Contacts of the strand formed by residues 103 - 112 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101T GLN 3.9 0.7 - - - -
102T PRO* 1.3 78.5 - - - +
104T ILE* 1.3 59.3 + - - +
139T VAL* 3.2 3.8 - - - -
140T VAL* 2.7 52.7 + - + +
147T TRP* 3.3 65.2 - - - +
236T MET* 3.8 33.4 - - + +
237T VAL 3.2 18.4 - - - +
238T ALA* 3.7 17.0 - - + +
239T VAL* 4.0 3.8 - - - -
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Residues in contact with ILE 104 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103T ARG* 1.3 73.7 - - - +
105T GLU* 1.3 60.9 + - - +
137T LEU* 4.2 21.3 - - + -
138T GLU 3.2 9.4 - - - +
139T VAL* 3.5 31.0 - - + -
185T MET* 3.9 13.1 - - + +
236T MET* 3.2 4.8 - - - -
237T VAL* 3.0 46.0 + - + +
239T VAL* 3.5 15.0 - - + -
245T PHE* 3.2 47.8 - - + -
257T ALA* 6.0 0.4 - - + -
259T PHE* 4.7 6.3 - - + -
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Residues in contact with GLU 105 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104T ILE* 1.3 74.3 - - - +
106T ALA* 1.3 60.2 + - - +
107T GLU* 3.0 22.5 - - + +
137T LEU* 3.4 7.8 - - - -
138T GLU* 2.8 42.0 + - + +
140T VAL* 3.8 9.3 - - + +
185T MET* 4.5 5.2 - - - -
232T ALA* 3.4 27.2 - - + +
234T GLY 4.2 7.0 - - - +
235T PRO 5.2 0.7 - - - -
236T MET* 3.7 23.6 + - + +
1262T PO4 2.8 40.2 + - - -
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Residues in contact with ALA 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105T GLU* 1.3 72.9 - - - +
107T GLU* 1.3 63.2 + - - +
136T ALA 3.6 7.0 - - - +
137T LEU* 4.3 2.9 - - + -
183T MET* 3.8 38.2 - - + +
185T MET* 4.4 6.8 - - - +
232T ALA* 3.6 1.0 - - - -
233T LEU* 2.9 32.2 + - + +
234T GLY 5.1 1.0 + - - -
247T ALA* 3.8 23.1 - - + -
249T ILE* 4.7 2.5 - - + -
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Residues in contact with GLU 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61T VAL 4.5 1.4 - - - +
105T GLU* 3.0 34.7 - - + +
106T ALA* 1.3 80.8 - - - +
108T ILE* 1.3 66.4 + - - +
109T ALA 4.1 0.2 - - - -
136T ALA* 2.8 41.7 + - + +
138T GLU* 3.1 23.2 - - + +
229T LEU* 3.3 22.1 - - + +
230T THR 4.9 0.2 - - - +
231T GLY* 2.9 38.3 + - - +
232T ALA* 3.5 7.8 + - - +
233T LEU* 4.1 5.6 - - - +
249T ILE* 3.6 8.3 - - - +
1262T PO4 4.1 2.1 + - - -
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Residues in contact with ILE 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107T GLU* 1.3 77.0 - - - +
109T ALA* 1.3 68.2 + - - +
110T LEU* 4.1 16.2 - - + -
133T VAL* 4.2 13.5 - - + -
134T LEU 3.8 4.5 - - - +
178T LEU* 4.2 8.5 - - + -
181T CYS* 3.5 31.9 - - - -
204T PRO* 3.8 23.8 - - + -
229T LEU* 4.1 0.4 - - - -
230T THR* 2.7 47.4 + - - +
231T GLY 4.4 1.6 + - - -
233T LEU* 4.2 17.5 - - + +
249T ILE* 4.5 5.2 - - + -
252T ILE* 3.8 18.8 - - + -
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Residues in contact with ALA 109 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107T GLU 4.0 1.0 + - - -
108T ILE* 1.3 73.2 - - - +
110T LEU* 1.3 65.0 + - - +
133T VAL* 3.4 5.4 - - - +
134T LEU* 2.8 50.6 + - + +
136T ALA* 4.1 8.5 - - + -
166T ILE* 4.9 2.0 - - + -
227T ILE* 4.2 17.3 - - + -
228T ILE 3.3 6.1 - - - +
229T LEU* 3.8 23.6 - - + -
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Residues in contact with LEU 110 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108T ILE* 4.1 11.0 - - + -
109T ALA* 1.3 83.3 - - - +
111T VAL* 1.3 65.5 + - - +
112T LEU* 5.1 4.3 - - + -
126T LEU* 4.7 1.1 - - + -
130T ILE* 4.4 20.6 - - + -
132T TRP 3.5 2.5 - - - +
133T VAL* 3.8 20.4 - - + -
178T LEU* 5.3 3.1 - - + -
204T PRO* 6.1 0.4 - - + -
205T LEU* 3.7 31.2 - - + -
208T ALA* 3.8 23.6 - - + -
226T ASP 3.7 0.7 - - - +
227T ILE* 3.3 6.3 - - - +
228T ILE* 2.8 45.8 + - + +
230T THR* 3.8 17.3 - - + -
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Residues in contact with VAL 111 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124Q ASP* 4.5 16.8 - - + +
128Q ASN* 6.0 2.5 - - + -
110T LEU* 1.3 78.2 - - - +
112T LEU* 1.3 59.4 + - - +
130T ILE* 3.6 3.8 - - - +
131T GLU* 2.7 48.2 + - - +
132T TRP* 3.0 29.3 + - + +
134T LEU* 3.9 22.7 - - + -
225T GLY* 3.9 17.0 - - - +
226T ASP 3.4 9.2 - - - +
227T ILE* 4.4 15.0 - - + -
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Residues in contact with LEU 112 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110T LEU* 5.1 7.2 - - + -
111T VAL* 1.3 77.6 - - - +
113T ASN* 1.4 59.3 + - - +
114T ARG 3.9 13.5 - - - +
116T LEU* 4.0 21.1 - - + -
126T LEU* 5.2 5.6 - - + -
129T ALA* 3.2 19.5 - - + +
130T ILE* 5.1 4.7 - - + -
131T GLU* 3.9 10.1 - - - +
222T LEU* 3.8 34.3 - - + -
223T ARG 3.9 14.8 - - - +
224T THR* 4.1 0.3 + - - -
225T GLY* 2.9 25.1 + - - -
226T ASP* 3.2 21.7 + - + +
228T 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