Contacts of the helix formed by residues 140 - 152 (chain A) in PDB entry 1KWV
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 ASN 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A PRO 3.4 1.2 - - - -
139A ARG* 1.3 86.4 + - - +
141A ALA* 1.3 59.3 + - - +
142A GLU* 2.8 28.7 + - - +
143A GLU* 2.8 27.4 + - - +
144A ASN* 3.0 28.4 + - - +
178A TYR* 3.5 19.8 - - + -
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Residues in contact with ALA 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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140A ASN* 1.3 72.7 - - - +
142A GLU* 1.3 59.1 - - - +
144A ASN* 3.3 2.8 + - - +
145A LYS* 3.0 29.5 + - - +
178A TYR* 3.6 21.6 - - + +
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Residues in contact with GLU 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 LYS* 3.3 40.2 - - - +
140A ASN* 2.8 20.8 + - - +
141A ALA* 1.3 74.4 - - - +
143A GLU* 1.3 66.3 + - - +
145A LYS* 3.2 22.0 + - - +
146A ALA* 2.9 28.5 + - + +
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Residues in contact with GLU 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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109A LYS* 5.9 3.3 - - + +
110A LYS* 3.1 40.0 + - + +
112A PHE* 4.2 10.8 - - + -
137A ILE 3.3 0.9 - - - +
138A PRO* 4.1 2.9 - - + -
139A ARG* 2.8 39.5 + - - +
140A ASN* 2.8 30.1 + - - +
142A GLU* 1.3 80.9 - - - +
144A ASN* 1.3 60.1 + - - +
146A ALA* 3.2 7.7 + - - +
147A ILE* 2.9 36.6 + - - +
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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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138A PRO* 3.3 23.1 - - + +
140A ASN 3.0 18.6 + - - +
141A ALA 3.6 5.4 - - - +
142A GLU 3.2 0.2 - - - -
143A GLU* 1.3 76.9 - - - +
145A LYS* 1.3 58.7 + - - +
147A ILE* 3.4 0.6 + - - -
148A GLN* 3.0 28.7 + - - +
178A TYR* 3.8 13.9 + - - +
180A ASN* 3.4 10.2 - - - +
198A ILE* 3.5 9.8 - - - +
202A GLY* 2.9 29.1 + - - -
204A TRP* 2.8 27.3 + - - -
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Residues in contact with LYS 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 ALA 3.0 15.9 + - - +
142A GLU* 3.5 20.6 - - - +
144A ASN* 1.3 77.6 - - - +
146A ALA* 1.3 61.6 + - - +
148A GLN* 3.2 16.7 + - - +
149A GLU* 2.8 48.8 + - + +
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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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112A PHE* 3.9 20.6 - - + -
142A GLU* 2.9 16.3 + - + +
143A GLU* 3.2 8.9 + - - +
145A LYS* 1.3 79.1 - - - +
147A ILE* 1.3 61.4 + - - +
149A GLU* 3.3 9.8 + - - +
150A VAL* 3.1 31.2 + - + +
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Residues in contact with ILE 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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112A PHE* 3.7 41.1 - - + -
136A ALA* 3.8 18.2 - - + -
137A ILE 3.8 0.7 - - - -
138A PRO* 3.4 39.0 - - + -
143A GLU 2.9 18.1 + - - +
144A ASN 3.7 4.0 - - - +
146A ALA* 1.3 75.5 - - - +
148A GLN* 1.3 58.2 + - - +
150A VAL* 3.4 5.1 + - - +
151A ALA* 2.9 31.2 + - + +
155A ALA* 5.7 0.4 - - + -
156A PHE 5.9 0.2 - - - +
157A LEU* 4.2 7.9 - - + -
198A ILE* 4.2 25.1 - - + -
216A VAL* 4.6 9.1 - - + +
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Residues in contact with GLN 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* 3.0 14.7 + - - +
145A LYS* 3.4 24.1 + - - +
147A ILE* 1.3 77.0 - - - +
149A GLU* 1.3 68.5 + - - +
151A ALA* 4.0 4.3 - - - +
152A LYS* 3.1 23.0 + - - +
198A ILE* 3.9 13.5 - - + -
199A VAL 4.8 4.6 - - - +
201A ASN* 3.4 14.0 + - - -
202A GLY* 3.3 32.1 + - - +
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Residues in contact with GLU 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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145A LYS* 2.8 46.3 + - + +
146A ALA* 3.6 7.9 - - - +
148A GLN* 1.3 85.2 + - - +
150A VAL* 1.3 59.7 + - + +
152A LYS* 3.0 35.8 - - - +
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Residues in contact with VAL 150 (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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112A PHE* 4.0 33.2 - - + +
113A VAL* 4.2 2.2 - - - -
114A THR* 3.6 41.0 - - + +
116A HIS* 3.7 3.6 - - - -
146A ALA* 3.1 19.5 + - + +
147A ILE* 3.8 4.3 - - - +
149A GLU* 1.3 79.9 - - + +
151A ALA* 1.3 62.1 + - - +
152A LYS* 3.7 7.8 + - - +
216A VAL* 4.3 9.0 - - + -
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Residues in contact with ALA 151 (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 THR* 4.9 2.2 - - - -
116A HIS* 4.0 10.6 + - - -
147A ILE* 2.9 20.7 + - + +
148A GLN* 4.0 3.6 - - - +
150A VAL* 1.3 77.3 - - - +
152A LYS* 1.3 67.0 + - - +
153A THR* 2.8 33.1 + - - +
155A ALA* 3.9 21.5 - - + -
198A ILE* 5.0 2.2 - - + -
214A THR* 4.4 5.3 - - + +
216A VAL* 4.0 14.1 - - + +
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Residues in contact with LYS 152 (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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116A HIS* 4.3 15.8 - - + +
148A GLN 3.1 14.5 + - - +
149A GLU* 3.0 24.5 - - - +
150A VAL* 3.7 6.0 + - - +
151A ALA* 1.3 77.2 - - - +
153A THR* 1.3 66.9 + - + +
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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