Contacts of the strand formed by residues 103 - 112 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101P GLN 4.0 0.7 - - - -
102P PRO* 1.3 77.8 - - - +
104P ILE* 1.3 58.8 + - - +
139P VAL* 3.2 3.4 - - - -
140P VAL* 2.7 52.4 + - + +
147P TRP* 3.3 63.2 - - - +
236P MET* 3.8 33.8 - - + +
237P VAL* 3.2 19.1 - - - +
238P ALA* 3.7 16.1 - - - +
239P VAL* 3.9 4.5 - - - -
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Residues in contact with ILE 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P ARG* 1.3 72.4 - - - +
105P GLU* 1.3 61.8 + - - +
137P LEU* 4.2 21.3 - - + -
138P GLU 3.2 8.7 - - - +
139P VAL* 3.5 31.6 - - + -
185P MET* 3.8 13.7 - - + +
236P MET* 3.3 5.3 - - - -
237P VAL* 3.0 45.5 + - + +
239P VAL* 3.4 15.3 - - + -
245P PHE* 3.1 47.6 - - + -
257P ALA* 6.1 0.7 - - + -
259P PHE* 4.7 5.2 - - + -
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Residues in contact with GLU 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104P ILE* 1.3 74.9 - - - +
106P ALA* 1.3 59.6 + - - +
107P GLU* 3.0 23.4 - - + +
137P LEU* 3.4 8.3 - - - +
138P GLU* 2.8 41.3 + - + +
140P VAL* 3.8 8.3 - - + +
185P MET* 4.5 6.1 - - - -
232P ALA* 3.4 29.5 - - + +
234P GLY 4.2 6.3 - - - +
235P PRO 5.2 0.4 - - - -
236P MET* 3.7 21.9 + - + +
1263P PO4 2.8 38.3 + - - -
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Residues in contact with ALA 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P GLU* 1.3 73.7 - - - +
107P GLU* 1.3 63.1 + - - +
136P ALA 3.6 6.5 - - - +
137P LEU* 4.3 3.4 - - + -
183P MET* 3.7 41.4 - - + +
185P MET* 4.5 5.2 - - - +
232P ALA* 3.6 0.3 - - - -
233P LEU* 2.9 32.0 + - + +
234P GLY 5.1 1.0 + - - -
247P ALA* 3.8 20.6 - - + -
249P ILE* 4.7 3.4 - - + -
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Residues in contact with GLU 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P VAL 4.5 3.1 - - - +
105P GLU* 3.0 33.9 - - + +
106P ALA* 1.3 81.4 - - - +
108P ILE* 1.3 66.1 + - - +
136P ALA* 2.8 40.2 + - + +
138P GLU* 3.1 23.7 - - + +
229P LEU* 3.3 22.9 - - + +
230P THR 4.9 0.2 - - - +
231P GLY* 2.9 38.1 + - - +
232P ALA* 3.5 8.0 + - - +
233P LEU* 4.0 6.5 - - - -
249P ILE* 3.6 8.3 - - - +
1263P PO4 4.8 0.9 + - - -
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Residues in contact with ILE 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P GLU* 1.3 76.4 - - - +
109P ALA* 1.3 69.6 + - - +
110P LEU* 4.1 16.6 - - + -
133P VAL* 4.2 14.1 - - + -
134P LEU 3.8 4.0 - - - +
178P LEU* 4.2 8.5 - - + -
181P CYS* 3.5 31.6 - - - -
204P PRO* 3.8 24.5 - - + -
229P LEU* 5.0 0.2 - - - -
230P THR* 2.6 47.6 + - - +
231P GLY 4.4 1.2 + - - -
233P LEU* 4.2 18.6 - - + +
249P ILE* 4.5 5.4 - - + -
252P ILE* 3.8 18.4 - - + -
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Residues in contact with ALA 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P GLU 4.1 1.0 + - - -
108P ILE* 1.3 72.1 - - - +
110P LEU* 1.3 64.4 + - - +
133P VAL* 3.4 5.2 - - - +
134P LEU* 2.8 50.8 + - + +
136P ALA* 4.1 8.3 - - + -
166P ILE* 4.9 2.5 - - + -
227P ILE* 4.2 17.5 - - + -
228P ILE 3.2 6.7 - - - +
229P LEU* 3.7 23.1 - - + -
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Residues in contact with LEU 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P ILE* 4.1 10.8 - - + -
109P ALA* 1.3 80.6 - - - +
111P VAL* 1.3 65.9 + - - +
112P LEU* 5.1 4.5 - - + -
126P LEU* 4.7 0.7 - - + -
130P ILE* 4.4 21.5 - - + -
132P TRP 3.5 2.9 - - - +
133P VAL* 3.8 20.2 - - + -
178P LEU* 5.3 2.7 - - + -
204P PRO* 6.1 0.2 - - + -
205P LEU* 3.6 32.1 - - + -
208P ALA* 3.8 16.4 - - + -
226P ASP 3.7 0.5 - - - +
227P ILE* 3.3 6.6 - - - +
228P ILE* 2.8 47.8 + - + +
230P THR* 3.7 25.4 - - + -
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Residues in contact with VAL 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P LEU* 1.3 77.3 - - - +
112P LEU* 1.3 58.9 + - - +
130P ILE* 3.6 4.0 - - - -
131P GLU* 2.6 48.9 + - - +
132P TRP* 2.9 27.6 + - + +
134P LEU* 3.9 22.9 - - + -
225P GLY* 3.9 16.4 - - - +
226P ASP 3.4 8.5 - - - +
227P ILE* 4.4 14.8 - - + -
124S ASP* 4.5 17.7 - - + +
128S ASN* 6.0 2.0 - - + -
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Residues in contact with LEU 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P LEU* 5.1 8.3 - - + -
111P VAL* 1.3 77.8 - - - +
113P ASN* 1.4 60.1 + - - +
114P ARG 4.0 13.9 - - - +
116P LEU* 3.9 21.1 - - + -
126P LEU* 5.2 5.4 - - + -
129P ALA* 3.2 18.6 - - + +
130P ILE* 5.1 4.7 - - + -
131P GLU* 3.9 9.7 - - - +
222P LEU* 3.8 34.8 - - + -
223P ARG 3.9 14.6 - - - +
224P THR* 4.1 0.3 + - - -
225P GLY* 3.0 24.6 + - - -
226P ASP* 3.3 21.9 + - + +
228P 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