Contacts of the helix formed by residues 169 - 181 (chain X) in PDB entry 5K0Y
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 169 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76X GLN* 4.3 12.1 - - - +
77X VAL* 4.0 26.4 + - - +
80X VAL* 4.0 27.5 - - - +
81X ARG* 6.2 0.4 - - - +
92X VAL 5.3 1.0 + - - -
93X VAL* 6.2 2.1 - - + +
133X LEU 5.0 0.4 - - - +
136X PRO* 6.3 0.2 - - - -
165X ASN 3.5 22.2 - - - +
166X VAL* 3.1 14.3 + - + +
168X HIS* 1.4 95.7 + - - +
170X VAL* 1.4 52.6 + - - +
171X GLU 2.9 13.6 + - - -
172X THR* 3.0 24.1 + - - -
173X PHE* 3.6 39.9 + - + -
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Residues in contact with VAL 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166X VAL* 3.3 14.8 + - + +
167X GLU* 3.3 23.3 - - - +
168X HIS 3.4 1.4 - - - -
169X LYS* 1.4 73.6 - - - +
171X GLU* 1.4 72.7 + - + +
172X THR 3.4 0.2 - - - -
173X PHE* 3.2 12.2 + - - +
174X SER* 3.1 31.3 + - - +
186X ASN* 5.6 0.4 - - - -
187X PHE* 4.1 41.8 - - + +
189X PHE* 5.5 7.0 - - + -
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Residues in contact with GLU 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X VAL* 5.1 2.8 - - - +
54X GLY 5.7 1.3 + - - -
55X GLY* 5.5 12.6 - - - +
167X GLU 4.0 6.4 - - - +
168X HIS* 3.0 21.0 - - - +
169X LYS 2.9 3.6 + - - -
170X VAL* 1.4 88.0 - - + +
172X THR* 1.4 62.4 + - - +
174X SER* 3.5 8.4 - - - -
175X GLY* 3.1 18.5 + - - -
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Residues in contact with THR 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X VAL* 3.9 12.7 - - + +
59X ALA* 4.0 11.0 - - + -
91X HIS* 3.1 51.2 + - + +
93X VAL* 5.9 6.1 - - + -
168X HIS 5.6 0.3 + - - -
169X LYS* 3.0 12.2 + - - -
171X GLU* 1.4 75.8 - - - +
173X PHE* 1.4 66.6 + - + +
175X GLY* 3.3 0.9 + - - -
176X VAL* 2.9 44.5 + - + +
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Residues in contact with PHE 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X VAL* 4.2 18.6 - - + -
133X LEU* 3.5 58.9 - - + +
134X VAL* 3.9 7.4 - - + -
166X VAL* 3.8 25.8 - - + -
169X LYS* 3.6 37.2 + - + -
170X VAL* 3.2 9.1 + - - +
172X THR* 1.4 86.0 - - + +
174X SER* 1.4 60.9 + - - +
176X VAL* 4.2 4.2 - - - +
177X TYR* 3.3 24.6 + - - +
185X VAL* 3.7 4.1 - - - +
187X PHE* 3.5 34.1 - + + -
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Residues in contact with SER 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170X VAL* 3.1 23.5 + - - +
171X GLU* 3.5 11.5 - - - -
172X THR 3.3 0.2 - - - -
173X PHE* 1.4 77.2 - - - +
175X GLY* 1.4 60.9 + - - +
177X TYR* 3.5 3.6 + - - +
178X LYS* 3.3 20.1 + - - +
184X ASP* 4.9 4.3 - - - +
185X VAL* 3.0 36.0 + - - +
186X ASN* 4.2 9.8 + - - -
187X PHE* 4.5 0.9 - - - -
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Residues in contact with GLY 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X VAL* 3.8 19.3 - - - -
54X GLY 5.4 2.0 - - - -
171X GLU 3.1 9.8 + - - -
172X THR 3.3 2.4 + - - -
174X SER* 1.4 77.1 - - - +
176X VAL* 1.4 62.5 + - - +
178X LYS* 3.2 9.9 + - - +
179X LYS* 3.1 30.8 + - - +
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Residues in contact with VAL 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X ILE* 4.1 9.6 - - + -
53X VAL* 3.7 15.9 - - + -
59X ALA* 3.8 20.0 - - + -
61X ILE* 3.9 16.4 - - + -
93X VAL* 5.6 5.6 - - + -
95X ILE* 3.8 18.2 - - + -
133X LEU* 5.9 3.8 - - + -
172X THR* 2.9 26.0 + - + +
173X PHE* 4.2 5.6 - - - +
175X GLY* 1.4 70.4 - - - +
177X TYR* 1.4 65.7 + - - +
179X LYS* 3.3 4.8 + - - +
180X LEU* 3.1 41.0 + - + +
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Residues in contact with TYR 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X HIS* 3.8 31.5 + + + +
129X ILE* 5.6 8.7 - - + -
130X LEU* 3.8 26.5 - - + +
133X LEU* 6.2 2.5 - - + -
154X ILE* 5.0 5.2 - - + -
173X PHE 3.3 17.2 + - - +
174X SER 3.8 1.1 - - - +
176X VAL* 1.4 76.9 - - - +
178X LYS* 1.4 56.9 + - - +
180X LEU* 3.3 8.3 + - + -
181X THR* 2.9 64.7 + - + +
183X LYS* 3.2 40.8 - - + +
185X VAL* 3.5 32.3 - - + -
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Residues in contact with LYS 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174X SER 3.3 10.7 + - - +
175X GLY* 3.2 13.1 + - - +
177X TYR* 1.4 77.9 - - - +
179X LYS* 1.4 65.3 + - + +
182X GLY* 3.0 28.8 + - - -
183X LYS 3.4 15.7 + - - +
184X ASP* 3.5 36.4 + - - +
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Residues in contact with LYS 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X ILE* 3.9 26.5 - - + -
52X GLU* 3.4 33.4 + - - +
53X VAL* 4.2 10.7 - - - +
54X GLY 5.2 0.6 - - - +
175X GLY* 3.1 19.7 + - - +
176X VAL 3.3 7.2 + - - +
178X LYS* 1.4 83.1 - - + +
180X LEU* 1.4 60.4 + - - +
182X GLY 5.0 0.2 + - - -
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Residues in contact with LEU 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736A C 3.8 10.4 - - - +
49X LYS* 5.6 9.0 - - + -
51X ILE* 4.4 15.5 - - + -
61X ILE* 5.3 2.7 - - + -
63X PHE* 5.7 9.0 - - + -
95X ILE* 3.8 24.0 - - + -
129X ILE* 5.6 6.7 - - + -
176X VAL* 3.1 36.6 + - + +
177X TYR* 3.9 9.0 - - + +
179X LYS* 1.4 78.6 - - - +
181X THR* 1.4 68.9 + - + +
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Residues in contact with THR 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736A C 3.9 14.2 - - - +
126X HIS* 3.5 37.0 - - + +
177X TYR* 2.9 53.7 + - + -
180X LEU* 1.4 79.5 - - + +
182X GLY* 1.4 61.7 + - - +
183X LYS* 3.4 12.4 + - - +
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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