Contacts of the strand formed by residues 103 - 112 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101O GLN 4.0 0.4 - - - -
102O PRO* 1.3 76.5 - - - +
104O ILE* 1.3 58.9 + - - +
139O VAL* 3.2 3.7 - - - -
140O VAL* 2.7 52.2 + - + +
147O TRP* 3.3 63.4 - - - +
236O MET* 3.8 34.1 - - + +
237O VAL* 3.2 19.7 - - - +
238O ALA* 3.7 15.9 - - + +
239O VAL* 3.9 4.0 - - - -
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Residues in contact with ILE 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O ARG* 1.3 72.8 - - - +
105O GLU* 1.3 61.8 + - - +
137O LEU* 4.2 21.1 - - + -
138O GLU 3.2 9.6 - - - +
139O VAL* 3.5 31.2 - - + -
185O MET* 3.9 12.6 - - + +
236O MET* 3.3 4.2 - - - -
237O VAL* 3.0 44.2 + - + +
239O VAL* 3.5 14.8 - - + -
245O PHE* 3.1 49.8 - - + -
257O ALA* 6.0 0.7 - - + -
259O PHE* 4.7 5.2 - - + -
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Residues in contact with GLU 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O ILE* 1.3 76.0 - - - +
106O ALA* 1.3 59.5 + - - +
107O GLU* 3.0 27.0 - - + +
137O LEU* 3.4 8.4 - - - +
138O GLU* 2.8 39.9 + - + +
140O VAL* 3.7 8.1 - - + +
185O MET* 4.4 5.8 - - - -
232O ALA* 3.5 26.9 - - + +
234O GLY 4.2 6.7 - - - +
235O PRO 5.2 0.2 - - - -
236O MET* 3.7 26.9 + - + +
1262O PO4 2.5 33.7 + - - -
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Residues in contact with ALA 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105O GLU* 1.3 74.0 - - - +
107O GLU* 1.3 63.2 + - - +
136O ALA 3.6 5.8 - - - +
137O LEU* 4.3 2.5 - - + -
183O MET* 3.7 39.6 - - + +
185O MET* 4.4 6.0 - - - +
232O ALA* 3.6 0.5 - - - -
233O LEU* 2.9 30.4 + - + +
234O GLY 5.2 0.8 + - - -
247O ALA* 3.8 22.7 - - + -
249O ILE* 4.7 2.7 - - + -
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Residues in contact with GLU 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61O VAL 4.5 2.6 - - - +
105O GLU* 3.0 35.5 - - + +
106O ALA* 1.3 82.2 - - - +
108O ILE* 1.3 66.8 + - - +
136O ALA* 2.8 40.7 + - + +
138O GLU* 3.1 22.9 - - + +
229O LEU* 3.3 22.1 - - + +
231O GLY* 2.9 40.3 + - - +
232O ALA* 3.6 6.7 + - - +
233O LEU* 4.0 5.8 - - - +
249O ILE* 3.6 7.1 - - - +
1262O PO4 4.7 0.2 + - - -
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Residues in contact with ILE 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O GLU* 1.3 76.6 - - - +
109O ALA* 1.3 67.7 + - - +
110O LEU* 4.1 16.4 - - + -
133O VAL* 4.2 13.7 - - + -
134O LEU 3.8 4.5 - - - +
178O LEU* 4.2 8.5 - - + -
181O CYS* 3.5 32.1 - - - -
204O PRO* 3.8 22.9 - - + -
229O LEU* 4.0 0.6 - - - -
230O THR* 2.7 47.7 + - - +
231O GLY 4.4 1.4 + - - -
233O LEU* 4.2 18.6 - - + +
249O ILE* 4.5 6.1 - - + -
252O ILE* 3.8 17.0 - - + -
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Residues in contact with ALA 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O GLU 4.1 1.0 + - - -
108O ILE* 1.3 74.2 - - - +
110O LEU* 1.3 63.9 + - - +
133O VAL* 3.4 5.0 - - - +
134O LEU* 2.8 50.1 + - + +
136O ALA* 4.1 8.1 - - + -
166O ILE* 4.9 2.2 - - + -
227O ILE* 4.2 17.7 - - + -
228O ILE 3.3 5.8 - - - +
229O LEU* 3.7 23.8 - - + -
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Residues in contact with LEU 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O ILE* 4.1 11.2 - - + -
109O ALA* 1.3 83.8 - - - +
111O VAL* 1.3 65.3 + - - +
112O LEU* 5.1 4.3 - - + -
126O LEU* 4.7 1.1 - - + -
130O ILE* 4.4 20.9 - - + -
132O TRP 3.5 2.7 - - - +
133O VAL* 3.8 20.9 - - + -
178O LEU* 5.3 2.7 - - + -
204O PRO* 6.1 0.4 - - + -
205O LEU* 3.7 33.2 - - + -
208O ALA* 3.8 22.9 - - + -
226O ASP 3.7 0.9 - - - +
227O ILE* 3.3 6.2 - - - +
228O ILE* 2.8 45.8 + - + +
230O THR* 3.8 17.5 - - + -
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Residues in contact with VAL 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L ASP* 4.8 14.4 - - + +
128L ASN* 6.4 0.7 - - + -
110O LEU* 1.3 79.7 - - - +
112O LEU* 1.3 58.8 + - - +
130O ILE* 3.6 4.3 - - - +
131O GLU* 2.7 48.8 + - - +
132O TRP* 3.0 27.2 + - + +
134O LEU* 3.9 23.6 - - + -
225O GLY* 4.0 15.5 - - - +
226O ASP 3.4 10.1 - - - +
227O ILE* 4.4 15.3 - - + -
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Residues in contact with LEU 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O LEU* 5.1 7.9 - - + -
111O VAL* 1.3 76.7 - - - +
113O ASN* 1.4 59.1 + - - +
114O ARG 3.9 12.6 - - - +
116O LEU* 4.0 21.8 - - + -
126O LEU* 5.2 5.8 - - + -
129O ALA* 3.2 19.7 - - + +
130O ILE* 5.0 5.2 - - + -
131O GLU* 3.9 10.4 - - - +
222O LEU* 3.8 34.5 - - + -
223O ARG 3.9 15.5 - - - +
224O THR* 4.1 0.5 + - - -
225O GLY* 3.0 24.7 + - - +
226O ASP* 3.2 20.0 + - + +
228O ILE* 3.9 20.4 - - + -
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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