Contacts of the helix formed by residues 135 - 147 (chain A) in PDB entry 3KHU
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LEU* 5.6 1.6 - - - -
134A VAL* 1.3 86.6 - - + +
136A ALA* 1.3 63.8 + - - +
137A ALA 3.3 2.7 - - - +
138A GLU* 3.2 38.0 + - - +
139A SER* 3.2 16.4 + - - +
214A TRP* 4.8 10.7 - - + +
217A GLU* 2.9 11.9 + - - -
286A TYR* 5.6 4.6 - - - -
287A LEU* 4.0 20.9 - - + +
290A ALA* 4.2 21.2 + - - +
291A LEU* 3.4 29.7 - - - +
244B THR* 5.9 3.5 - - + +
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Residues in contact with ALA 136 (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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106A LEU* 4.1 22.0 - - + -
109A ILE* 5.1 4.3 - - + +
128A GLU* 3.0 18.8 - - - +
132A VAL* 3.5 18.8 - - + -
133A PRO* 3.1 19.7 + - - +
134A VAL 3.4 0.6 + - - -
135A ARG* 1.3 77.1 - - - +
137A ALA* 1.3 62.0 + - - +
139A SER* 3.1 17.9 + - - -
140A ILE* 3.1 15.6 + - - +
217A GLU* 3.6 1.5 + - - +
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Residues in contact with ALA 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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128A GLU* 3.0 11.8 + - - +
135A ARG 3.3 0.4 - - - -
136A ALA* 1.3 75.1 - - - +
138A GLU* 1.3 62.2 + - - +
140A ILE* 3.2 8.5 + - - +
141A ARG* 2.9 24.7 + - - +
156A VAL* 3.9 18.3 - - + +
157A LEU 5.4 0.2 - - - +
213A THR* 3.4 33.0 - - + -
217A GLU* 2.9 15.8 + - - +
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Residues in contact with GLU 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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135A ARG* 3.2 35.0 + - - +
137A ALA* 1.3 77.4 - - - +
139A SER* 1.3 58.4 + - - +
141A ARG* 3.4 8.2 + - + +
142A ARG* 2.9 63.5 + - - +
214A TRP* 4.3 26.1 + - + +
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.1 11.8 - - - +
109A ILE* 6.1 1.8 - - - -
135A ARG* 3.2 10.5 + - - +
136A ALA* 3.1 11.2 + - - -
138A GLU* 1.3 77.5 + - - +
140A ILE* 1.3 67.1 + - - +
142A ARG* 3.1 12.3 + - - +
143A ILE* 3.1 21.0 + - - +
323E PHE* 3.2 45.1 - - - +
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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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87A ILE* 4.2 12.6 - - + -
109A ILE* 3.8 29.2 - - + -
113A ALA* 4.3 15.0 - - + -
126A VAL* 4.7 6.3 - - + -
128A GLU* 3.7 37.0 - - + +
136A ALA 3.1 8.3 + - - +
137A ALA* 3.5 7.4 - - - +
139A SER* 1.3 74.5 - - - +
141A ARG* 1.3 63.8 + - - +
143A ILE* 3.2 7.2 + - + +
144A PHE* 3.0 54.8 + - + -
156A VAL* 3.7 13.7 - - + -
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Residues in contact with ARG 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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137A ALA 2.9 17.1 + - - +
138A GLU* 3.6 9.4 - - + +
140A ILE* 1.3 76.7 - - - +
142A ARG* 1.3 56.9 + - + +
144A PHE* 3.4 25.3 + - - +
145A ASP* 2.9 69.8 + - - +
154A LEU* 2.8 34.2 + - - +
155A GLN* 4.1 5.9 + - - +
156A VAL* 4.1 25.5 - - + +
183A ASP* 5.4 7.6 + - - -
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Residues in contact with ARG 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 GLU* 2.9 50.3 + - + +
139A SER 3.1 6.0 + - - +
141A ARG* 1.3 74.9 - - + +
143A ILE* 1.3 66.2 + - - +
145A ASP* 3.4 7.5 + - + +
146A ALA* 3.0 26.2 + - - +
321E SER* 5.7 3.8 + - - +
323E PHE* 4.3 25.1 - - + -
435E PRO* 4.6 7.4 - - + +
458E GLN* 5.7 9.5 - - - +
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Residues in contact with ILE 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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110A GLU* 3.7 26.7 - - + +
113A ALA* 3.9 28.9 - - + +
114A ARG* 3.9 31.9 - - + +
117A VAL* 4.4 4.0 - - + -
139A SER* 3.1 15.9 + - - +
140A ILE* 3.6 6.3 - - + +
142A ARG* 1.3 76.3 - - - +
144A PHE* 1.3 64.0 + - + +
146A ALA 3.3 1.0 + - - -
147A ASN* 2.9 43.5 + - - +
323E PHE* 3.6 30.7 - - + -
435E PRO* 4.6 6.3 - - + -
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Residues in contact with PHE 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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113A ALA* 3.4 37.0 - - + -
116A ILE* 4.3 6.3 - - + -
117A VAL* 4.2 9.4 - - + +
126A VAL* 3.9 22.4 - - + -
140A ILE* 3.0 34.7 + - + -
141A ARG* 3.6 21.8 - - - +
143A ILE* 1.3 78.9 - - + +
145A ASP* 1.3 62.7 + - - +
147A ASN* 3.2 23.2 + - - +
148A THR* 3.6 5.5 + - - -
152A LEU* 5.8 1.0 - - - +
154A LEU* 3.7 45.5 - - + -
156A VAL* 3.7 22.7 - - + -
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Residues in contact with ASP 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 ARG* 2.9 54.3 + - - +
142A ARG* 3.9 7.4 - - + +
143A ILE 3.3 0.2 - - - -
144A PHE* 1.3 76.4 - - - +
146A ALA* 1.3 59.1 - - - +
148A THR* 4.2 14.5 - - - +
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Residues in contact with ALA 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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142A ARG 3.0 17.6 + - - +
143A ILE 3.8 3.8 - - - +
145A ASP* 1.3 77.6 - - - +
147A ASN* 1.3 58.6 + - - +
148A THR* 3.6 2.4 + - - -
434E LYS* 3.4 17.9 - - + +
435E PRO* 3.5 39.9 - - + -
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Residues in contact with ASN 147 (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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114A ARG* 4.2 4.4 + - - +
117A VAL* 3.1 39.4 - - + +
143A ILE* 2.9 35.6 + - - +
144A PHE 3.2 4.8 + - - +
146A ALA* 1.3 78.4 - - - +
148A THR* 1.3 63.5 + - - +
149A LYS* 3.9 2.4 + - - +
152A LEU* 4.3 1.4 - - - +
434E LYS* 2.8 48.2 + - - +
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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