Contacts of the helix formed by residues 168 - 180 (chain B) in PDB entry 2KXN
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 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B PRO* 4.4 17.8 - - + +
166B PHE* 3.6 5.4 - - - +
167B GLU* 1.3 93.1 + - - +
169B VAL* 1.3 63.7 + - - +
170B ASP* 3.4 15.4 - - + +
171B ASP* 4.6 14.5 + - + +
172B ALA* 3.2 24.1 + - - +
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Residues in contact with VAL 169 (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 ASN 4.3 9.9 - - - +
118B CYS* 3.8 34.5 - - + -
120B LEU* 5.6 3.1 - - + -
166B PHE* 5.1 6.3 - - + +
168B ASN* 1.3 75.7 - - - +
170B ASP* 1.3 60.5 + - - +
171B ASP 2.9 10.6 + - - -
172B ALA* 3.7 11.4 - - + -
173B LYS* 3.3 31.6 + - + +
193B PHE* 5.0 11.9 - - + -
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Residues in contact with ASP 170 (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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168B ASN* 3.4 10.9 - - + +
169B VAL* 1.3 80.5 + - - +
171B ASP* 1.3 67.5 + - - +
173B LYS* 2.8 29.8 + - - +
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Residues in contact with ASP 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR 3.9 18.7 - - - +
142B GLY* 5.2 6.3 - - - -
143B PRO* 5.4 4.9 - - + -
166B PHE* 5.5 0.4 - - - -
168B ASN* 4.0 13.9 + - + +
169B VAL* 2.9 0.4 - - - +
170B ASP* 1.3 91.5 - - - +
172B ALA* 1.3 63.6 + - - +
173B LYS* 3.1 8.4 + - - +
174B GLU* 3.2 16.6 + - - +
175B ALA 3.6 5.9 + - - -
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Residues in contact with ALA 172 (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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120B LEU* 3.6 16.6 - - + +
166B PHE* 3.3 41.0 - - + -
168B ASN 3.2 22.4 + - - +
169B VAL* 3.5 11.6 + - + -
171B ASP* 1.3 74.0 - - - +
173B LYS* 1.3 64.0 + - - +
174B GLU 3.1 0.2 - - - -
175B ALA* 3.1 16.3 + - - +
176B LYS* 3.2 9.0 + - - +
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Residues in contact with LYS 173 (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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169B VAL* 3.3 27.0 + - + +
170B ASP* 2.8 28.0 + - - +
171B ASP* 4.3 5.2 + - - +
172B ALA* 1.3 77.6 - - - +
174B GLU* 1.3 67.7 + - + +
176B LYS* 3.5 14.0 - - - +
177B GLU* 3.4 33.7 + - - +
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Residues in contact with GLU 174 (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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141B TYR* 4.8 7.5 - - + +
171B ASP* 3.2 9.3 + - - +
172B ALA 3.1 0.4 - - - -
173B LYS* 1.3 87.6 + - + +
175B ALA* 1.3 59.4 + - - +
176B LYS 3.0 2.0 - - - -
177B GLU* 3.8 9.8 - - + +
178B ARG* 2.9 80.3 + - + +
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Residues in contact with ALA 175 (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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120B LEU* 4.8 1.3 - - + -
138B PHE* 4.9 4.9 - - + -
141B TYR* 3.4 37.2 - - + +
166B PHE* 3.7 30.5 - - + -
171B ASP 3.6 2.2 + - - +
172B ALA* 3.1 13.4 + - - +
174B GLU* 1.3 78.3 - - - +
176B LYS* 1.3 58.3 + - - +
178B ARG 4.2 0.2 - - - -
179B ALA* 3.2 30.0 + - - +
191B VAL* 4.2 3.5 - - - +
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Residues in contact with LYS 176 (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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120B LEU* 4.1 15.9 - - + +
172B ALA 3.2 9.0 + - - +
173B LYS* 3.5 16.8 - - - +
174B GLU 3.0 0.2 - - - -
175B ALA* 1.3 77.2 - - - +
177B GLU* 1.3 72.4 + - + +
180B ASN* 3.3 21.8 + - - +
191B VAL* 3.4 14.2 - - - +
192B ASP* 3.6 24.0 - - + +
193B PHE* 3.1 65.0 - - - +
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Residues in contact with GLU 177 (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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173B LYS* 3.4 25.9 + - - +
174B GLU* 3.2 9.5 + - + +
176B LYS* 1.3 90.0 - - + +
178B ARG* 1.3 63.9 + - + +
180B ASN* 4.3 9.4 + - - +
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Residues in contact with ARG 178 (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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141B TYR* 3.3 34.4 + - + +
174B GLU* 2.9 55.8 + - + +
177B GLU* 1.3 79.7 - - + +
179B ALA* 1.3 63.2 + - - +
180B ASN 3.2 8.4 + - - +
182B MET* 4.9 3.5 - - - +
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Residues in contact with ALA 179 (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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137B VAL* 6.0 0.2 - - + -
138B PHE* 4.4 10.3 - - + -
141B TYR* 4.5 18.2 - - + +
175B ALA 3.2 19.4 + - - +
178B ARG* 1.3 77.7 - - - +
180B ASN* 1.3 63.9 + - - +
182B MET* 3.1 40.6 + - - +
191B VAL* 3.4 22.9 - - + +
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Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LYS* 3.3 19.0 + - + +
177B GLU* 4.4 8.7 - - - +
178B ARG 3.2 8.2 - - - +
179B ALA* 1.3 78.1 - - - +
181B GLY* 1.3 66.5 + - - +
182B MET* 3.0 6.5 + - - -
189B ILE 3.8 2.6 - - - +
190B ARG* 4.0 2.8 - - - -
191B VAL* 3.2 30.8 + - - +
192B ASP* 4.6 4.2 - - - +
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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