Contacts of the helix formed by residues 170 - 184 (chain A) in PDB entry 1K89
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 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A GLY* 1.3 71.7 - - - -
171A ARG* 1.3 65.9 + - - +
173A LEU* 3.8 1.9 - - - +
174A GLY* 3.0 20.6 + - - -
194A GLY 4.2 15.5 - - - +
195A LYS 5.6 0.2 - - - -
196A ALA* 5.4 12.0 + - + +
199A PHE* 5.8 0.2 - - - -
205A ARG* 4.0 17.9 - - - +
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Residues in contact with ARG 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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132A PRO* 5.4 5.7 + - - +
135A LYS 5.0 3.0 + - - -
136A SER 4.6 0.6 - - - -
137A ASP* 3.2 41.9 + - - +
140A VAL* 3.8 27.1 - - - +
169A GLY 3.1 0.8 + - - -
170A ALA* 1.3 82.2 - - - +
172A GLU* 1.3 97.1 + - - +
174A GLY* 3.3 1.8 + - - -
175A TYR* 3.1 43.8 + - + +
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Residues in contact with GLU 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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94A PHE* 4.4 7.4 - - + -
132A PRO* 5.3 3.2 - - + +
140A VAL* 3.5 17.4 - - + +
144A CYS* 3.9 16.6 - - - -
167A GLY 3.8 19.6 - - - +
168A VAL* 3.7 20.1 - - + -
169A GLY* 2.7 30.3 + - - +
171A ARG* 1.3 111.3 + - - +
173A LEU* 1.3 66.8 + - - +
175A TYR* 3.2 2.6 + - - +
176A MET* 2.9 32.1 + - + +
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Residues in contact with LEU 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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163A ALA* 4.8 2.5 - - - -
164A GLY* 4.4 10.8 - - - +
168A VAL* 4.2 14.1 - - + -
169A GLY 3.0 24.0 + - - +
170A ALA 3.8 3.1 - - - +
172A GLU* 1.3 78.3 - - - +
174A GLY* 1.3 57.3 + - - +
176A MET* 3.7 10.3 - - + +
177A TYR* 2.9 33.1 + - - +
192A LEU* 4.1 13.9 - - + +
193A THR 3.8 21.3 - - - +
194A GLY* 4.3 16.2 - - - +
195A LYS* 5.1 5.2 - - + -
199A PHE* 5.3 1.3 - - - -
205A ARG* 5.3 0.9 - - - +
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Residues in contact with GLY 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 ALA 3.0 15.0 + - - -
171A ARG 3.7 3.4 - - - -
173A LEU* 1.3 78.0 - - - +
175A TYR* 1.3 65.8 + - - +
177A TYR* 3.4 2.4 + - - +
178A GLY* 2.9 21.1 + - - -
199A PHE* 3.9 24.7 - - - -
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Residues in contact with TYR 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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137A ASP* 2.3 39.7 + - - -
140A VAL* 4.4 7.0 - - + -
141A MET* 3.5 52.7 - - + +
144A CYS* 3.8 13.5 - - + -
145A GLN* 4.5 7.8 + - + +
171A ARG* 3.1 37.8 + - + +
172A GLU* 3.8 4.9 - - - +
174A GLY* 1.3 80.0 - - - +
176A MET* 1.3 61.4 + - - +
178A GLY* 3.4 2.3 + - - -
179A GLN* 3.3 20.3 + - - +
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Residues in contact with MET 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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92A LEU* 3.7 32.1 - - + -
94A PHE* 4.5 7.9 - - + -
144A CYS* 3.7 25.8 - - + +
147A PHE* 3.9 20.0 - - + -
148A MET* 3.5 30.4 - - + +
168A VAL* 3.8 18.4 - - + -
172A GLU* 2.9 31.8 + - + +
173A LEU* 3.7 9.0 - - + +
175A TYR* 1.3 74.1 - - - +
177A TYR* 1.3 62.3 + - - +
179A GLN 3.2 1.6 + - - +
180A TYR* 2.9 28.4 + - - +
192A LEU* 4.3 9.9 - - + -
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Residues in contact with TYR 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 LEU 2.9 17.5 + - - +
174A GLY 3.8 3.1 - - - +
176A MET* 1.3 79.2 - - - +
178A GLY* 1.3 66.1 + - - +
180A TYR* 3.0 7.0 + + - +
181A ARG* 2.9 52.4 + - + +
187A PHE* 2.8 55.4 + + - -
189A ASN* 3.8 22.8 - - + +
191A VAL* 3.8 23.1 - - + -
192A LEU* 3.7 13.8 - - + +
195A LYS* 5.1 3.6 - - + -
199A PHE* 3.7 37.2 - + + -
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Residues in contact with GLY 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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145A GLN* 6.2 0.4 - - - -
174A GLY 2.9 16.5 + - - -
175A TYR* 3.4 2.9 + - - -
176A MET 3.3 0.2 - - - -
177A TYR* 1.3 83.6 - - - +
179A GLN* 1.3 60.9 + - - +
181A ARG* 3.6 10.0 + - - +
182A LYS* 3.3 21.0 + - - +
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Residues in contact with GLN 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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145A GLN* 3.6 51.1 + - + +
148A MET* 4.1 9.6 - - + -
149A THR* 3.0 22.4 + - - +
175A TYR 3.3 10.9 + - - +
176A MET 3.2 8.4 + - - +
177A TYR 3.2 0.4 - - - -
178A GLY* 1.3 73.7 - - - +
180A TYR* 1.3 67.5 + - - +
182A LYS* 3.3 10.9 + - - +
183A ILE* 2.9 42.2 + - + +
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Residues in contact with TYR 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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148A MET* 3.8 19.2 - - + +
152A TYR* 3.7 34.0 + - + -
155A ILE* 4.2 4.5 + - + -
156A GLY* 3.9 18.2 - - - -
157A PRO* 4.1 5.9 - - - +
176A MET 2.9 14.1 + - - +
177A TYR* 3.0 18.4 + + + +
179A GLN* 1.3 79.9 - - - +
181A ARG* 1.3 67.6 + - - +
183A ILE* 3.2 3.2 + - - -
184A VAL* 3.0 56.1 + - + +
187A PHE 4.6 0.7 - - - -
188A TYR* 4.0 15.8 - - + +
191A VAL* 3.7 41.7 - - + +
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Residues in contact with ARG 181 (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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177A TYR* 2.9 47.8 + - + +
178A GLY* 4.3 9.5 + - - +
180A TYR* 1.3 81.7 - - - +
182A LYS* 1.3 61.5 + - - +
184A VAL* 4.4 0.7 - - - -
185A GLY* 2.9 28.1 + - - -
186A GLY 3.4 22.5 + - - +
187A PHE* 4.4 8.3 - - - +
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Residues in contact with LYS 182 (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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178A GLY 3.3 17.2 + - - +
179A GLN* 3.6 12.8 - - - +
180A TYR 3.1 0.4 - - - -
181A ARG* 1.3 84.3 - - + +
183A ILE* 1.3 67.2 + - + +
185A GLY* 3.7 5.9 + - - -
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Residues in contact with ILE 183 (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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148A MET 4.3 2.5 - - - +
149A THR* 3.8 35.4 - - + +
152A TYR* 3.7 45.5 - - + +
179A GLN* 2.9 41.6 + - + +
180A TYR* 3.9 2.9 - - - +
182A LYS* 1.3 82.4 - - + +
184A VAL* 1.3 63.9 + - + +
185A GLY* 4.4 0.3 - - - -
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Residues in contact with VAL 184 (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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152A TYR* 3.7 29.6 - - + -
180A TYR* 3.0 57.9 + - + +
181A ARG 4.3 1.1 - - - +
183A ILE* 1.3 76.8 - - - +
185A GLY* 1.3 62.4 + - - +
186A GLY 3.5 6.0 + - - +
188A TYR* 3.8 26.4 - - + -
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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