Contacts of the helix formed by residues 136 - 146 (chain A) in PDB entry 1KHI
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 SER 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASP* 5.3 7.2 + - - -
134A GLN 3.2 2.4 + - - +
135A SER* 1.3 76.8 - - - +
137A LEU* 1.3 63.5 + - - +
138A TRP 3.3 3.4 - - - +
139A ASN* 3.3 24.9 + - - +
140A ARG* 3.0 27.5 + - - +
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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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131A VAL* 3.7 23.8 - - + -
132A ILE* 3.7 17.3 - - + +
133A ASP* 5.7 0.4 + - - +
134A GLN 3.1 16.6 + - - +
135A SER 3.1 1.6 + - - -
136A SER* 1.3 75.9 - - - +
138A TRP* 1.3 57.9 + - - +
140A ARG* 3.3 20.0 + - - +
141A LEU* 2.8 37.5 + - + +
154A VAL* 6.2 0.2 - - + -
165A ALA* 3.7 5.4 - - + +
166A VAL 3.4 33.0 - - - +
167A ASP* 3.5 24.9 - - - +
168A MET* 3.8 18.8 - - + +
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Residues in contact with TRP 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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111A MET* 3.8 24.0 - - + -
112A GLN 4.2 6.7 - - - -
113A ASP* 4.5 5.8 - - - -
114A GLY* 3.3 48.7 - - - -
115A SER 3.4 21.3 - - - -
116A ILE* 3.8 13.7 - - + -
131A VAL* 4.0 20.5 - - + +
132A ILE 4.8 3.4 + - - +
133A ASP* 6.0 3.1 - - - +
136A SER* 3.3 1.0 - - - -
137A LEU* 1.3 78.5 - - - +
139A ASN* 1.3 70.7 + - - +
141A LEU* 3.3 4.8 + - - +
142A GLN* 2.9 54.1 + - - +
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Residues in contact with ASN 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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136A SER* 3.3 26.8 + - - +
138A TRP* 1.3 89.9 - - - +
140A ARG* 1.3 63.2 + - + +
142A GLN* 3.9 6.4 - - - +
143A LYS* 3.0 24.7 + - - +
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Residues in contact with ARG 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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134A GLN 3.9 2.8 + - - -
135A SER* 2.9 37.2 + - - -
136A SER* 3.0 16.0 + - - +
137A LEU* 3.3 27.0 - - - +
139A ASN* 1.3 76.7 - - + +
141A LEU* 1.3 63.5 + - - +
143A LYS* 3.4 10.2 + - + +
144A ALA* 3.1 24.1 + - - +
167A ASP* 4.3 10.5 + - - -
168A MET* 3.7 29.7 - - - +
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Residues in contact with LEU 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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108A VAL* 4.3 4.5 - - + -
111A MET* 3.7 22.0 - - + -
116A ILE* 4.2 7.0 - - + -
131A VAL* 4.2 29.6 - - + -
137A LEU* 2.8 21.3 + - + +
138A TRP* 3.6 4.9 - - + +
140A ARG* 1.3 77.4 - - - +
142A GLN* 1.3 57.2 + - - +
144A ALA* 3.2 3.6 + - - +
145A PHE* 2.9 29.5 + - - +
152A VAL* 3.6 30.2 - - + +
154A VAL* 3.7 30.3 - - + -
168A MET* 3.6 20.1 - - + -
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Residues in contact with GLN 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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111A MET* 3.5 29.0 + - + +
138A TRP* 2.9 47.3 + - - +
139A ASN* 3.9 7.5 - - - +
141A LEU* 1.3 76.3 - - - +
143A LYS* 1.3 62.5 + - - +
145A PHE* 3.5 1.4 - - + +
146A GLU* 3.0 51.7 + - + +
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Residues in contact with LYS 143 (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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139A ASN 3.0 17.9 + - - +
140A ARG* 3.6 9.9 - - + +
141A LEU 3.2 0.2 - - - -
142A GLN* 1.3 80.8 - - - +
144A ALA* 1.3 62.2 + - - +
146A GLU* 3.5 15.7 + - - +
147A SER* 3.4 14.6 + - - -
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Residues in contact with ALA 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 ARG 3.1 5.9 + - - +
141A LEU 3.7 2.2 - - - +
143A LYS* 1.3 77.5 - - - +
145A PHE* 1.3 66.0 + - - +
147A SER* 3.2 16.4 + - - -
148A GLY* 3.3 10.7 + - - -
152A VAL* 3.3 18.0 - - + +
168A MET* 3.5 32.8 - - + -
170A VAL* 4.0 11.7 - - + -
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Residues in contact with PHE 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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108A VAL* 3.6 37.9 - - + -
109A LEU 3.5 19.1 - - - -
110A ASP* 3.6 10.3 - - - -
111A MET* 3.7 35.2 - - + -
141A LEU* 2.9 17.3 + - + +
142A GLN* 3.5 6.3 - - + +
143A LYS 3.3 0.2 - - - -
144A ALA* 1.3 77.4 - - - +
146A GLU* 1.3 60.6 + - + +
147A SER 3.0 5.0 + - - -
149A ARG* 2.7 98.7 + - + +
152A VAL* 3.7 9.4 - - + +
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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
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142A GLN* 3.0 41.5 + - + +
143A LYS* 3.5 9.3 + - - +
144A ALA 3.3 0.4 - - - -
145A PHE* 1.3 82.0 - - + +
147A SER* 1.3 58.8 + - - +
148A GLY 3.8 0.4 - - - -
149A ARG* 4.6 14.8 - - - +
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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