Contacts of the helix formed by residues 167 - 180 (chain A) in PDB entry 1KYH
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 LYS 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A GLU* 3.3 27.5 + - - -
164A LEU 3.0 6.6 + - - -
166A LYS* 1.3 89.2 - - + +
168A ARG* 1.3 64.0 + - - +
169A ALA 3.4 2.5 - - - -
170A GLU* 3.2 40.6 + - + +
171A TYR* 3.1 40.1 + - + -
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Residues in contact with ARG 168 (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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150A PRO* 4.1 3.2 - - - +
164A LEU* 3.0 15.7 + - - +
165A GLN* 3.1 49.4 + - - +
166A LYS 3.9 0.4 - - - -
167A LYS* 1.3 74.6 - - - +
169A ALA* 1.3 58.6 + - - +
171A TYR* 3.4 1.0 + - - +
172A ALA* 2.9 31.6 + - - +
185A LEU* 2.9 52.2 + - + +
186A LYS 3.1 25.2 + - - -
187A GLY* 3.7 9.7 - - - +
188A ASN* 5.1 1.0 - - - +
189A GLN* 3.1 27.7 + - - +
191A VAL* 3.9 8.7 - - + +
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Residues in contact with ALA 169 (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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3A VAL* 3.8 28.5 - - + -
167A LYS 3.4 0.4 - - - -
168A ARG* 1.3 78.5 - - - +
170A GLU* 1.3 59.7 + - + +
172A ALA* 3.8 0.2 - - - +
173A LYS* 2.9 40.6 + - + +
191A VAL* 4.1 23.6 - - + +
201A LEU* 4.7 3.8 - - + -
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Residues in contact with GLU 170 (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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167A LYS* 3.2 46.8 + - + +
169A ALA* 1.3 77.5 - - + +
171A TYR* 1.3 59.5 + - + +
173A LYS* 3.9 6.8 - - + +
174A GLU* 2.9 33.5 + - - +
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Residues in contact with TYR 171 (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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153A PHE* 3.9 5.8 - - + -
159A VAL* 3.8 27.7 - - + +
163A GLU* 3.0 53.0 + - + +
164A LEU* 3.5 36.3 - - + -
167A LYS* 3.1 40.9 + - + +
170A GLU* 1.3 74.4 - - + +
172A ALA* 1.3 61.0 + - - +
174A GLU* 3.8 24.7 - - - -
175A TRP* 2.9 37.7 + - - +
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Residues in contact with ALA 172 (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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153A PHE* 4.3 11.8 - - - -
168A ARG 2.9 18.3 + - - +
169A ALA 3.8 3.1 - - - +
171A TYR* 1.3 75.5 - - - +
173A LYS* 1.3 58.6 + - - +
175A TRP 3.9 0.2 - - - -
176A ALA* 2.9 31.9 + - - +
183A ILE* 4.0 8.7 - - + +
185A LEU* 4.1 19.7 - - + +
191A VAL* 3.9 21.3 - - + -
193A ALA* 3.6 9.4 - - + +
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Residues in contact with LYS 173 (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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3A VAL* 4.6 8.3 - - + -
169A ALA* 2.9 30.2 + - + +
170A GLU* 3.9 6.5 - - + +
172A ALA* 1.3 74.8 - - + +
174A GLU* 1.3 63.9 + - - +
176A ALA* 3.5 2.0 + - - +
177A ALA* 3.2 24.1 + - - +
191A VAL* 5.3 1.1 - - + -
193A ALA* 3.8 10.3 - - + -
194A PHE 5.3 1.5 - - - +
197A GLY* 3.0 24.5 + - - -
199A CYS* 2.8 48.3 - - + +
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Residues in contact with GLU 174 (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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170A GLU* 2.9 20.8 + - - +
171A TYR* 3.4 26.6 - - - +
173A LYS* 1.3 78.7 - - - +
175A TRP* 1.3 80.0 + - + +
177A ALA* 3.4 5.6 + - - +
178A GLN* 3.1 32.5 + - - +
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Residues in contact with TRP 175 (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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153A PHE* 3.7 15.9 - + + -
156A MSE 4.6 5.2 - - - -
157A THR* 3.2 51.3 - - + -
159A VAL* 4.0 12.3 - - + +
171A TYR* 2.9 28.0 + + - +
174A GLU* 1.3 93.9 + - - +
176A ALA* 1.3 60.1 + - - +
177A ALA 3.1 1.6 - - - -
178A GLN* 3.4 38.4 - - - -
179A LEU* 2.8 64.4 + - + +
183A ILE* 3.7 16.2 - - + -
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Residues in contact with ALA 176 (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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172A ALA 2.9 19.7 + - - +
173A LYS 3.8 2.7 - - - +
175A TRP* 1.3 76.2 - - - +
177A ALA* 1.3 54.4 + - - +
180A GLN* 2.7 33.3 + - - -
181A THR* 3.1 24.1 + - - +
183A ILE* 3.5 9.6 - - + +
193A ALA* 3.7 28.0 - - + +
194A PHE 4.1 7.0 - - - +
195A PRO* 3.8 4.7 - - - +
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Residues in contact with ALA 177 (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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173A LYS 3.2 14.7 + - - +
174A GLU* 3.6 5.4 - - - +
175A TRP 3.1 0.2 - - - -
176A ALA* 1.3 77.8 - - - +
178A GLN* 1.3 64.6 + - - +
180A GLN* 2.8 32.9 + - - +
194A PHE 5.0 1.1 + - - +
195A PRO* 4.3 9.1 - - - +
197A GLY* 6.0 2.9 - - - +
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Residues in contact with GLN 178 (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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174A GLU* 3.1 24.8 + - - +
175A TRP* 3.3 51.9 + - + +
177A ALA* 1.3 78.2 - - - +
179A LEU* 1.3 62.4 + - + +
180A GLN* 4.8 2.3 - - - +
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Residues in contact with LEU 179 (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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135A ARG 3.7 23.1 - - - +
136A THR* 5.0 6.7 - - + -
137A TYR* 4.3 23.6 + - + +
146A LEU* 4.1 5.2 - - + -
156A MSE 3.9 28.9 - - + +
157A THR* 5.4 0.2 - - + -
175A TRP* 2.8 53.5 + - + +
178A GLN* 1.3 77.1 - - + +
180A GLN* 1.3 70.3 + - - +
181A THR* 3.5 28.0 - - + +
183A ILE* 4.3 4.3 - - + -
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Residues in contact with GLN 180 (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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137A TYR* 5.7 0.9 - - - +
144A VAL* 5.3 3.6 + - - +
176A ALA 2.7 12.4 + - - -
177A ALA* 2.8 27.3 + - - +
178A GLN 3.4 2.2 - - - +
179A LEU* 1.3 83.1 - - - +
181A THR* 1.3 58.1 + - - +
195A PRO* 3.2 45.6 + - - +
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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