Contacts of the helix formed by residues 128 - 141 (chain B) in PDB entry 1KNY
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 ALA 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B VAL 3.9 2.0 + - - -
127B GLU* 1.3 71.2 - - + +
129B GLN* 1.3 60.1 + - - +
131B PHE* 3.4 12.7 + - - +
132B HIS* 3.0 25.1 + - - +
182B ARG* 3.7 30.9 + - - +
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Residues in contact with GLN 129 (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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127B GLU* 3.1 11.5 - - + +
128B ALA* 1.3 75.5 - - - +
130B THR* 1.3 60.5 + - - +
132B HIS* 2.6 44.4 + - - +
133B ASP* 2.7 52.3 + - - +
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Residues in contact with THR 130 (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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90B SER 4.9 2.5 - - - +
92B VAL* 3.0 39.9 - - + +
126B VAL* 3.9 6.9 - - + +
127B GLU* 2.8 29.2 + - - +
129B GLN* 1.3 82.3 - - - +
131B PHE* 1.3 53.7 + - - -
133B ASP* 3.5 10.9 + - - +
134B ALA* 3.2 23.6 + - - +
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Residues in contact with PHE 131 (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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92B VAL* 3.7 12.8 - - + -
96B TRP* 3.2 47.6 - + - -
123B ALA 5.7 0.2 - - - -
126B VAL* 3.7 40.8 - - + -
127B GLU 3.2 21.9 + - - -
128B ALA* 3.8 6.1 - - - +
129B GLN 3.0 0.6 - - - -
130B THR* 1.3 75.4 - - - +
132B HIS* 1.3 57.6 + - - +
134B ALA* 3.3 7.6 + - - +
135B ILE* 2.8 39.1 + - - +
179B LEU* 3.8 23.5 - - + +
182B ARG* 3.2 46.2 - - + +
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Residues in contact with HIS 132 (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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128B ALA 3.0 13.8 + - - +
129B GLN* 2.6 43.2 + - - +
131B PHE* 1.3 73.9 - - - +
133B ASP* 1.3 64.1 + - - -
134B ALA 3.4 0.2 + - - -
135B ILE* 3.5 4.5 + - - +
136B CYS* 3.4 37.2 + - - -
241B HIS 5.3 1.6 - - - -
242B GLY 3.1 25.2 + - - -
243B TYR* 3.3 36.4 - + + -
244B ILE 5.0 4.9 - - - -
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Residues in contact with ASP 133 (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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129B GLN* 2.7 52.6 + - - +
130B THR* 3.5 9.6 + - - +
132B HIS* 1.3 78.1 + - - +
134B ALA* 1.4 61.7 + - - +
136B CYS* 3.1 8.8 + - - +
137B ALA* 3.0 24.2 + - - +
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Residues in contact with ALA 134 (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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92B VAL* 4.1 17.0 - - + +
93B GLU* 4.4 5.8 - - - +
94B SER* 5.1 3.7 + - - +
130B THR 3.2 15.3 + - - +
131B PHE* 3.5 9.9 - - - +
132B HIS 3.3 0.4 - - - -
133B ASP* 1.4 73.8 - - - +
135B ILE* 1.3 65.4 + - - +
137B ALA* 3.3 5.8 + - - +
138B LEU* 3.1 22.3 + - - +
179B LEU* 3.5 33.4 - - + +
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Residues in contact with ILE 135 (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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131B PHE* 2.8 18.4 - - + +
132B HIS 3.6 6.3 - - - +
134B ALA* 1.3 75.5 - - - +
136B CYS* 1.4 62.8 + - - +
138B LEU* 3.0 15.6 + - - +
139B ILE* 3.1 25.7 + - + +
176B LEU* 3.6 26.5 - - + +
179B LEU* 4.1 14.8 - - + +
180B HIS* 4.1 24.2 - - + +
182B ARG* 6.3 0.2 - - - +
237B TRP* 4.5 2.2 - - + -
243B TYR* 3.3 56.5 - - + +
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Residues in contact with CYS 136 (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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132B HIS* 3.4 34.5 + - - -
133B ASP* 3.1 11.6 + - - +
135B ILE* 1.4 78.0 - - - +
137B ALA* 1.3 61.9 + - - +
139B ILE* 3.6 9.7 + - - +
140B VAL* 3.3 28.2 + - - +
243B TYR* 4.1 22.9 - - - -
244B ILE 4.2 4.0 - - - -
245B VAL* 3.6 28.1 - - + +
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Residues in contact with ALA 137 (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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94B SER* 5.8 3.6 - - - +
133B ASP 3.0 15.5 + - - +
134B ALA* 3.6 7.0 - - - +
136B CYS* 1.3 73.9 - - - +
138B LEU* 1.3 67.9 + - - +
140B VAL* 4.7 1.6 - - - -
141B GLU* 2.7 50.4 + - - +
142B GLU* 5.0 0.4 - - - -
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Residues in contact with LEU 138 (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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94B SER* 4.1 11.8 - - - +
134B ALA 3.1 7.2 + - - +
135B ILE 3.0 10.8 + - - +
137B ALA* 1.3 76.4 - - - +
139B ILE* 1.3 58.1 + - - +
142B GLU* 2.6 58.6 + - + +
143B LEU* 2.9 42.3 + - + -
172B ALA* 3.8 16.2 - - + +
175B MET* 3.9 18.6 - - + -
176B LEU* 3.8 16.4 - - + +
179B LEU* 3.7 29.2 - - + -
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Residues in contact with ILE 139 (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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1A MET* 4.0 23.8 - - + -
135B ILE* 3.2 29.2 - - + +
136B CYS* 3.7 10.8 - - - +
138B LEU* 1.3 84.0 - - + +
140B VAL* 1.3 59.1 + - + +
143B LEU* 3.1 11.6 + - + +
144B PHE* 2.6 35.0 + - - +
176B LEU* 4.5 13.5 - - + -
231B TRP* 4.8 13.7 - - + -
234B ILE* 4.8 10.5 - - + -
235B GLN* 5.5 0.9 - - - +
238B THR* 3.5 31.4 - - + -
243B TYR* 4.6 5.6 - - + +
245B VAL* 6.3 0.9 - - + -
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Residues in contact with VAL 140 (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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1A MET* 5.1 3.8 - - + -
67A GLU 4.2 18.4 - - - +
68A TRP* 4.4 10.3 - - - -
69A THR* 3.9 24.2 - - + +
74A LYS* 3.5 21.2 + - + +
136B CYS 3.3 16.5 + - - +
137B ALA* 3.8 3.1 - - - +
138B LEU 3.2 0.4 - - - -
139B ILE* 1.3 82.3 - - + +
141B GLU* 1.3 74.9 + - + +
142B GLU 3.0 5.7 + - - -
144B PHE* 3.3 18.8 - - - +
145B GLU 3.9 0.5 + - - -
245B VAL* 4.5 18.4 - - + -
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Residues in contact with GLU 141 (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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67A GLU* 3.4 34.0 - - + +
74A LYS* 3.0 13.9 + - - -
137B ALA* 2.7 36.5 + - - +
140B VAL* 1.3 79.8 - - + +
142B GLU* 1.3 66.8 + - - +
145B GLU* 3.1 12.0 - - - +
559B KAN 2.5 54.3 + - - +
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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