Contacts of the strand formed by residues 103 - 112 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101K GLN 4.0 0.7 - - - -
102K PRO* 1.3 78.0 - - - +
104K ILE* 1.3 58.4 + - - +
139K VAL* 3.2 3.4 - - - -
140K VAL* 2.7 53.5 + - + +
147K TRP* 3.3 63.8 - - - +
236K MET* 3.8 33.4 - - + +
237K VAL 3.2 20.0 - - - +
238K ALA* 3.7 16.7 - - - +
239K VAL* 3.9 4.0 - - - -
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Residues in contact with ILE 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K ARG* 1.3 73.3 - - - +
105K GLU* 1.3 61.8 + - - +
137K LEU* 4.2 20.2 - - + -
138K GLU 3.2 9.2 - - - +
139K VAL* 3.5 31.2 - - + -
185K MET* 3.7 13.7 - - + +
236K MET* 3.3 4.8 - - - -
237K VAL* 3.0 41.0 + - + +
239K VAL* 3.5 14.8 - - + -
245K PHE* 3.0 50.9 - - + -
257K ALA* 6.0 0.7 - - + -
259K PHE* 4.7 5.6 - - + -
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Residues in contact with GLU 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K ILE* 1.3 75.5 - - - +
106K ALA* 1.3 58.9 + - - +
107K GLU* 3.0 23.8 - - + +
137K LEU* 3.4 9.1 - - - +
138K GLU* 2.8 43.6 + - + +
140K VAL* 3.8 8.8 - - + +
185K MET* 4.4 6.1 - - - -
232K ALA* 3.4 30.6 + - + +
234K GLY 4.2 7.0 - - - +
235K PRO 5.2 0.4 - - - -
236K MET* 3.7 24.9 + - + +
1264K PO4 2.5 31.5 + - - -
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Residues in contact with ALA 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K GLU* 1.3 73.7 - - - +
107K GLU* 1.3 62.4 + - - +
136K ALA 3.6 6.5 - - - +
137K LEU* 4.2 2.7 - - + +
183K MET* 3.6 41.1 - - + +
185K MET* 4.6 5.4 - - - +
232K ALA* 3.6 0.3 - - - -
233K LEU* 2.9 32.0 + - + +
234K GLY 5.2 0.8 + - - -
247K ALA* 3.9 21.1 - - + -
249K ILE* 4.6 2.7 - - + -
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Residues in contact with GLU 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60K LYS* 4.9 0.2 + - - -
61K VAL 4.5 3.3 - - - +
105K GLU* 3.0 33.7 - - + +
106K ALA* 1.3 81.5 - - - +
108K ILE* 1.3 67.3 + - - +
136K ALA* 2.8 40.9 + - + +
138K GLU* 3.1 23.7 - - + +
229K LEU* 3.3 21.9 - - + +
231K GLY* 3.0 39.3 + - - +
232K ALA* 3.5 8.1 + - - +
233K LEU* 4.0 6.0 - - - +
249K ILE* 3.3 7.4 - - - +
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Residues in contact with ILE 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K GLU* 1.3 77.5 - - - +
109K ALA* 1.3 69.4 + - - +
110K LEU* 4.1 16.4 - - + -
133K VAL* 4.1 13.5 - - + -
134K LEU 3.8 4.7 - - - +
178K LEU* 4.1 9.0 - - + -
181K CYS* 3.6 31.2 - - - -
204K PRO* 3.8 23.3 - - + -
230K THR* 2.7 47.0 + - - +
231K GLY 4.4 1.2 + - - -
233K LEU* 4.2 17.0 - - + +
249K ILE* 4.2 6.5 - - + -
252K ILE* 3.7 19.1 - - + -
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Residues in contact with ALA 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K GLU 4.1 1.0 + - - -
108K ILE* 1.3 74.4 - - - +
110K LEU* 1.3 63.2 + - - +
133K VAL* 3.4 5.5 - - - +
134K LEU* 2.8 51.5 + - + +
136K ALA* 4.1 8.1 - - + -
166K ILE* 4.9 2.9 - - + -
227K ILE* 4.2 16.6 - - + -
228K ILE 3.3 6.3 - - - +
229K LEU* 3.8 23.6 - - + -
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Residues in contact with LEU 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K ILE* 4.1 11.4 - - + -
109K ALA* 1.3 81.1 - - - +
111K VAL* 1.3 65.8 + - - +
112K LEU* 5.1 4.4 - - + +
126K LEU* 4.7 0.9 - - + -
130K ILE* 4.3 22.7 - - + -
132K TRP 3.5 2.7 - - - +
133K VAL* 3.8 20.6 - - + -
178K LEU* 5.2 2.9 - - + -
204K PRO* 6.0 0.2 - - + -
205K LEU* 3.7 32.8 - - + -
208K ALA* 3.7 15.9 - - + -
226K ASP 3.7 0.5 - - - +
227K ILE* 3.3 6.3 - - - +
228K ILE* 2.8 48.0 + - + +
230K THR* 3.7 24.7 - - + -
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Residues in contact with VAL 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K LEU* 1.3 77.0 - - - +
112K LEU* 1.3 60.7 + - - +
130K ILE* 3.6 5.0 - - - +
131K GLU* 2.7 49.7 + - - +
132K TRP* 2.9 28.8 + - + +
134K LEU* 3.9 22.7 - - + -
225K GLY* 3.9 15.0 - - - +
226K ASP 3.4 9.0 - - - +
227K ILE* 4.4 9.2 - - + -
124N ASP* 4.4 22.4 - - + +
128N ASN* 6.2 1.3 - - + -
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Residues in contact with LEU 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K LEU* 5.1 7.9 - - + -
111K VAL* 1.3 78.5 - - - +
113K ASN* 1.4 59.1 + - - +
114K ARG 3.3 13.0 - - - +
116K LEU* 3.9 21.5 - - + -
126K LEU* 5.2 5.2 - - + -
129K ALA* 3.2 19.5 - - + +
130K ILE* 5.1 5.2 - - + -
131K GLU* 3.8 10.7 - - - +
222K LEU* 3.8 33.9 - - + -
223K ARG 3.9 15.5 - - - +
224K THR* 4.2 0.3 + - - -
225K GLY* 3.0 23.9 + - - -
226K ASP* 3.2 21.3 + - + +
228K ILE* 3.9 21.3 - - + -
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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