Contacts of the helix formed by residues 159 - 171 (chain A) in PDB entry 3K9O
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 SER 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLN* 5.1 14.3 + - - +
158A SER* 1.3 74.1 + - - +
160A PRO* 1.4 68.9 - - - +
161A GLU* 3.0 22.4 + - - -
162A TYR* 3.2 47.5 + - - +
163A THR* 3.0 23.8 + - - -
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Residues in contact with PRO 160 (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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157A VAL* 5.5 3.6 - - + -
158A SER 3.2 10.1 - - - +
159A SER* 1.4 83.8 - - - +
161A GLU* 1.3 70.9 + - + +
163A THR* 3.5 8.9 + - - +
164A LYS* 3.0 27.4 + - - +
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Residues in contact with GLU 161 (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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159A SER* 3.0 20.9 + - - +
160A PRO* 1.3 93.0 - - + +
162A TYR* 1.3 70.5 + - + +
164A LYS* 3.3 6.8 + - - +
165A LYS* 3.1 33.5 + - - +
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Residues in contact with TYR 162 (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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140A MET* 3.8 18.1 - - + +
143A GLN* 3.5 42.7 - - + +
144A THR* 3.9 0.2 + - - -
147A LEU* 4.0 18.2 - - + -
159A SER* 3.2 32.4 + - - +
161A GLU* 1.3 81.9 - - + +
163A THR* 1.3 64.7 + - - +
165A LYS* 3.1 8.6 + - + +
166A ILE* 3.0 26.0 + - - +
188A TRP* 3.4 77.0 + + + -
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Residues in contact with THR 163 (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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147A LEU* 4.3 11.3 - - - +
150A HIS* 5.4 6.2 + - + -
157A VAL* 5.6 2.8 - - - +
158A SER* 4.5 3.8 + - - -
159A SER 3.0 12.8 + - - -
160A PRO* 3.6 12.7 - - - +
162A TYR* 1.3 79.3 - - - +
164A LYS* 1.3 57.0 + - - +
166A ILE* 3.2 12.7 + - + +
167A GLU* 2.8 54.3 + - + +
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Residues in contact with LYS 164 (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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160A PRO 3.0 17.1 + - - +
161A GLU* 3.8 7.2 - - - +
162A TYR 3.2 0.2 - - - -
163A THR* 1.3 73.8 - - - +
165A LYS* 1.3 66.3 + - + +
167A GLU* 3.2 24.3 + - - +
168A ASN* 2.9 56.3 + - - +
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Residues in contact with LYS 165 (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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161A GLU* 3.1 25.4 + - - +
162A TYR* 3.1 11.1 + - + +
164A LYS* 1.3 78.2 - - + +
166A ILE* 1.3 62.3 + - - +
168A ASN* 3.4 8.0 + - - +
169A LEU* 3.2 27.5 + - - +
183A LEU* 4.0 13.7 - - + -
188A TRP* 2.8 49.3 + - + +
190A VAL* 3.8 24.2 - - + +
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Residues in contact with ILE 166 (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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147A LEU* 4.0 25.1 - - + -
151A VAL* 5.2 2.7 - - + -
162A TYR 3.0 23.6 + - - +
163A THR* 3.5 12.6 - - + +
165A LYS* 1.3 75.0 - - - +
167A GLU* 1.3 54.7 + - + +
169A LEU* 3.3 1.9 + - - -
170A CYS* 2.8 42.4 + - - -
176A ARG* 3.7 26.0 - - + +
179A VAL* 3.8 10.5 - - + +
180A ILE* 3.8 36.1 - - + -
183A LEU* 3.9 14.8 - - + +
188A TRP* 4.0 8.1 - - + -
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Residues in contact with GLU 167 (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 THR* 2.8 46.9 + - + +
164A LYS* 3.6 26.0 - - - +
166A ILE* 1.3 76.5 - - + +
168A ASN* 1.3 69.5 + - - +
170A CYS* 3.3 7.8 + - - +
171A ALA* 3.0 24.0 + - - +
176A ARG* 5.0 8.5 - - - +
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Residues in contact with ASN 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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164A LYS* 2.9 54.7 + - - +
165A LYS* 3.7 7.9 - - - +
167A GLU* 1.3 79.7 + - - +
169A LEU* 1.3 64.6 + - + +
171A ALA* 3.4 19.5 + - - +
172A MET* 3.7 12.1 - - - +
190A VAL* 6.3 3.4 - - + -
6B LYS* 6.1 1.2 - - - +
68B HIS* 5.6 0.3 + - - -
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Residues in contact with LEU 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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165A LYS 3.2 9.7 + - - +
168A ASN* 1.3 75.4 - - + +
170A CYS* 1.3 66.1 + - - +
171A ALA 3.1 1.6 - - - -
172A MET* 3.0 40.5 + - - +
173A GLY 3.8 0.7 + - - -
174A PHE* 3.5 18.3 + - + -
179A VAL* 3.7 24.9 - - + -
183A LEU* 3.9 36.8 - - + -
190A VAL* 4.8 9.6 - - + +
193A ALA* 4.4 5.4 - - + -
194A THR* 3.3 28.5 - - - +
197A LEU* 4.2 11.9 - - + -
8B LEU* 4.5 5.4 - - + -
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Residues in contact with CYS 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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166A ILE* 2.8 30.5 + - - +
167A GLU* 3.7 5.4 - - - +
169A LEU* 1.3 73.0 - - - +
171A ALA* 1.3 57.4 + - - +
173A GLY* 2.8 22.0 + - - -
174A PHE 3.9 11.7 - - - +
176A ARG* 3.5 64.6 - - - +
179A VAL* 4.1 7.0 - - - -
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Residues in contact with ALA 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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167A GLU 3.0 13.4 + - - +
168A ASN* 3.4 15.5 - - - +
169A LEU 3.1 0.6 - - - -
170A CYS* 1.3 71.7 - - - +
172A MET* 1.3 59.4 + - - +
173A GLY 3.1 5.9 + - - -
6B LYS* 6.1 3.1 - - - +
68B HIS* 3.5 18.4 - - - +
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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