Contacts of the helix formed by residues 140 - 152 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C PRO 3.4 1.0 - - - -
139C ARG* 1.3 83.0 + - - +
141C ALA* 1.3 58.8 + - - +
142C GLU* 2.9 33.6 + - - +
143C GLU* 2.9 30.8 + - - +
144C ASN* 2.9 28.1 + - - +
178C TYR* 3.6 18.8 - - + -
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ASN* 1.3 75.4 - - - +
142C GLU* 1.3 63.3 + - - +
144C ASN* 3.5 2.2 - - - +
145C LYS* 3.0 27.0 + - - +
178C TYR* 3.3 27.3 - - + +
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Residues in contact with GLU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LYS* 3.2 40.9 + - - +
140C ASN* 2.9 13.3 + - - +
141C ALA* 1.3 75.7 - - - +
143C GLU* 1.3 65.2 + - + +
145C LYS* 3.1 8.3 + - + +
146C ALA* 2.9 31.7 + - - +
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Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LYS* 2.6 39.4 + - + +
112C PHE* 4.5 7.6 - - + -
137C ILE 3.5 5.9 - - - +
138C PRO* 3.9 9.9 - - + -
139C ARG* 2.7 42.2 + - - +
140C ASN* 2.9 28.1 + - - +
142C GLU* 1.3 82.1 - - + +
144C ASN* 1.3 57.7 + - - +
146C ALA* 3.0 10.1 + - - +
147C ILE* 2.9 34.3 + - - +
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Residues in contact with ASN 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C PRO* 3.4 20.8 - - + +
140C ASN 2.9 17.0 + - - +
141C ALA* 3.5 6.9 + - - +
142C GLU 3.1 0.2 - - - -
143C GLU* 1.3 78.5 - - - +
145C LYS* 1.3 61.9 + - - +
147C ILE* 3.4 1.4 + - - +
148C GLN* 3.1 18.2 + - - +
178C TYR* 3.6 16.9 + - - +
180C ASN* 3.7 7.7 - - - +
198C ILE* 3.4 15.7 - - - +
202C GLY* 2.8 32.1 + - - -
204C TRP* 2.9 26.6 + - - -
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Residues in contact with LYS 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C ALA* 3.0 18.6 + - - +
142C GLU* 3.1 6.0 + - - +
144C ASN* 1.3 75.0 - - - +
146C ALA* 1.3 66.7 + - - +
148C GLN* 3.2 21.7 + - - +
149C GLU* 3.0 44.9 + - + +
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Residues in contact with ALA 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C PHE* 4.0 18.8 - - + -
142C GLU* 2.9 18.8 + - - +
143C GLU* 3.0 12.1 + - - +
145C LYS* 1.3 77.4 - - - +
147C ILE* 1.3 62.0 + - - +
149C GLU* 3.4 12.9 + - - +
150C VAL* 3.2 28.6 + - + +
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C PHE* 3.8 29.6 - - + -
136C ALA* 3.7 25.6 - - + -
137C ILE 3.9 0.4 - - - -
138C PRO* 3.6 43.3 - - + -
143C GLU 2.9 15.9 + - - +
144C ASN 3.8 4.3 - - - +
146C ALA* 1.3 72.8 - - - +
148C GLN* 1.3 66.3 + - - +
150C VAL* 3.2 5.5 + - - +
151C ALA* 3.0 23.1 + - + +
155C ALA* 5.4 0.4 - - + -
156C PHE 5.9 0.2 - - - +
157C LEU* 4.2 8.5 - - + -
198C ILE* 4.2 22.2 - - + -
216C VAL* 4.4 13.5 - - + -
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Residues in contact with GLN 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ASN* 3.1 12.3 + - - +
145C LYS* 3.2 29.7 + - - +
147C ILE* 1.3 76.2 - - - +
149C GLU* 1.3 61.1 + - + +
151C ALA* 4.2 3.0 - - - +
152C LYS* 3.0 29.5 + - - -
153C THR 5.5 0.4 - - - +
198C ILE* 3.9 13.9 - - + +
199C VAL 4.4 7.6 - - - +
200C ASP* 4.1 5.5 - - - +
201C ASN* 3.4 24.5 + - - +
202C GLY* 3.5 22.8 + - - +
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Residues in contact with GLU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LYS* 3.0 32.3 + - + +
146C ALA* 3.7 11.8 - - - +
148C GLN* 1.3 81.2 - - + +
150C VAL* 1.3 61.4 + - + +
152C LYS* 3.3 25.5 + - - +
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Residues in contact with VAL 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C PHE* 3.8 43.1 - - + +
113C VAL* 4.2 0.9 - - - -
114C THR* 3.6 36.0 - - + +
116C HIS* 3.9 8.5 - - - -
146C ALA* 3.2 16.3 + - + +
147C ILE 3.2 6.0 + - - +
149C GLU* 1.3 79.7 - - + +
151C ALA* 1.3 62.1 + - - +
152C LYS* 4.1 4.9 + - - +
216C VAL* 4.3 7.0 - - + -
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Residues in contact with ALA 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C THR* 4.8 0.9 - - - -
116C HIS* 4.3 9.5 + - - -
147C ILE* 3.0 17.7 + - + +
148C GLN* 4.2 3.1 - - - +
150C VAL* 1.3 77.1 - - - +
152C LYS* 1.3 66.6 + - - +
153C THR* 2.8 33.2 + - - +
155C ALA* 3.7 22.7 - - + -
198C ILE* 5.2 1.6 - - + -
214C THR* 4.4 9.1 - - + +
216C VAL* 3.8 14.1 - - + -
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Residues in contact with LYS 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C HIS* 4.2 20.4 - - + +
148C GLN 3.0 17.0 + - - -
149C GLU 3.3 21.7 + - - +
150C VAL* 4.1 4.8 + - - +
151C ALA* 1.3 75.8 - - - +
153C THR* 1.3 65.9 + - + +
200C ASP* 2.9 14.2 - - - +
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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