Contacts of the helix formed by residues 122 - 128 (chain P) 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 THR 122 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120P ASP 3.8 8.1 - - - +
121P ILE* 1.3 78.3 - - - +
123P PHE* 1.3 65.0 + - - +
124P ASP* 2.8 23.6 + - - +
125P GLU* 2.9 43.5 + - - +
126P LEU* 3.0 11.8 + - - +
209P VAL* 4.3 3.4 - - - -
213P ARG* 4.2 5.6 - - - +
57Q VAL* 4.9 2.9 - - + -
84Q ALA* 3.8 34.5 - - + +
87Q CYS* 3.8 13.9 - - + -
164Q TYR* 5.0 1.6 - - - +
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Residues in contact with PHE 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P THR* 1.3 72.1 - - - +
124P ASP* 1.3 61.8 + - - +
126P LEU* 3.4 5.0 + - - +
127P TYR* 3.3 30.6 + + - -
203P HIS* 3.8 28.3 - + - -
205P LEU* 3.5 30.6 - - + +
206P ASN* 3.3 28.0 - - - -
209P VAL* 3.8 15.6 - - + +
213P ARG* 5.2 1.0 - - - +
87Q CYS* 4.3 9.6 + - - -
88Q TYR 4.6 0.7 - - - +
89Q GLY* 3.4 20.4 - - - +
90Q ASP* 3.7 15.5 - - + -
166Q ILE* 3.4 31.9 - - + -
167Q GLY 3.4 16.2 - - - -
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Residues in contact with ASP 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P THR* 2.8 22.5 + - - +
123P PHE* 1.3 76.4 - - - +
125P GLU* 1.3 76.5 + - - +
127P TYR* 3.3 23.3 + - - +
128P ASN* 3.6 6.4 + - - +
87Q CYS* 3.7 2.4 - - - -
111Q VAL* 4.5 14.8 - - + +
132Q TRP* 5.4 3.1 - - - -
134Q LEU* 4.7 7.8 - - + +
164Q TYR* 4.4 3.6 + - - -
166Q ILE* 3.5 37.0 - - + +
225Q GLY 5.3 3.6 - - - +
227Q ILE* 3.8 29.1 - - + +
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Residues in contact with GLU 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P ARG* 5.7 0.5 + - - -
116P LEU* 5.5 0.3 - - - +
118P ALA* 5.5 1.6 - - - +
121P ILE* 3.5 17.9 - - + +
122P THR* 2.9 36.4 + - - +
124P ASP* 1.3 84.0 - - - +
126P LEU* 1.3 65.6 + - - +
128P ASN* 3.3 16.3 + - - +
129P ALA* 3.6 10.0 + - - +
55Q ARG* 3.1 38.2 + - - -
57Q VAL* 4.0 11.6 - - - +
225Q GLY 5.8 3.9 - - - +
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Residues in contact with LEU 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P LEU* 4.7 1.8 - - + -
112P LEU* 5.2 6.7 - - + -
116P LEU* 4.2 23.8 - - + -
121P ILE* 4.0 9.9 - - + +
122P THR 3.0 11.4 + - - +
123P PHE 3.6 8.3 - - - +
125P GLU* 1.3 75.4 - - - +
127P TYR* 1.3 65.2 + - - +
129P ALA* 2.9 15.5 + - + +
130P ILE* 3.4 14.4 + - + +
205P LEU* 3.7 37.0 - - + +
208P ALA* 3.5 46.9 - - + +
209P VAL* 4.0 10.1 - - + +
212P ALA* 4.4 4.3 - - + -
228P ILE* 5.6 0.9 - - + -
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Residues in contact with TYR 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P PHE* 3.3 26.9 + + - -
124P ASP* 3.3 12.0 + - - +
125P GLU 3.3 0.6 - - - -
126P LEU* 1.3 79.1 - - - +
128P ASN* 1.3 61.8 - - - +
129P ALA 3.1 1.0 + - - -
130P ILE* 3.3 27.0 + - + +
173P PRO* 4.6 18.9 - - + +
176P LEU 4.8 1.4 + - - -
178P LEU* 4.2 18.5 + - + +
203P HIS* 4.5 6.8 + - - -
205P LEU* 3.6 24.0 - - + +
132Q TRP* 4.5 14.2 - + + +
134Q LEU* 3.8 18.2 - - + -
167Q GLY 3.5 20.1 + - - -
168Q GLY* 3.6 17.3 - - - -
169Q PRO* 3.7 3.6 - - - +
170Q ALA* 3.6 35.5 + - + -
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Residues in contact with ASN 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113P ASN* 2.6 24.1 + - - -
114P ARG* 3.1 31.9 + - - +
124P ASP 3.6 6.1 + - - +
125P GLU* 3.3 11.5 + - - +
126P LEU 3.2 1.0 - - - -
127P TYR* 1.3 77.8 - - - +
129P ALA* 1.3 50.3 + - - +
130P ILE 3.5 1.8 - - - +
111Q VAL* 6.2 1.6 - - + -
131Q GLU* 3.0 32.0 + - - +
132Q TRP* 2.7 37.9 - - + +
172Q ARG* 4.8 1.4 - - - +
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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