Contacts of the strand formed by residues 130 - 140 (chain D) in PDB entry 2WQT
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 ILE 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D LEU* 4.4 19.1 - - + -
111D VAL 3.7 4.5 - - - +
112D LEU* 4.7 3.8 - - + +
113D ASN* 3.6 8.3 + - - +
126D LEU* 3.6 19.1 - - + +
127D TYR* 3.3 20.5 + - + +
128D ASN 4.8 0.7 - - - +
129D ALA* 1.3 77.3 - - - +
131D GLU* 1.3 63.4 + - - +
132D TRP 3.6 24.9 - - - +
133D VAL* 4.1 5.6 - - + -
173D PRO* 3.5 33.9 - - + +
178D LEU* 5.1 2.7 - - + -
205D LEU* 3.6 39.9 - - + -
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Residues in contact with GLU 131 (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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128C ASN* 2.8 35.4 + - - +
111D VAL* 2.7 30.8 + - - +
112D LEU 3.9 8.4 - - - +
113D ASN* 3.9 23.6 - - - +
129D ALA 3.6 2.0 + - - -
130D ILE* 1.3 73.6 - - - +
132D TRP* 1.3 72.3 + - + +
172D ARG* 3.3 38.9 + - - +
173D PRO* 3.8 6.5 - - - +
225D GLY* 5.3 2.3 - - - -
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Residues in contact with TRP 132 (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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124C ASP 5.4 2.5 - - - -
127C TYR* 4.5 16.8 - - + -
128C ASN* 2.8 38.0 - - + +
173C PRO* 4.9 9.2 - - + -
174C ALA* 3.7 34.5 - - + -
109D ALA 3.9 0.2 - - - +
110D LEU* 3.4 4.3 - - - -
111D VAL* 2.9 43.2 + - + -
130D ILE* 3.6 5.6 - - - +
131D GLU* 1.3 100.4 - - + +
133D VAL* 1.3 64.2 + - - +
134D LEU* 4.2 16.2 - - + -
170D ALA* 3.7 28.7 - - + -
171D GLN 3.4 20.9 - - - -
172D ARG* 3.3 39.0 - - - -
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Residues in contact with VAL 133 (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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108D ILE* 4.2 9.9 - - + -
109D ALA 3.4 2.9 - - - -
110D LEU* 3.8 15.0 - - + -
130D ILE* 4.1 9.4 - - + -
132D TRP* 1.3 75.5 - - - +
134D LEU* 1.3 62.6 + - - +
171D GLN* 2.8 39.1 + - - +
173D PRO* 4.0 17.9 - - + -
176D LEU* 3.6 33.2 - - + -
178D LEU* 4.0 22.2 - - + -
252D ILE* 4.3 13.0 - - + -
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Residues in contact with LEU 134 (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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124C ASP* 4.8 6.1 - - + +
127C TYR* 3.8 33.2 - - + -
108D ILE* 3.8 2.3 - - - +
109D ALA* 2.8 52.5 + - + +
111D VAL* 3.9 26.7 - - + -
132D TRP* 4.2 8.3 - - + -
133D VAL* 1.3 79.2 - - - +
135D PRO* 1.4 74.9 - - + +
166D ILE* 3.9 23.3 - - + -
167D GLY 4.4 3.1 - - - +
169D PRO 4.4 4.5 - - - +
170D ALA* 3.9 14.8 - - + -
227D ILE* 5.0 2.9 - - + -
252D ILE* 4.2 5.2 - - - -
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Residues in contact with PRO 135 (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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107D GLU 3.9 5.2 - - - +
108D ILE* 5.0 0.7 - - - -
134D LEU* 1.4 91.0 - - + +
136D ALA* 1.3 60.8 + - - +
166D ILE* 3.8 2.3 - - - +
167D GLY 2.9 26.5 + - - -
168D GLY 3.6 22.2 - - - +
169D PRO 3.9 12.8 - - - +
249D ILE* 3.8 20.2 - - + -
252D ILE* 3.8 17.7 - - + -
253D GLY 3.9 2.2 - - - -
254D SER 3.6 25.6 - - - +
255D VAL* 3.8 9.8 - - + +
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Residues in contact with ALA 136 (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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106D ALA* 3.6 5.2 - - - +
107D GLU* 2.8 37.0 + - + +
109D ALA* 4.1 10.1 - - + -
134D LEU 3.7 0.2 + - - -
135D PRO* 1.3 76.7 - - - +
137D LEU* 1.3 63.0 + - - +
164D TYR* 5.6 0.4 - - + -
165D VAL 3.2 12.6 - - - +
166D ILE* 4.5 4.9 - - + -
229D LEU* 3.9 28.3 - - + -
249D ILE* 4.7 0.2 - - - +
255D VAL* 3.7 11.4 - - - +
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Residues in contact with LEU 137 (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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104D ILE* 4.2 14.4 - - + -
105D GLU 3.4 8.7 - - - +
106D ALA* 4.3 1.1 - - - -
136D ALA* 1.3 79.1 - - - +
138D GLU* 1.3 60.8 + - - +
139D VAL 4.1 0.2 - - - -
164D TYR* 3.3 5.5 - - - +
165D VAL* 2.8 44.3 + - + +
185D MET* 3.9 19.5 - - - -
245D PHE* 4.5 10.3 - - + +
246D GLU 5.3 0.4 - - - -
247D ALA* 3.8 28.3 - - + +
255D VAL* 3.7 23.8 - - + +
256D ALA 4.0 2.5 - - - -
257D ALA* 3.9 36.8 - - + +
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Residues in contact with GLU 138 (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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60D LYS* 3.1 47.7 + - - +
82D LEU* 5.1 1.4 - - + +
86D MET* 5.7 0.5 - - - +
104D ILE* 3.2 3.8 - - - -
105D GLU* 2.8 41.4 + - + +
107D GLU* 3.1 34.3 - - - +
136D ALA 4.2 0.2 - - - -
137D LEU* 1.3 73.3 - - - +
139D VAL* 1.3 62.8 + - - +
140D VAL* 3.4 17.2 + - - +
161D CYS* 3.7 15.8 - - - -
162D GLY 4.6 1.4 + - - -
163D VAL 3.8 10.0 - - - +
164D TYR* 4.2 1.3 - - + -
229D LEU* 3.8 17.3 - - + -
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Residues in contact with VAL 139 (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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94D ILE* 4.4 7.6 - - + -
99D VAL* 4.1 15.0 - - + -
102D PRO* 4.0 23.8 - - + -
103D ARG 3.2 11.2 - - - +
104D ILE* 3.5 19.5 - - + -
138D GLU* 1.3 70.1 - - - +
140D VAL* 1.3 58.9 - - - +
162D GLY* 3.2 8.0 + - - -
163D VAL* 2.9 52.8 + - + +
165D VAL* 4.7 8.3 - - + -
257D ALA* 5.9 0.4 - - + -
259D PHE* 3.8 25.8 - - + -
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Residues in contact with VAL 140 (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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60D LYS* 4.0 4.7 - - - +
99D VAL* 3.7 2.3 - - - +
102D PRO* 3.3 4.3 - - - +
103D ARG* 2.7 55.6 + - + +
105D GLU* 3.7 23.6 - - - +
138D GLU* 3.4 21.9 + - - +
139D VAL* 1.3 74.9 - - - +
141D GLY* 1.3 59.3 + - - +
147D TRP* 3.7 22.9 - - + -
160D SER 3.2 16.8 - - - +
162D GLY 4.1 0.7 - - - +
236D MET* 3.9 12.6 - - - -
1263D PO4 3.8 11.9 - - - +
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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