Contacts of the strand formed by residues 103 - 112 (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 ARG 103 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101N GLN 4.0 0.7 - - - -
102N PRO* 1.3 79.5 - - - +
104N ILE* 1.3 59.3 + - - +
139N VAL* 3.2 3.5 - - - -
140N VAL* 2.7 51.4 + - + +
147N TRP* 3.3 63.2 - - - +
236N MET* 3.8 33.6 - - + +
237N VAL* 3.2 19.3 - - - +
238N ALA* 3.7 17.2 - - - +
239N VAL* 3.9 3.8 - - - -
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Residues in contact with ILE 104 (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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103N ARG* 1.3 73.3 - - - +
105N GLU* 1.3 60.6 + - - +
137N LEU* 4.2 21.3 - - + -
138N GLU 3.2 9.6 - - - +
139N VAL* 3.5 31.4 - - + -
185N MET* 3.9 13.3 - - + +
236N MET* 3.3 4.6 - - - -
237N VAL* 3.0 43.3 + - + +
239N VAL* 3.4 14.8 - - + -
245N PHE* 3.0 47.8 - - + -
257N ALA* 6.0 0.7 - - + -
259N PHE* 4.7 5.2 - - + -
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Residues in contact with GLU 105 (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* 1.3 76.4 - - - +
106N ALA* 1.3 59.1 + - - +
107N GLU* 3.1 26.7 - - + +
137N LEU* 3.4 9.0 - - - +
138N GLU* 2.8 43.9 + - + +
140N VAL* 3.7 8.1 - - - +
185N MET* 4.5 6.3 - - - -
232N ALA* 3.5 26.1 - - + +
234N GLY 4.2 4.0 - - - +
235N PRO 5.2 0.4 - - - -
236N MET* 3.7 26.4 + - + +
1262N PO4 2.9 33.2 + - - -
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Residues in contact with ALA 106 (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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105N GLU* 1.3 74.2 - - - +
107N GLU* 1.3 62.0 + - - +
136N ALA 3.6 6.5 - - - +
137N LEU* 4.3 3.1 - - + -
183N MET* 3.7 40.9 - - + +
185N MET* 4.5 5.6 - - - +
232N ALA* 3.6 0.7 - - - -
233N LEU* 2.9 32.0 + - + +
234N GLY 5.2 0.6 + - - -
247N ALA* 3.8 21.8 - - + -
249N ILE* 4.7 2.5 - - + -
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Residues in contact with GLU 107 (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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61N VAL 4.5 1.9 - - - +
105N GLU* 3.1 34.0 - - + +
106N ALA* 1.3 81.8 - - - +
108N ILE* 1.3 66.3 + - - +
136N ALA* 2.8 40.3 + - + +
138N GLU* 3.1 22.6 - - + +
229N LEU* 3.3 22.4 - - + +
231N GLY* 3.0 39.0 + - - +
232N ALA* 3.6 8.2 + - - +
233N LEU* 4.0 6.7 - - - +
249N ILE* 3.6 7.4 - - - +
1262N PO4 4.4 1.9 + - - -
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Residues in contact with ILE 108 (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* 1.3 77.3 - - - +
109N ALA* 1.3 69.7 + - - +
110N LEU* 4.1 16.8 - - + -
133N VAL* 4.2 13.5 - - + -
134N LEU 3.9 4.0 - - - +
136N ALA* 5.1 0.2 - - - -
178N LEU* 4.2 8.7 - - + -
181N CYS* 3.5 32.5 - - - -
204N PRO* 3.9 21.5 - - + -
229N LEU* 4.0 0.6 - - - -
230N THR* 2.7 46.9 + - - +
231N GLY 4.5 1.0 + - - -
233N LEU* 4.2 17.7 - - + +
249N ILE* 4.5 5.8 - - + -
252N ILE* 3.7 18.4 - - + -
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Residues in contact with ALA 109 (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 4.0 0.6 + - - -
108N ILE* 1.3 73.2 - - - +
110N LEU* 1.3 63.5 + - - +
133N VAL* 3.4 5.2 - - - +
134N LEU* 2.8 51.8 + - + +
136N ALA* 4.1 8.3 - - + -
166N ILE* 4.9 2.0 - - + -
227N ILE* 4.1 17.0 - - + -
228N ILE 3.3 5.2 - - - +
229N LEU* 3.7 23.3 - - + -
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Residues in contact with LEU 110 (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* 4.1 11.0 - - + -
109N ALA* 1.3 81.3 - - - +
111N VAL* 1.3 66.2 + - - +
112N LEU* 5.1 4.3 - - + -
126N LEU* 4.7 0.9 - - + -
130N ILE* 4.4 21.1 - - + -
132N TRP 3.4 2.9 - - - +
133N VAL* 3.8 21.3 - - + -
178N LEU* 5.2 3.6 - - + -
204N PRO* 6.1 0.2 - - + -
205N LEU* 3.7 31.0 - - + -
208N ALA* 3.8 15.9 - - + -
226N ASP 3.7 0.5 - - - +
227N ILE* 3.3 6.1 - - - +
228N ILE* 2.8 44.3 + - + +
230N THR* 3.8 24.0 - - + -
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Residues in contact with VAL 111 (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* 4.7 14.1 - - + +
128M ASN* 5.9 1.8 - - + +
110N LEU* 1.3 77.9 - - - +
112N LEU* 1.3 60.2 + - - +
130N ILE* 3.6 4.7 - - - +
131N GLU* 2.7 48.0 + - - +
132N TRP* 3.0 27.3 + - + +
134N LEU* 3.9 22.7 - - + -
225N GLY* 3.9 16.2 - - - +
226N ASP 3.4 9.6 - - - +
227N ILE* 4.4 15.0 - - + -
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Residues in contact with LEU 112 (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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110N LEU* 5.1 7.6 - - + -
111N VAL* 1.3 76.9 - - - +
113N ASN* 1.4 59.2 + - - +
114N ARG 3.3 13.5 - - - +
116N LEU* 4.0 21.5 - - + -
126N LEU* 5.2 5.6 - - + -
129N ALA* 3.2 19.3 - - + +
130N ILE* 5.0 4.5 - - + -
131N GLU* 3.9 10.1 - - - +
222N LEU* 3.8 28.7 - - + -
223N ARG 3.9 15.3 - - - +
224N THR* 4.1 0.3 + - - -
225N GLY* 2.9 26.6 + - - +
226N ASP* 3.2 20.6 + - + +
228N ILE* 3.9 26.0 - - + -
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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