Contacts of the helix formed by residues 169 - 177 (chain B) in PDB entry 5KX8
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 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B SER 3.8 1.6 + - - -
168B PHE* 1.3 74.5 - - - +
170B PHE* 1.3 65.6 + - - +
171B TYR* 3.6 15.8 + - - +
172B GLU* 3.0 34.0 + - - +
173B LEU* 3.2 13.2 + - - +
252B SER* 3.5 0.7 - - - -
254B ASP* 3.7 13.5 + - - -
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Residues in contact with PHE 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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169B SER* 1.3 71.3 + - - +
171B TYR* 1.3 75.6 + + + +
173B LEU* 3.3 4.9 + - + +
174B LYS* 2.8 52.3 + - + +
180B PHE* 3.7 32.1 - + - -
214B LYS* 4.8 1.6 - - + -
252B SER* 3.0 19.7 + - - +
254B ASP* 3.3 7.2 + - - +
255B GLY* 3.6 26.2 - - - +
256B ASP* 4.6 8.1 - - + -
257B ASP* 4.0 47.3 - - + -
259B CYS* 4.5 9.0 - - - -
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Residues in contact with TYR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER* 3.2 10.2 + - - +
170B PHE* 1.3 89.9 - + + +
172B GLU* 1.4 58.5 + - - +
174B LYS* 3.8 34.0 + - + +
175B ASN* 3.0 29.8 + - - +
254B ASP* 5.2 4.5 - - - -
255B GLY* 5.8 2.9 - - - -
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Residues in contact with GLU 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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168B PHE* 3.6 27.2 - - + -
169B SER* 3.0 27.9 + - - +
171B TYR* 1.4 76.2 - - - +
173B LEU* 1.3 59.0 + - + +
175B ASN* 3.5 3.8 + - - +
176B VAL* 3.1 44.5 + - + +
205B VAL* 4.4 18.7 - - + +
206B ASN* 5.2 4.0 + - - +
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Residues in contact with LEU 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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168B PHE* 3.9 22.9 - - + -
169B SER 3.2 6.8 + - - +
170B PHE* 3.8 6.1 - - - +
172B GLU* 1.3 76.1 - - - +
174B LYS* 1.4 56.7 + - - +
176B VAL* 3.5 8.6 + - + +
177B THR* 2.8 38.8 + - - +
180B PHE* 3.9 12.8 - - + -
205B VAL* 5.0 4.0 - - + -
212B VAL* 3.9 22.7 - - + -
252B SER* 3.8 20.4 - - - +
259B CYS* 3.7 28.0 - - + -
261B VAL* 3.7 33.4 - - + -
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Residues in contact with LYS 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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170B PHE* 2.8 42.5 + - + +
171B TYR* 4.0 30.1 - - + +
173B LEU* 1.4 71.2 - - - +
175B ASN* 1.3 58.8 + - - +
177B THR* 3.4 3.9 + - - -
179B ASN* 2.7 64.3 + - - +
180B PHE* 3.5 23.9 - - + -
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Residues in contact with ASN 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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171B TYR 3.0 20.0 + - - +
172B GLU* 3.7 6.1 - - - +
173B LEU 3.3 0.2 - - - -
174B LYS* 1.3 76.2 - - - +
176B VAL* 1.3 68.9 + - - +
178B ASN* 3.2 22.9 + - - +
179B ASN* 5.3 2.2 - - - -
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Residues in contact with VAL 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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172B GLU* 3.1 31.4 + - + +
173B LEU* 3.6 15.7 - - + +
175B ASN* 1.3 85.0 - - - +
177B THR* 1.4 60.1 + - + +
178B ASN* 3.4 9.2 + - - +
190B ASN* 4.3 1.7 + - - -
202B LYS 3.9 1.4 - - - +
203B GLY* 3.6 18.0 - - - -
204B TYR* 3.1 47.9 + - + +
205B VAL* 4.5 10.8 - - + -
212B VAL* 5.1 1.3 - - + -
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Residues in contact with THR 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 LEU 2.8 21.8 + - - +
174B LYS 3.4 2.3 + - - -
176B VAL* 1.4 77.8 - - + +
178B ASN* 1.4 69.1 + - - +
180B PHE* 3.0 33.3 + - + -
181B ASP 3.2 14.6 + - - -
190B ASN* 3.8 9.8 - - - +
201B TYR* 3.8 24.7 - - + -
202B LYS 3.9 16.8 - - - +
212B VAL* 4.0 24.0 - - + -
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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