Contacts of the strand formed by residues 103 - 112 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101G GLN 4.0 0.7 - - - -
102G PRO* 1.3 76.8 - - - +
104G ILE* 1.3 57.3 + - - +
139G VAL* 3.2 3.7 - - - -
140G VAL* 2.7 52.1 + - + +
147G TRP* 3.3 64.3 - - - +
236G MET* 3.8 32.7 - - + +
237G VAL 3.2 20.6 - - - +
238G ALA* 3.6 16.9 - - - +
239G VAL* 3.9 5.6 - - - -
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Residues in contact with ILE 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G ARG* 1.3 70.7 - - - +
105G GLU* 1.3 61.3 + - - +
137G LEU* 4.2 21.1 - - + -
138G GLU 3.2 9.9 - - - +
139G VAL* 3.5 30.5 - - + -
185G MET* 3.7 13.5 - - + +
236G MET* 3.3 4.1 - - - -
237G VAL* 3.1 39.0 + - + +
239G VAL* 3.4 15.3 - - + -
245G PHE* 3.0 51.8 - - + -
257G ALA* 6.0 0.9 - - + -
259G PHE* 4.7 5.8 - - + -
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Residues in contact with GLU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ILE* 1.3 74.9 - - - +
106G ALA* 1.3 60.8 + - - +
107G GLU* 3.1 26.3 - - - +
137G LEU* 3.4 7.9 - - - +
138G GLU* 2.8 43.5 + - + +
140G VAL* 3.7 8.0 - - - +
185G MET* 4.5 5.2 - - - -
232G ALA* 3.5 26.4 - - + +
234G GLY 4.2 4.3 - - - +
235G PRO 5.2 0.4 - - - -
236G MET* 3.7 27.5 + - + +
1263G PO4 3.2 34.2 + - - -
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Residues in contact with ALA 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G GLU* 1.3 73.1 - - - +
107G GLU* 1.3 63.5 + - - +
136G ALA 3.6 5.8 - - - +
137G LEU* 4.3 2.9 - - + -
183G MET* 3.7 35.6 - - + +
185G MET* 4.3 5.4 - - - +
232G ALA* 3.6 0.7 - - - -
233G LEU* 2.9 31.0 + - + +
234G GLY 5.2 0.2 + - - -
247G ALA* 3.6 29.6 - - + -
249G ILE* 4.7 2.0 - - + -
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Residues in contact with GLU 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G VAL 4.5 1.4 - - - +
105G GLU* 3.1 34.7 - - + +
106G ALA* 1.3 81.1 - - - +
108G ILE* 1.3 65.5 + - - +
136G ALA* 2.8 41.0 + - + +
138G GLU* 3.1 23.0 - - + +
229G LEU* 3.3 22.1 - - + +
230G THR 4.9 0.2 - - - +
231G GLY* 3.0 38.7 + - - +
232G ALA* 3.5 8.1 + - - +
233G LEU* 4.0 6.3 - - - +
249G ILE* 3.5 8.0 - - - +
1263G PO4 4.3 2.3 + - - -
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Residues in contact with ILE 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G GLU* 1.3 77.0 - - - +
109G ALA* 1.3 68.0 + - - +
110G LEU* 4.1 16.6 - - + -
133G VAL* 4.2 13.5 - - + -
134G LEU 3.8 3.1 - - - +
178G LEU* 4.2 8.1 - - + -
181G CYS* 3.5 32.5 - - - -
204G PRO* 3.9 22.9 - - + -
229G LEU* 4.9 0.2 - - - -
230G THR* 2.7 46.7 + - - +
231G GLY 4.4 1.4 + - - -
233G LEU* 4.2 16.1 - - + +
249G ILE* 4.5 6.3 - - + -
252G ILE* 3.6 19.3 - - + -
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Residues in contact with ALA 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G GLU 4.1 0.8 + - - -
108G ILE* 1.3 74.3 - - - +
110G LEU* 1.3 63.6 + - - +
133G VAL* 3.4 5.0 - - - +
134G LEU* 2.8 49.3 + - + +
136G ALA* 4.1 7.9 - - + -
166G ILE* 4.9 2.2 - - + -
227G ILE* 4.2 17.0 - - + -
228G ILE 3.3 5.8 - - - +
229G LEU* 3.7 23.6 - - + -
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Residues in contact with LEU 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G ILE* 4.1 11.0 - - + -
109G ALA* 1.3 82.4 - - - +
111G VAL* 1.3 65.0 + - - +
112G LEU* 5.1 4.4 - - + +
126G LEU* 4.7 1.1 - - + -
130G ILE* 4.4 21.8 - - + -
132G TRP 3.4 3.4 - - - +
133G VAL* 3.8 20.6 - - + -
178G LEU* 5.3 3.1 - - + -
205G LEU* 3.7 32.1 - - + -
208G ALA* 3.8 15.9 - - + -
226G ASP 3.7 0.7 - - - +
227G ILE* 3.3 6.1 - - - +
228G ILE* 2.8 45.6 + - + +
230G THR* 3.8 25.1 - - + -
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Residues in contact with VAL 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ASP* 4.6 16.6 - - + +
128F ASN* 5.8 2.7 - - + +
110G LEU* 1.3 78.3 - - - +
112G LEU* 1.3 59.5 + - - +
130G ILE* 3.6 4.3 - - - -
131G GLU* 2.6 49.1 + - - +
132G TRP* 2.9 26.7 + - + +
134G LEU* 3.9 23.6 - - + -
225G GLY* 3.9 16.2 - - - +
226G ASP 3.4 8.7 - - - +
227G ILE* 4.4 14.6 - - + -
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Residues in contact with LEU 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G LEU* 5.1 7.6 - - + -
111G VAL* 1.3 76.5 - - - +
113G ASN* 1.4 59.7 + - - +
114G ARG 3.9 12.1 - - - +
116G LEU* 3.9 22.2 - - + -
126G LEU* 5.2 5.8 - - + -
129G ALA* 3.2 18.8 - - + +
130G ILE* 5.0 5.2 - - + -
131G GLU* 3.9 10.0 - - - +
222G LEU* 3.8 34.1 - - + -
223G ARG 3.8 15.9 - - - +
224G THR* 4.1 0.5 + - - -
225G GLY* 2.9 25.5 + - - -
226G ASP* 3.2 21.2 + - + +
228G ILE* 3.9 20.9 - - + -
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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