Contacts of the helix formed by residues 134 - 149 (chain A) in PDB entry 6U81
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 PRO 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A THR* 5.1 3.6 - - + -
128A ALA* 4.9 0.2 - - + -
132A GLY 4.2 4.0 - - - +
133A LEU* 1.3 91.2 - - + +
135A GLU* 1.3 66.6 + - - +
136A SER* 4.1 9.4 - - - +
137A ARG* 2.9 37.8 + - + +
138A ILE* 3.0 10.9 + - - +
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Residues in contact with GLU 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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21A ARG* 2.6 34.7 + - - -
61A PRO* 5.7 0.7 - - - +
62A ARG* 5.0 0.9 + - - -
121A ILE* 3.8 1.7 - - - +
124A ARG* 2.9 46.9 + - + -
125A GLU* 4.2 19.3 - - + -
128A ALA* 3.9 19.4 - - + +
133A LEU 3.4 3.4 + - - -
134A PRO* 1.3 71.1 - - - +
136A SER* 1.3 76.5 + - - +
138A ILE* 3.1 7.9 + - - +
139A GLN* 2.9 26.0 + - - +
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO* 3.7 36.7 - - - +
62A ARG* 5.6 1.8 - - - +
96A ARG* 5.1 3.5 + - - -
134A PRO* 3.1 8.9 - - - +
135A GLU* 1.3 89.9 + - - +
137A ARG* 1.3 88.3 + - - +
139A GLN* 3.4 9.2 + - - +
140A ILE* 3.2 26.7 + - - +
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Residues in contact with ARG 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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64A GLN* 3.8 21.8 + - - -
96A ARG* 3.7 25.3 - - - +
99A THR* 3.4 19.3 - - + +
101A VAL* 6.5 0.2 - - + -
133A LEU* 5.2 4.7 - - + -
134A PRO* 2.9 31.6 + - + +
136A SER* 1.3 100.3 + - - +
138A ILE* 1.3 61.6 + - - +
140A ILE* 3.1 33.7 + - - +
141A TRP* 2.9 28.6 + - - +
5C G 6.2 0.2 - - - -
6C A 2.9 53.5 + - - +
7C T 4.0 8.5 + - - -
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Residues in contact with ILE 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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109A LEU* 3.9 22.7 - - + -
124A ARG* 4.0 13.2 - - + +
127A LEU* 3.5 20.2 - - + +
128A ALA* 3.3 44.0 - - + +
131A THR* 3.8 7.6 - - - +
133A LEU* 3.8 19.3 - - + +
134A PRO 3.0 9.5 + - - +
135A GLU* 3.5 6.7 - - - +
137A ARG* 1.3 76.4 - - - +
139A GLN* 1.3 61.7 + - - +
141A TRP* 3.2 7.9 + - - +
142A PHE* 3.1 35.7 + - + -
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Residues in contact with GLN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.7 9.4 + - - -
65A ILE* 5.9 2.8 - - - +
124A ARG* 3.5 36.5 - - - +
135A GLU* 2.9 21.7 + - - +
136A SER* 3.6 11.3 - - - +
138A ILE* 1.3 78.8 - - - +
140A ILE* 1.3 63.7 + - + +
142A PHE* 3.3 5.7 + - - +
143A GLN* 3.1 36.2 + - - +
7B T 3.2 39.6 + - - +
8B C 3.9 14.8 + - - +
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Residues in contact with ILE 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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136A SER 3.2 15.2 + - - +
137A ARG* 3.1 33.2 + - - +
139A GLN* 1.3 75.1 - - + +
141A TRP* 1.3 68.4 + - - +
143A GLN* 3.1 24.1 + - + +
144A ASN* 3.0 38.9 + - - +
5C G 4.8 1.3 - - + -
6C A 4.1 17.0 - - + +
7C T 3.8 32.3 - - + -
8C T 6.3 0.4 - - + -
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Residues in contact with TRP 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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101A VAL* 5.3 5.4 - - + -
106A THR* 4.7 4.0 + - + +
109A LEU* 3.5 63.0 - - + +
110A LEU* 3.9 15.9 - - + -
113A PHE* 4.1 10.1 - + + -
137A ARG 2.9 12.9 + - - +
138A ILE* 3.2 13.4 + - - +
140A ILE* 1.3 77.9 - - - +
142A PHE* 1.3 76.5 + + - +
144A ASN* 3.3 4.8 + - - +
145A ARG* 2.8 57.0 + - + +
202A EDO 3.3 39.9 + - - -
5C G 3.1 35.3 + - - +
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Residues in contact with PHE 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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109A LEU* 4.1 10.1 - - + -
112A ALA* 4.1 16.2 - - + -
113A PHE* 3.6 25.4 - + + -
116A ASP 3.6 12.8 - - - -
117A ARG 3.2 18.6 - - - -
119A PRO* 3.4 30.1 - - + -
124A ARG* 5.4 1.1 - - + -
127A LEU* 3.8 28.9 - - + -
138A ILE* 3.1 30.2 + - + +
139A GLN* 3.7 8.3 - - - +
140A ILE 3.2 0.2 - - - -
141A TRP* 1.3 89.7 - + - +
143A GLN* 1.3 66.7 + - - +
145A ARG* 4.2 1.1 - - - -
146A ARG* 2.8 42.8 + - - +
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Residues in contact with GLN 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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139A GLN* 3.1 30.0 + - - +
140A ILE* 3.1 30.1 + - + +
142A PHE* 1.3 77.2 - - - +
144A ASN* 1.3 64.4 + - - +
146A ARG* 3.8 23.6 - - - +
147A ALA* 3.1 22.5 + - - +
7B T 5.2 1.2 - - - +
8B C 4.3 21.8 + - - +
9B T 3.5 34.4 + - + +
10B A 5.0 0.9 + - - -
7C T 4.9 7.3 - - - +
8C T 4.9 5.4 - - - +
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Residues in contact with ASN 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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140A ILE* 3.0 33.0 + - - +
141A TRP* 3.8 5.5 - - - +
143A GLN* 1.3 77.2 - - - +
145A ARG* 1.3 60.9 - - - +
147A ALA* 3.3 6.3 + - - +
148A ARG* 3.1 50.6 + - - +
202A EDO 5.8 1.1 - - - +
11B A 4.3 4.7 + - - -
4C T 5.7 0.2 - - + -
5C G 3.9 18.3 + - - +
6C A 2.6 50.6 + - - +
7C T 4.3 2.4 - - - +
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Residues in contact with ARG 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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110A LEU* 3.4 28.7 - - - +
113A PHE* 3.5 30.8 - - + -
141A TRP* 2.8 44.8 + - + +
142A PHE 3.3 3.1 + - - +
144A ASN* 1.3 73.0 - - - +
146A ARG* 1.3 67.3 + - - +
148A ARG* 3.0 11.7 + - - -
149A HIS* 3.0 58.7 + - - +
202A EDO 3.0 37.7 + - - +
4C T 5.0 3.2 + - - -
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Residues in contact with ARG 146 (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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113A PHE* 3.6 20.9 - - + -
117A ARG* 3.1 57.4 + - - +
118A PHE* 3.3 40.1 - - - +
119A PRO* 4.6 1.6 - - - +
142A PHE* 2.8 41.7 + - - +
143A GLN* 3.8 20.7 - - - +
145A ARG* 1.3 73.7 - - - +
147A ALA* 1.3 61.0 + - - +
148A ARG 3.5 0.2 + - - -
149A HIS 3.8 6.6 + - - -
150A PRO* 4.3 2.9 - - - +
8B C 3.4 30.5 + - - -
9B T 2.9 31.8 + - - +
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLN 3.1 17.1 + - - +
144A ASN* 3.5 9.2 - - - +
145A ARG 3.1 1.0 - - - -
146A ARG* 1.3 78.1 - - - +
148A ARG* 1.3 65.8 + - + +
149A HIS 3.5 0.7 + - - -
150A PRO* 4.4 8.7 - - - +
9B T 5.7 4.0 - - + +
10B A 5.0 27.5 + - + +
11B A 6.0 3.4 - - - +
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Residues in contact with ARG 148 (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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144A ASN* 3.1 33.4 + - - +
145A ARG* 3.0 2.6 + - - -
147A ALA* 1.3 83.1 - - + +
149A HIS* 1.3 84.8 + - + +
150A PRO* 3.8 5.8 - - - +
202A EDO 5.8 3.6 - - - -
12B T 3.1 22.8 + - - +
13B C 4.4 0.8 - - - +
4C T 3.4 43.0 + - + +
5C G 2.7 48.5 + - - -
6C A 3.2 6.5 - - - +
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Residues in contact with HIS 149 (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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113A PHE* 4.6 8.0 - - + -
117A ARG* 2.6 33.0 + - - -
145A ARG* 3.0 67.0 + - - +
146A ARG 4.1 3.3 - - - +
147A ALA 3.5 0.2 - - - -
148A ARG* 1.3 102.4 + - + +
150A PRO* 1.3 61.8 - - - +
202A EDO 4.2 4.7 - - - -
4C T 5.1 6.5 + - - -
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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