Contacts of the strand formed by residues 130 - 140 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110N LEU* 4.4 19.3 - - + -
111N VAL 3.7 5.2 - - - +
112N LEU* 4.7 4.0 - - + +
113N ASN* 3.2 8.9 + - - +
126N LEU* 3.6 18.4 - - + +
127N TYR* 3.3 20.2 + - + +
128N ASN 3.5 0.9 - - - +
129N ALA* 1.3 74.6 - - - +
131N GLU* 1.3 61.7 + - - +
132N TRP 3.6 24.9 - - - +
133N VAL* 4.1 5.8 - - + -
173N PRO* 3.4 36.4 - - + +
178N LEU* 5.2 2.7 - - + -
205N LEU* 3.6 38.8 - - + -
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Residues in contact with GLU 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M ASN* 3.1 32.8 + - - +
111N VAL* 2.7 27.5 + - - +
112N LEU 3.9 11.2 - - - +
113N ASN* 3.2 25.1 + - - +
129N ALA 3.6 0.8 + - - -
130N ILE* 1.3 74.8 - - - +
132N TRP* 1.3 71.4 + - + +
172N ARG* 3.2 39.5 + - - +
173N PRO* 3.8 5.4 - - - +
225N GLY* 5.3 2.4 - - - -
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Residues in contact with TRP 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124M ASP 5.6 2.2 - - - -
127M TYR* 4.7 15.0 - + + -
128M ASN* 2.7 39.7 - - + +
173M PRO* 5.0 9.2 - - + -
174M ALA* 3.7 33.4 - - + -
110N LEU* 3.4 4.3 - - - -
111N VAL* 3.0 41.4 + - + -
130N ILE* 3.6 5.5 - - - +
131N GLU* 1.3 101.4 - - + +
133N VAL* 1.3 64.6 + - - +
134N LEU* 4.2 16.2 - - + -
170N ALA* 3.6 28.3 - - + -
171N GLN 3.3 21.8 - - - -
172N ARG* 3.3 40.4 - - - -
173N PRO* 5.0 0.2 - - - -
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Residues in contact with VAL 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108N ILE* 4.2 10.3 - - + -
109N ALA 3.4 2.9 - - - -
110N LEU* 3.8 13.5 - - + -
130N ILE* 4.1 9.2 - - + -
132N TRP* 1.3 76.0 - - - +
134N LEU* 1.3 63.7 + - - +
171N GLN* 2.8 37.3 + - - +
173N PRO* 4.0 18.2 - - + -
176N LEU* 3.6 33.4 - - + -
178N LEU* 4.0 22.2 - - + -
252N ILE* 4.3 12.8 - - + -
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Residues in contact with LEU 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124M ASP* 4.8 7.2 - - + +
127M TYR* 3.9 22.9 - - + -
108N ILE* 3.8 1.9 - - - -
109N ALA* 2.8 56.6 + - + +
111N VAL* 3.9 27.1 - - + -
132N TRP* 4.2 8.5 - - + -
133N VAL* 1.3 78.9 - - - +
135N PRO* 1.3 76.7 - - + +
166N ILE* 3.9 21.5 - - + -
167N GLY 4.3 2.2 - - - +
169N PRO 4.4 4.0 - - - +
170N ALA* 3.8 24.7 - - + -
227N ILE* 5.0 3.6 - - + -
252N ILE* 4.2 5.6 - - - -
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Residues in contact with PRO 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107N GLU 3.9 4.9 - - - +
108N ILE* 5.0 0.7 - - - -
109N ALA* 5.3 0.2 - - - -
134N LEU* 1.3 92.3 - - + +
136N ALA* 1.3 60.0 + - - +
166N ILE* 3.8 2.3 - - - +
167N GLY 2.9 27.4 + - - -
168N GLY 3.6 22.4 - - - +
169N PRO 3.9 12.3 - - - +
249N ILE* 3.8 22.0 - - + -
252N ILE* 3.8 16.6 - - + +
253N GLY 3.9 2.2 - - - -
254N SER 3.7 24.7 - - - +
255N VAL* 3.7 10.7 - - + +
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Residues in contact with ALA 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106N ALA* 3.6 4.2 - - - +
107N GLU* 2.8 38.5 + - + +
109N ALA* 4.1 10.3 - - + -
135N PRO* 1.3 76.0 - - - +
137N LEU* 1.3 64.8 + - - +
164N TYR* 5.6 0.4 - - + -
165N VAL 3.2 12.3 - - - +
166N ILE* 4.5 4.9 - - + -
229N LEU* 3.9 28.0 - - + -
249N ILE* 4.8 0.5 - - - +
255N VAL* 3.7 10.6 - - - +
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Residues in contact with LEU 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N ILE* 4.2 13.5 - - + -
105N GLU 3.4 9.0 - - - +
106N ALA* 4.3 1.6 - - - -
107N GLU* 5.3 0.2 - - - -
136N ALA* 1.3 78.2 - - - +
138N GLU* 1.3 59.5 + - - +
139N VAL 4.1 0.2 - - - -
164N TYR* 3.3 6.4 - - - +
165N VAL* 2.9 42.6 + - + +
185N MET* 4.0 19.5 - - + -
229N LEU* 5.7 0.2 - - - -
245N PHE* 4.5 11.4 - - + +
246N GLU 5.3 0.2 - - - -
247N ALA* 3.8 28.0 - - + +
255N VAL* 3.8 23.5 - - + +
256N ALA* 4.0 1.8 - - - -
257N ALA* 4.0 36.1 - - + +
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Residues in contact with GLU 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N LYS* 3.1 50.7 + - - +
82N LEU* 5.0 1.6 - - + +
86N MET* 5.7 0.3 - - - +
104N ILE* 3.2 3.5 - - - -
105N GLU* 2.8 41.9 + - + +
107N GLU* 3.1 33.0 - - - +
137N LEU* 1.3 73.3 - - - +
139N VAL* 1.3 63.6 + - - +
140N VAL* 3.5 14.6 + - - +
161N CYS* 3.7 15.8 - - - -
162N GLY 4.7 1.0 + - - -
163N VAL 3.8 10.5 - - - +
164N TYR* 4.2 1.3 - - + -
229N LEU* 3.8 18.2 - - + -
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Residues in contact with VAL 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94N ILE* 4.4 8.3 - - + -
99N VAL* 4.1 14.6 - - + -
102N PRO* 4.0 24.2 - - + -
103N ARG 3.2 11.7 - - - +
104N ILE* 3.5 18.6 - - + -
138N GLU* 1.3 70.0 - - - +
140N VAL* 1.3 59.2 + - - +
162N GLY* 3.2 8.0 + - - -
163N VAL* 2.9 51.9 + - + +
165N VAL* 4.7 8.7 - - + -
239N VAL* 4.9 0.2 - - + -
259N PHE* 3.9 25.1 - - + -
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Residues in contact with VAL 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N LYS* 4.0 2.9 - - - +
99N VAL* 3.7 2.4 - - - +
101N GLN 4.0 0.2 - - - +
102N PRO* 3.3 4.7 - - - +
103N ARG* 2.7 55.3 + - + +
105N GLU* 3.7 15.5 - - - +
138N GLU* 3.5 18.6 + - - +
139N VAL* 1.3 74.8 - - - +
141N GLY* 1.3 58.3 + - - +
147N TRP* 3.7 22.4 - - + -
160N SER* 3.2 17.5 - - - +
162N GLY 4.2 0.7 - - - +
236N MET* 3.9 13.0 - - + -
1262N PO4 3.3 24.0 - - - +
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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