Contacts of the strand formed by residues 103 - 112 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101L GLN 4.0 0.7 - - - -
102L PRO* 1.3 78.0 - - - +
104L ILE* 1.3 58.3 + - - +
139L VAL* 3.2 3.6 - - - -
140L VAL* 2.7 52.2 + - + +
147L TRP* 3.3 65.6 - - - +
236L MET* 3.8 33.6 - - + +
237L VAL* 3.1 19.7 - - - +
238L ALA* 3.6 17.4 - - - +
239L VAL* 3.8 4.9 - - - -
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Residues in contact with ILE 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103L ARG* 1.3 72.9 - - - +
105L GLU* 1.3 61.4 + - - +
137L LEU* 4.2 21.1 - - + -
138L GLU 3.2 9.6 - - - +
139L VAL* 3.5 31.0 - - + -
185L MET* 3.7 14.5 - - + +
236L MET* 3.3 5.1 - - - -
237L VAL* 3.0 43.7 + - + +
239L VAL* 3.5 14.6 - - + -
245L PHE* 3.1 47.8 - - + -
257L ALA* 6.0 0.4 - - + -
259L PHE* 4.7 4.9 - - + -
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Residues in contact with GLU 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104L ILE* 1.3 75.1 - - - +
106L ALA* 1.3 59.4 + - - +
107L GLU* 3.0 19.3 - - + +
137L LEU* 3.4 8.3 - - - +
138L GLU* 2.8 42.7 + - + +
140L VAL* 3.8 7.6 - - - +
185L MET* 4.2 5.8 - - - -
232L ALA* 3.4 30.8 - - + +
234L GLY 4.2 6.3 - - - +
235L PRO 5.1 0.2 - - - -
236L MET* 3.7 24.5 + - + +
1262L PO4 3.0 39.0 + - - -
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Residues in contact with ALA 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L GLU* 1.3 73.3 - - - +
107L GLU* 1.3 63.8 + - - +
136L ALA 3.6 6.3 - - - +
137L LEU* 4.2 2.9 - - + -
183L MET* 3.6 41.6 - - + +
185L MET* 4.4 5.9 - - - +
232L ALA* 3.6 0.9 - - - -
233L LEU* 2.9 28.6 + - - +
234L GLY 5.2 0.4 + - - -
247L ALA* 3.8 21.3 - - + -
249L ILE* 4.5 4.5 - - + -
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Residues in contact with GLU 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L VAL 4.5 1.9 - - - +
105L GLU* 3.0 33.9 - - + +
106L ALA* 1.3 81.2 - - - +
108L ILE* 1.3 65.4 + - - +
136L ALA* 2.8 41.0 + - + +
138L GLU* 3.1 23.1 - - + +
229L LEU* 3.3 21.6 - - + +
231L GLY* 3.0 38.4 + - - +
232L ALA* 3.6 8.2 + - - +
233L LEU* 4.0 6.7 - - - -
249L ILE* 3.5 7.8 - - - +
1262L PO4 4.1 2.3 + - - -
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Residues in contact with ILE 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L GLU* 1.3 75.5 - - - +
109L ALA* 1.3 69.8 + - - +
110L LEU* 4.1 15.9 - - + -
133L VAL* 4.2 13.2 - - + -
134L LEU 3.8 4.7 - - - +
178L LEU* 4.2 8.5 - - + -
181L CYS* 3.5 31.6 - - - -
204L PRO* 3.9 24.7 - - + -
229L LEU* 4.0 0.6 - - - -
230L THR* 2.7 46.5 + - - +
231L GLY 4.4 1.4 + - - -
233L LEU* 4.1 17.0 - - + +
249L ILE* 4.3 5.4 - - + -
252L ILE* 3.7 18.8 - - + -
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Residues in contact with ALA 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L GLU 4.0 0.4 + - - -
108L ILE* 1.3 74.0 - - - +
110L LEU* 1.3 64.7 + - - +
133L VAL* 3.3 5.9 - - - +
134L LEU* 2.8 50.3 + - + +
136L ALA* 4.1 8.3 - - + -
166L ILE* 4.9 2.2 - - + -
227L ILE* 4.2 16.8 - - + -
228L ILE 3.3 6.1 - - - +
229L LEU* 3.7 23.3 - - + -
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Residues in contact with LEU 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ILE* 4.1 10.3 - - + -
109L ALA* 1.3 84.2 - - - +
111L VAL* 1.3 65.8 + - - +
112L LEU* 5.1 4.5 - - + -
126L LEU* 4.7 0.9 - - + -
130L ILE* 4.4 21.3 - - + -
132L TRP 3.5 2.5 - - - +
133L VAL* 3.8 20.4 - - + -
178L LEU* 5.3 2.9 - - + -
204L PRO* 6.1 0.7 - - + -
205L LEU* 3.7 31.6 - - + -
208L ALA* 3.8 23.6 - - + -
226L ASP 3.7 0.9 - - - +
227L ILE* 3.3 5.7 - - - +
228L ILE* 2.8 45.0 + - + +
230L THR* 3.8 17.3 - - + -
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Residues in contact with VAL 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124K ASP* 4.6 16.2 - - + +
128K ASN* 5.9 2.5 - - + +
110L LEU* 1.3 79.5 - - - +
112L LEU* 1.3 58.6 + - - +
130L ILE* 3.6 5.0 - - - +
131L GLU* 2.7 48.2 + - - +
132L TRP* 2.9 27.7 + - + +
134L LEU* 3.9 22.7 - - + -
225L GLY* 3.9 16.2 - - - +
226L ASP 3.4 9.2 - - - +
227L ILE* 4.4 15.3 - - + -
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Residues in contact with LEU 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L LEU* 5.1 8.1 - - + -
111L VAL* 1.3 79.1 - - - +
113L ASN* 1.3 59.8 + - - +
114L ARG 3.9 12.6 - - - +
116L LEU* 3.9 20.6 - - + -
126L LEU* 5.2 5.6 - - + -
129L ALA* 3.2 18.2 - - + +
130L ILE* 5.0 4.9 - - + -
131L GLU* 3.9 10.0 - - - +
222L LEU* 3.8 34.5 - - + -
223L ARG 3.9 15.3 - - - +
224L THR* 4.1 0.3 + - - -
225L GLY* 2.9 26.0 + - - -
226L ASP* 3.2 20.2 + - + +
228L 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