
163D HIS* 3.5 15.0 + - - -
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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