Contacts of the helix formed by residues 159 - 170 (chain B) in PDB entry 6CKX
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 HIS 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASP* 3.5 30.3 - - + +
72B ALA* 3.2 18.3 - - + +
73B THR* 3.0 49.5 + - - -
76B ILE* 3.8 17.0 - - + +
107B GLU* 4.8 0.7 - - - -
157B VAL* 3.8 20.9 + - + -
158B GLU* 1.3 77.5 + - - +
160B PRO* 1.3 78.2 - - + +
161B TYR* 3.2 18.0 + - + -
162B GLN* 3.2 14.3 + - - +
163B PHE* 3.2 17.7 - - - -
193B LEU* 5.6 1.2 - - - +
203B PRO* 3.4 6.1 - - - -
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Residues in contact with PRO 160 (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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159B HIS* 1.3 90.5 - - + +
161B TYR* 1.3 54.6 + - + +
163B PHE* 3.0 6.8 + - + +
164B LEU* 2.8 35.2 + - - +
189B VAL* 4.0 27.6 - - + -
192B SER* 5.3 1.1 - - - +
193B LEU* 5.9 6.5 - - + -
203B PRO* 3.8 25.1 - - + +
206B ILE* 3.6 36.6 - - + -
207B ALA* 3.7 7.2 - - - +
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Residues in contact with TYR 161 (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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58B PHE* 4.7 2.9 - - - -
68B TYR* 3.5 53.1 + + + +
69B ASP* 4.2 1.3 - - - +
72B ALA* 4.2 12.1 - - + -
159B HIS* 3.2 15.6 - - + -
160B PRO* 1.3 76.4 - - + +
162B GLN* 1.3 63.9 + - - +
164B LEU* 3.0 19.2 + - - +
165B LEU* 3.0 19.3 + - - +
186B TRP* 3.4 45.0 - + + -
189B VAL* 3.5 32.8 - - + +
190B ASN* 2.7 29.2 + - - -
193B LEU* 3.6 18.6 - - + +
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Residues in contact with GLN 162 (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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68B TYR* 5.2 4.4 - - + +
69B ASP* 4.5 17.0 + - - +
158B GLU* 3.4 27.5 + - - +
159B HIS* 3.2 32.0 + - - +
161B TYR* 1.3 78.1 - - - +
163B PHE* 1.3 84.4 + - + +
165B LEU* 3.6 11.3 + - - +
166B LYS* 3.2 25.1 + - - +
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Residues in contact with PHE 163 (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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158B GLU* 4.2 9.4 - - + -
159B HIS 3.2 27.8 - - - -
160B PRO 3.0 5.0 + - - +
162B GLN* 1.3 98.7 - - + +
164B LEU* 1.3 66.5 + - - +
165B LEU 3.2 1.1 - - - -
166B LYS* 3.9 27.8 - - - +
167B TYR* 2.9 63.4 + + + -
203B PRO* 4.1 11.9 - - + -
204B GLU* 3.7 41.7 - - + -
207B ALA* 3.9 7.2 - - + -
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Residues in contact with LEU 164 (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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160B PRO 2.8 12.9 + - - +
161B TYR* 3.3 10.3 - - - +
163B PHE* 1.3 76.7 - - - +
165B LEU* 1.3 56.3 + - - +
167B TYR* 4.2 0.7 - - - +
168B ALA* 3.0 32.1 + - + +
182B VAL* 3.8 27.6 - - + +
185B ALA* 3.8 14.6 - - + +
186B TRP* 3.6 50.0 - - + +
189B VAL* 4.7 6.7 - - + -
207B ALA* 3.9 11.5 - - + +
210B VAL* 4.8 3.4 - - + -
211B MET* 3.5 31.4 - - + -
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Residues in contact with LEU 165 (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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68B TYR* 4.3 16.2 - - - +
161B TYR 3.0 18.8 + - - +
162B GLN* 3.9 8.1 - - - +
164B LEU* 1.3 75.7 - - + +
166B LYS* 1.3 64.5 + - - +
168B ALA* 4.3 3.3 - - - +
169B LYS* 3.1 28.5 + - + +
182B VAL* 4.5 19.1 - - + -
186B TRP* 4.0 27.6 - - + -
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Residues in contact with LYS 166 (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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162B GLN 3.2 18.3 + - - +
163B PHE* 3.3 28.5 + - - +
165B LEU* 1.3 78.1 - - - +
167B TYR* 1.3 83.7 + - + +
169B LYS* 3.5 9.7 + - - +
170B GLN* 3.3 30.2 - - + +
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Residues in contact with TYR 167 (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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163B PHE* 2.9 38.0 + - + +
166B LYS* 1.3 103.6 + - + +
168B ALA* 1.3 60.7 + - - +
170B GLN* 3.2 12.7 + - - +
171B LEU* 3.8 4.5 + - - +
204B GLU* 3.7 32.9 - - - +
207B ALA* 4.4 2.5 - - + -
208B VAL* 3.9 22.4 - - + -
211B MET* 4.0 20.6 - - - -
238B PHE* 3.5 82.8 + + + -
239B VAL* 4.4 0.7 - - + -
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Residues in contact with ALA 168 (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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164B LEU* 3.0 23.3 + - + +
165B LEU* 4.3 2.9 - - - +
167B TYR* 1.3 76.7 - - - +
169B LYS* 1.3 64.1 + - - +
170B GLN 3.2 0.5 + - - -
171B LEU* 3.2 34.4 + - + +
178B ILE* 4.1 10.3 - - + +
181B LEU* 5.4 1.1 - - + -
182B VAL* 3.3 32.5 - - + -
211B MET* 4.5 4.6 - - + +
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Residues in contact with LYS 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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165B LEU* 3.1 20.4 + - + +
166B LYS* 3.6 9.2 - - - +
167B TYR 3.2 0.4 - - - -
168B ALA* 1.3 77.0 - - - +
170B GLN* 1.3 61.8 + - + +
171B LEU 3.3 6.5 - - - +
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Residues in contact with GLN 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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166B LYS* 3.3 32.0 - - + +
167B TYR* 3.2 8.3 + - - +
168B ALA 3.1 0.8 - - - -
169B LYS* 1.3 78.0 - - + +
171B LEU* 1.3 65.3 + - - +
172B LYS* 3.8 3.5 + - - +
225B TRP 4.4 2.1 - - - +
226B THR* 5.5 1.7 - - - -
227B SER 5.9 0.3 + - - -
237B GLN* 5.3 7.4 + - - +
238B PHE* 4.1 26.3 - - + -
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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