Contacts of the helix formed by residues 133 - 147 (chain A) in PDB entry 2UYQ
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 GLN 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ASP* 1.3 91.3 + - - +
134A PRO* 1.4 79.3 - - + +
135A LYS* 3.3 3.6 - - + +
136A VAL* 3.3 14.9 + - + +
137A LEU* 3.2 18.0 + - - +
160A ILE 3.8 0.8 + - - -
161A ASP* 3.4 48.5 + - - +
163A ARG* 4.6 4.8 - - - +
1311A SAM 4.0 22.8 + - + +
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Residues in contact with PRO 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ASP 3.7 2.0 - - - +
133A GLN* 1.4 95.0 - - + +
135A LYS* 1.3 60.6 + - + +
137A LEU* 3.2 4.8 + - + +
138A ALA* 2.9 30.0 + - - +
159A PRO* 3.9 34.1 - - + +
160A ILE* 5.0 1.3 - - - -
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 5.5 3.7 + - - +
133A GLN* 3.3 3.3 - - + +
134A PRO* 1.3 80.5 - - + +
136A VAL* 1.3 61.2 + - + +
138A ALA* 3.8 7.9 - - + +
139A TYR* 2.9 29.6 + - - +
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.4 34.9 - - + +
15A GLY 5.1 2.9 - - - +
18A ALA* 6.2 0.2 - - + -
112A GLY* 3.8 23.6 - - - +
113A LEU* 5.2 0.6 - - + +
132A ASP* 3.6 27.8 - - + +
133A GLN* 3.5 16.8 - - + +
135A LYS* 1.3 75.5 - - + +
137A LEU* 1.3 67.9 + - + +
139A TYR* 3.3 4.2 + - - +
140A LYS* 3.2 21.5 + - - +
1311A SAM 3.9 19.7 - - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 3.5 24.7 - - - +
130A GLU* 4.0 18.4 - - + +
132A ASP* 3.7 31.2 - - + +
133A GLN 3.2 8.3 + - - +
134A PRO* 3.2 6.7 + - + +
136A VAL* 1.3 79.6 - - + +
138A ALA* 1.3 61.0 + - - +
140A LYS* 3.3 9.3 + - - +
141A SER* 3.1 26.9 + - - -
155A ARG* 4.4 8.5 + - - +
157A GLU* 3.9 30.5 - - + +
158A VAL 4.0 7.2 - - - +
159A PRO* 3.8 25.4 - - + -
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PRO 2.9 17.7 + - - +
135A LYS* 3.8 9.0 - - + +
137A LEU* 1.3 76.1 - - - +
139A TYR* 1.3 60.2 + - - +
141A SER* 3.6 7.4 - - - -
142A THR* 2.9 38.9 + - + +
157A GLU* 5.1 0.9 + - - -
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Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.2 30.5 - - + +
44A LEU* 2.6 34.6 + - + -
47A ASN* 2.9 39.5 - - - +
48A THR* 3.1 12.3 + - - -
113A LEU* 3.8 18.2 - - + -
135A LYS 2.9 19.1 + - - +
136A VAL 3.6 4.0 - - - +
137A LEU 3.3 0.2 - - - -
138A ALA* 1.3 77.2 - - - +
140A LYS* 1.3 63.8 + - - +
142A THR* 3.2 4.7 + - - -
143A THR* 2.8 51.7 + - - -
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Residues in contact with LYS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.8 26.9 - - + -
111A SER* 3.7 7.3 + - - -
112A GLY 2.8 25.7 + - - +
113A LEU* 3.8 18.4 - - + -
114A ASP 2.9 26.8 + - - +
115A SER* 5.2 0.7 - - - +
118A TYR* 4.8 5.2 - - + +
130A GLU* 2.7 31.7 + - - -
136A VAL 3.2 11.3 + - - +
137A LEU* 3.3 9.2 + - - +
139A TYR* 1.3 80.2 - - - +
141A SER* 1.3 58.9 + - - +
143A THR* 3.8 0.5 - - - -
144A LEU* 2.9 49.4 + - + +
155A ARG* 3.7 13.7 - - - +
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Residues in contact with SER 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TYR* 4.7 9.0 - - - -
137A LEU 3.1 18.2 + - - -
138A ALA* 3.2 10.6 + - - -
140A LYS* 1.3 77.7 - - - +
142A THR* 1.3 61.7 + - - +
144A LEU* 3.4 2.5 + - - +
145A ALA* 2.9 30.4 + - - +
149A VAL 5.2 0.2 - - - +
155A ARG* 4.8 5.6 - - - +
157A GLU* 3.6 19.9 + - - -
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Residues in contact with THR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ALA* 2.9 27.7 + - + +
139A TYR* 3.2 8.8 + - - -
141A SER* 1.3 77.4 + - - +
143A THR* 1.3 73.3 + - - +
145A ALA* 3.3 6.6 + - - +
146A GLU* 3.0 24.8 + - - +
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Residues in contact with THR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.8 16.6 - - + +
44A LEU* 4.0 16.4 - - + -
47A ASN* 3.7 32.6 - - + +
139A TYR* 2.8 42.4 + - - +
140A LYS 3.8 2.2 - - - -
142A THR* 1.3 85.0 + - - +
144A LEU* 1.3 62.1 + - - +
146A GLU* 3.4 11.1 + - - +
147A HIS* 3.1 23.0 + - - -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR* 4.1 22.2 - - + -
43A LEU* 3.4 24.9 - - + -
44A LEU* 4.1 13.0 - - + -
115A SER* 5.8 0.7 - - - -
118A TYR* 3.4 46.0 - - + +
140A LYS* 2.9 33.3 + - + +
141A SER* 3.9 3.6 - - - +
143A THR* 1.3 73.2 - - - +
145A ALA* 1.3 59.7 + - - +
147A HIS* 2.9 20.1 + - - +
149A VAL* 3.0 41.8 + - + +
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A SER 2.9 19.0 + - - +
142A THR* 3.3 8.0 + - - +
144A LEU* 1.3 75.5 - - - +
146A GLU* 1.3 57.1 + - - +
148A GLY* 2.9 20.0 + - - -
149A VAL 3.7 11.1 + - - +
150A THR* 5.6 6.1 - - + -
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Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 6.0 1.1 - - - +
142A THR 3.0 15.8 + - - +
143A THR* 3.7 9.4 - - - +
144A LEU 3.2 0.4 - - - -
145A ALA* 1.3 75.6 - - - +
147A HIS* 1.3 66.1 + - + +
148A GLY 3.4 1.2 + - - -
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Residues in contact with HIS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.3 39.4 - - + +
46A THR* 6.1 0.6 - - - +
47A ASN* 3.2 36.4 + - - -
143A THR 3.1 18.1 + - - -
144A LEU 2.9 9.4 + - - +
146A GLU* 1.3 84.1 - - + +
148A GLY* 1.3 60.4 + - - +
149A VAL* 3.3 8.4 + - + +
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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