Contacts of the strand formed by residues 103 - 112 (chain M) 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 ARG 103 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101M GLN 4.0 0.4 - - - -
102M PRO* 1.3 78.9 - - - +
104M ILE* 1.3 57.6 + - - +
139M VAL* 3.2 3.7 - - - -
140M VAL* 2.7 52.6 + - + +
147M TRP* 3.3 64.6 - - - +
236M MET* 3.8 34.9 - - + +
237M VAL 3.2 19.5 - - - +
238M ALA* 3.7 15.9 - - + +
239M VAL* 3.9 3.8 - - - -
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Residues in contact with ILE 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M ARG* 1.3 72.2 - - - +
105M GLU* 1.3 61.7 + - - +
137M LEU* 4.2 22.0 - - + -
138M GLU 3.2 9.6 - - - +
139M VAL* 3.5 31.2 - - + -
185M MET* 3.8 13.4 - - + +
236M MET* 3.3 3.9 - - - -
237M VAL* 3.1 41.2 + - + +
239M VAL* 3.4 15.0 - - + -
245M PHE* 3.1 48.9 - - + -
257M ALA* 6.0 0.4 - - + -
259M PHE* 4.6 5.8 - - + -
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Residues in contact with GLU 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M ILE* 1.3 75.1 - - - +
106M ALA* 1.3 59.3 + - - +
107M GLU* 3.0 24.0 - - - +
137M LEU* 3.4 8.7 - - - +
138M GLU* 2.8 42.8 + - + +
140M VAL* 3.7 10.9 - - - +
185M MET* 4.5 5.8 - - - -
232M ALA* 3.5 26.9 - - + +
234M GLY 4.2 6.7 - - - +
235M PRO 5.2 0.4 - - - -
236M MET* 3.7 27.2 + - + +
1262M PO4 2.5 31.2 + - - -
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Residues in contact with ALA 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105M GLU* 1.3 73.5 - - - +
107M GLU* 1.3 62.4 + - - +
136M ALA 3.6 6.5 - - - +
137M LEU* 4.3 2.7 - - + -
183M MET* 3.7 38.6 - - + +
185M MET* 4.5 6.0 - - - +
232M ALA* 3.6 0.5 - - - -
233M LEU* 2.9 30.7 + - + +
234M GLY 5.1 0.8 + - - -
247M ALA* 3.8 23.3 - - + -
249M ILE* 4.6 3.1 - - + -
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Residues in contact with GLU 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M VAL 4.5 2.1 - - - +
105M GLU* 3.0 34.0 - - + +
106M ALA* 1.3 81.0 - - - +
108M ILE* 1.3 65.8 + - - +
135M PRO 3.8 0.2 - - - -
136M ALA* 2.8 40.0 + - + +
138M GLU* 3.1 23.3 - - + +
229M LEU* 3.3 22.6 - - + +
231M GLY* 3.0 38.1 + - - +
232M ALA* 3.5 8.2 + - - +
233M LEU* 4.0 6.3 - - - +
249M ILE* 3.6 8.5 - - - +
1262M PO4 4.4 1.6 + - - -
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Residues in contact with ILE 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M GLU* 1.3 77.1 - - - +
109M ALA* 1.3 69.9 + - - +
110M LEU* 4.1 16.6 - - + -
133M VAL* 4.2 13.5 - - + -
134M LEU 3.9 3.4 - - - +
178M LEU* 4.2 8.5 - - + -
181M CYS* 3.5 32.3 - - - -
204M PRO* 3.8 23.3 - - + -
229M LEU* 4.0 0.7 - - - -
230M THR* 2.7 47.7 + - - +
231M GLY 4.4 1.6 + - - -
233M LEU* 4.2 17.5 - - + +
249M ILE* 4.5 6.5 - - + -
252M ILE* 3.8 17.7 - - + -
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Residues in contact with ALA 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M GLU 4.1 0.8 + - - -
108M ILE* 1.3 73.3 - - - +
110M LEU* 1.3 64.2 + - - +
133M VAL* 3.4 5.4 - - - +
134M LEU* 2.8 49.8 + - + +
136M ALA* 4.1 8.3 - - + -
166M ILE* 4.9 2.0 - - + -
227M ILE* 4.2 17.0 - - + -
228M ILE 3.3 5.6 - - - +
229M LEU* 3.7 23.6 - - + -
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Residues in contact with LEU 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108M ILE* 4.1 10.8 - - + -
109M ALA* 1.3 81.7 - - - +
111M VAL* 1.3 66.1 + - - +
112M LEU* 5.1 3.8 - - + -
126M LEU* 4.7 1.1 - - + -
130M ILE* 4.4 20.6 - - + -
132M TRP 3.5 2.9 - - - +
133M VAL* 3.8 20.2 - - + -
178M LEU* 5.2 3.1 - - + -
204M PRO* 6.1 0.4 - - + -
205M LEU* 3.7 31.6 - - + -
208M ALA* 3.7 24.0 - - + -
226M ASP 3.7 0.7 - - - +
227M ILE* 3.3 6.5 - - - +
228M ILE* 2.8 45.5 + - + +
230M THR* 3.8 17.3 - - + -
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Residues in contact with VAL 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M LEU* 1.3 79.1 - - - +
112M LEU* 1.3 58.0 + - - +
130M ILE* 3.6 4.5 - - - +
131M GLU* 2.7 48.7 + - - +
132M TRP* 2.9 27.3 + - + +
134M LEU* 3.9 23.1 - - + -
225M GLY* 4.0 16.4 - - - +
226M ASP 3.4 9.9 - - - +
227M ILE* 4.4 8.1 - - + -
124O ASP* 4.4 24.2 - - + +
128O ASN* 6.0 2.2 - - + -
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Residues in contact with LEU 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M LEU* 5.1 7.4 - - + -
111M VAL* 1.3 78.0 - - - +
113M ASN* 1.3 58.4 + - - +
114M ARG 3.9 12.6 - - - +
116M LEU* 3.9 22.0 - - + -
126M LEU* 5.2 5.8 - - + -
129M ALA* 3.2 19.3 - - + +
130M ILE* 5.1 4.7 - - + -
131M GLU* 3.9 9.9 - - - +
222M LEU* 3.8 33.7 - - + -
223M ARG 3.9 15.9 - - - +
224M THR* 4.1 0.5 + - - -
225M GLY* 2.9 25.7 + - - +
226M ASP* 3.3 20.6 + - + +
228M ILE* 3.9 21.8 - - + -
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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