Contacts of the helix formed by residues 147 - 158 (chain B) in PDB entry 1KCX
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 GLY 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B TYR* 3.2 5.5 + - - -
146B ASP* 1.3 80.9 + - - +
148B VAL* 1.3 65.1 + - - +
149B ARG* 3.2 3.6 + - - +
150B GLU* 3.3 30.2 + - - +
151B GLU* 3.5 17.0 + - - +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.7 23.6 - - + -
141B ILE* 4.4 15.7 - - + -
143B SER 4.4 1.1 - - - +
144B TRP* 3.6 39.5 - - + +
145B TYR* 3.0 45.8 + - + +
147B GLY* 1.3 76.8 - - - +
149B ARG* 1.3 72.1 + - + +
151B GLU* 3.2 3.0 + - - +
152B LEU* 2.9 35.1 + - + +
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B TRP* 4.7 7.5 - - + +
147B GLY 3.2 1.3 - - - +
148B VAL* 1.3 91.2 - - + +
150B GLU* 1.3 77.9 + - - +
152B LEU* 3.0 5.1 + - - +
153B GLU* 3.0 27.9 + - - +
183B GLU* 4.1 31.3 + - - +
187B PHE* 3.0 63.2 - - + +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLY* 3.3 29.9 + - - +
148B VAL 3.3 0.4 - - - -
149B ARG* 1.3 89.2 - - - +
151B GLU* 1.3 62.6 + - + +
153B GLU* 3.3 18.2 + - - +
154B VAL* 3.3 25.0 + - - +
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Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B SER* 2.6 32.9 + - - -
116B LEU* 3.1 10.7 + - + -
117B LEU* 2.9 43.2 + - + +
145B TYR* 2.6 33.2 + - - +
147B GLY 3.5 9.4 + - - +
148B VAL 3.2 7.2 + - - +
150B GLU* 1.3 74.1 - - + +
152B LEU* 1.3 65.4 + - - +
154B VAL* 3.2 4.3 + - - +
155B LEU* 3.0 28.2 + - - +
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.4 23.6 - - + -
141B ILE* 3.9 9.2 - - + -
144B TRP* 3.3 38.6 - - + -
148B VAL* 2.9 23.3 + - + +
149B ARG 3.0 6.5 + - - +
151B GLU* 1.3 77.6 - - - +
153B GLU* 1.3 62.4 + - - +
155B LEU* 3.2 6.0 + - + +
156B VAL* 3.1 26.9 + - - +
164B PHE* 3.6 31.9 - - + -
187B PHE* 3.9 20.6 - - + -
188B LEU* 4.4 4.9 - - + -
191B LEU* 4.0 7.4 - - + -
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ARG* 3.0 16.6 + - - +
150B GLU* 3.5 25.4 + - - +
151B GLU 3.3 0.2 - - - -
152B LEU* 1.3 76.2 - - - +
154B VAL* 1.3 59.6 + - + +
156B VAL* 3.5 1.6 + - - +
157B GLN* 3.0 33.1 + - - +
187B PHE* 3.7 22.9 - - + -
191B LEU* 3.8 21.4 - - + +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 3.9 29.2 - - + -
150B GLU 3.3 14.3 + - - +
151B GLU 3.2 7.5 + - - +
152B LEU 3.2 0.6 - - - -
153B GLU* 1.3 75.3 - - + +
155B LEU* 1.3 60.6 + - - +
157B GLN* 5.1 0.4 - - - -
158B ASP* 2.8 54.2 + - + +
159B LYS* 3.1 15.3 + - - -
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.8 37.2 - - + -
117B LEU* 3.8 17.7 - - + -
120B PHE* 3.7 39.3 - - + -
139B VAL* 4.2 8.5 - - + -
151B GLU 3.0 20.3 + - - +
152B LEU* 3.2 6.5 + - - +
154B VAL* 1.3 76.6 - - - +
156B VAL* 1.3 56.7 + - - +
159B LYS* 3.2 13.0 + - + +
160B GLY 3.0 13.2 + - - -
161B VAL* 3.0 30.5 + - + -
164B PHE* 4.2 22.2 - - + -
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU 3.1 14.7 + - - +
153B GLU* 3.9 4.0 - - - +
155B LEU* 1.3 78.0 - - - +
157B GLN* 1.3 66.2 + - + +
160B GLY* 4.0 11.4 + - - -
161B VAL 3.2 21.3 + - - +
162B ASN* 4.8 2.2 - - - -
164B PHE* 3.4 24.2 - - + -
191B LEU* 3.9 41.5 - - + +
193B ALA* 4.8 2.7 - - + -
471B ARG 4.8 1.0 - - - +
473B PRO* 3.9 30.3 - - + +
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Residues in contact with GLN 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B GLU 3.0 17.4 + - - +
154B VAL* 5.1 0.2 - - - -
156B VAL* 1.3 82.1 - - + +
158B ASP* 1.3 87.4 + - - +
160B GLY* 5.0 0.5 + - - -
473B PRO* 6.1 0.7 - - - -
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B VAL* 2.8 44.6 + - + +
157B GLN* 1.3 103.0 + - - +
159B LYS* 1.3 69.3 + - + +
160B GLY 3.4 2.1 + - - -
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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