Contacts of the strand formed by residues 103 - 112 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101Q GLN 4.0 0.9 - - - -
102Q PRO* 1.3 78.0 - - - +
104Q ILE* 1.3 59.3 + - - +
139Q VAL* 3.2 3.4 - - - -
140Q VAL* 2.7 52.2 + - + +
147Q TRP* 3.3 62.3 - - - +
236Q MET* 3.8 35.2 - - + +
237Q VAL 3.2 18.8 - - - +
238Q ALA* 3.7 16.3 - - - +
239Q VAL* 3.9 3.6 - - - -
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Residues in contact with ILE 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q ARG* 1.3 73.0 - - - +
105Q GLU* 1.3 61.3 + - - +
137Q LEU* 4.2 20.6 - - + -
138Q GLU 3.2 8.7 - - - +
139Q VAL* 3.5 32.3 - - + -
185Q MET* 3.6 14.8 - - + +
236Q MET* 3.3 4.7 - - - -
237Q VAL* 3.0 42.1 + - + +
239Q VAL* 3.5 14.4 - - + -
245Q PHE* 3.0 50.9 - - + -
257Q ALA* 6.0 0.7 - - + -
259Q PHE* 4.7 5.2 - - + -
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Residues in contact with GLU 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q ILE* 1.3 75.8 - - - +
106Q ALA* 1.3 59.6 - - - +
107Q GLU* 3.1 19.6 - - + +
137Q LEU* 3.4 6.6 - - - +
138Q GLU* 2.8 43.1 + - + +
140Q VAL* 3.7 8.3 - - + +
185Q MET* 4.1 7.6 - - - -
232Q ALA* 3.4 29.5 - - + +
234Q GLY 4.2 6.1 - - - +
236Q MET* 3.7 23.8 + - + +
1262Q PO4 2.8 37.8 + - - -
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Residues in contact with ALA 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105Q GLU* 1.3 73.1 - - - +
107Q GLU* 1.3 63.5 + - - +
136Q ALA 3.6 6.5 - - - +
137Q LEU* 4.3 2.7 - - + -
183Q MET* 3.8 39.3 - - + +
185Q MET* 4.3 6.0 - - - +
232Q ALA* 3.6 0.5 - - - -
233Q LEU* 2.9 31.5 + - + +
234Q GLY 5.2 0.6 + - - -
247Q ALA* 3.8 23.1 - - + -
249Q ILE* 4.7 2.5 - - + -
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Residues in contact with GLU 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Q VAL 4.5 1.2 - - - +
105Q GLU* 3.1 33.7 - - + +
106Q ALA* 1.3 81.3 - - - +
108Q ILE* 1.3 67.2 + - - +
135Q PRO 3.8 0.2 - - - -
136Q ALA* 2.9 40.8 + - + +
138Q GLU* 3.1 23.8 - - + +
229Q LEU* 3.3 22.3 - - + +
230Q THR 4.9 0.2 - - - +
231Q GLY* 3.0 39.0 + - - +
232Q ALA* 3.6 7.5 + - - +
233Q LEU* 4.0 6.3 - - - -
249Q ILE* 3.6 8.1 - - - +
1262Q PO4 4.2 2.1 + - - -
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Residues in contact with ILE 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Q GLU* 1.3 77.1 - - - +
109Q ALA* 1.3 69.6 + - - +
110Q LEU* 4.1 17.0 - - + -
133Q VAL* 4.2 13.7 - - + -
134Q LEU 3.8 4.3 - - - +
178Q LEU* 4.2 8.1 - - + -
181Q CYS* 3.5 32.3 - - - -
204Q PRO* 3.8 24.0 - - + -
229Q LEU* 4.0 0.7 - - - -
230Q THR* 2.7 46.1 + - - +
231Q GLY 4.4 1.4 + - - -
233Q LEU* 4.2 17.7 - - + +
249Q ILE* 4.5 6.3 - - + -
252Q ILE* 3.8 17.9 - - + -
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Residues in contact with ALA 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Q GLU 4.1 0.8 + - - -
108Q ILE* 1.3 74.5 - - - +
110Q LEU* 1.3 63.3 + - - +
133Q VAL* 3.4 5.7 - - - +
134Q LEU* 2.8 50.3 + - + +
136Q ALA* 4.1 8.5 - - + -
166Q ILE* 4.9 2.5 - - + -
227Q ILE* 4.2 17.3 - - + -
228Q ILE 3.3 5.4 - - - +
229Q LEU* 3.7 23.8 - - + -
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Residues in contact with LEU 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Q ILE* 4.1 11.4 - - + -
109Q ALA* 1.3 82.9 - - - +
111Q VAL* 1.3 63.6 + - - +
112Q LEU* 5.1 4.5 - - + -
126Q LEU* 4.7 1.1 - - + -
130Q ILE* 4.4 22.9 - - + -
132Q TRP 3.5 2.5 - - - +
133Q VAL* 3.8 20.6 - - + -
178Q LEU* 5.3 2.9 - - + -
204Q PRO* 6.1 0.4 - - + -
205Q LEU* 3.7 31.9 - - + -
208Q ALA* 3.8 15.3 - - + -
226Q ASP 3.7 0.9 - - - +
227Q ILE* 3.3 7.2 - - - +
228Q ILE* 2.8 44.2 + - + +
230Q THR* 3.7 24.5 - - + -
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Residues in contact with VAL 111 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124P ASP* 4.5 16.6 - - + +
128P ASN* 6.1 1.6 - - + -
110Q LEU* 1.3 78.4 - - - +
112Q LEU* 1.3 61.0 + - - +
130Q ILE* 3.6 4.5 - - - -
131Q GLU* 2.7 50.0 + - - +
132Q TRP* 2.9 27.6 + - + +
134Q LEU* 4.0 22.7 - - + -
225Q GLY* 3.9 14.6 - - - +
226Q ASP 3.4 9.2 - - - +
227Q ILE* 4.4 13.2 - - + -
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Residues in contact with LEU 112 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q LEU* 5.1 7.9 - - + -
111Q VAL* 1.3 77.4 - - - +
113Q ASN* 1.3 59.9 + - - +
114Q ARG 3.9 13.0 - - - +
116Q LEU* 4.0 22.2 - - + -
126Q LEU* 5.2 5.4 - - + -
129Q ALA* 3.2 18.6 - - + +
130Q ILE* 5.0 4.7 - - + -
131Q GLU* 3.9 10.2 - - - +
222Q LEU* 3.8 34.1 - - + -
223Q ARG 3.9 15.3 - - - +
224Q THR* 4.1 0.2 + - - -
225Q GLY* 3.0 24.1 + - - -
226Q ASP* 3.2 21.5 + - + +
228Q 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