Contacts of the helix formed by residues 163 - 172 (chain X) in PDB entry 5LIK
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 163 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161X ASN 4.1 0.2 + - - -
162X PHE* 1.3 76.3 - - - +
164X HIS* 1.3 64.5 + - - +
165X PHE* 3.2 18.4 + - - +
166X GLN* 2.5 34.3 + - - -
167X ILE* 3.0 13.4 + - - +
196X LEU* 4.2 3.1 - - - -
311X PRO* 3.5 25.4 + - - +
314X ALA* 4.3 5.4 - - - +
316X TYR* 3.5 20.4 - - - -
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Residues in contact with HIS 164 (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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163X SER* 1.3 72.1 - - - +
165X PHE* 1.3 109.5 + + - +
167X ILE* 3.6 1.2 - - - +
168X GLU* 2.8 40.0 + - + +
196X LEU* 3.7 3.7 - - + +
199X TYR* 3.6 37.6 + + + -
316X TYR* 2.7 80.5 + + + +
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Residues in contact with PHE 165 (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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163X SER* 3.1 6.9 + - - +
164X HIS* 1.3 117.9 + + - +
166X GLN* 1.3 56.8 + - + +
168X GLU* 3.5 8.2 + - + +
169X LYS* 3.1 26.3 + - - +
314X ALA* 3.7 28.9 - - + -
315X GLU 5.5 1.6 - - - -
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Residues in contact with GLN 166 (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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113X PRO* 3.5 22.9 - - + +
138X PHE* 4.1 17.7 - - + -
162X PHE* 3.1 22.5 - - + -
163X SER* 2.5 44.6 + - - +
165X PHE* 1.3 77.1 - - + +
167X ILE* 1.3 66.1 + - - +
169X LYS* 3.1 10.1 + - + +
170X LEU* 2.9 22.0 + - - +
309X ASP* 2.7 42.6 + - - +
310X TYR 4.0 1.2 + - - -
311X PRO* 3.4 15.7 - - - +
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Residues in contact with ILE 167 (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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159X VAL* 5.0 5.2 - - + -
162X PHE* 4.2 16.4 - - + -
163X SER 3.0 13.3 + - - +
164X HIS* 3.6 3.8 - - - +
166X GLN* 1.3 75.1 - - - +
168X GLU* 1.3 57.4 + - - +
170X LEU* 3.1 8.7 + - - +
171X LEU* 2.8 36.6 + - + +
180X PRO* 5.0 3.1 - - + -
183X ASN* 3.9 14.1 - - + +
196X LEU* 4.3 2.2 - - + -
199X TYR* 3.1 40.2 - - + +
200X CYS* 3.5 26.9 - - - -
205X ILE* 3.7 25.6 - - + -
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Residues in contact with GLU 168 (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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164X HIS* 2.8 25.7 + - + +
165X PHE* 3.6 10.5 - - + +
167X ILE* 1.3 76.7 - - - +
169X LYS* 1.3 56.7 + - - +
171X LEU* 3.2 6.0 + - - +
172X ASN* 2.8 59.3 + - - +
199X TYR* 2.8 28.2 + - + +
203X MLY 3.5 28.7 - - - -
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Residues in contact with LYS 169 (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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137X THR* 5.7 6.7 - - - +
138X PHE* 3.7 24.7 - - + -
139X LEU* 3.9 26.4 - - + +
165X PHE 3.1 15.4 + - - +
166X GLN* 3.3 11.7 - - + +
168X GLU* 1.3 74.7 - - - +
170X LEU* 1.3 62.6 + - - +
172X ASN* 4.0 3.2 - - - -
173X LYS* 3.4 21.1 + - - +
308X GLU* 4.3 11.5 + - - -
309X ASP* 3.1 29.5 + - - +
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Residues in contact with LEU 170 (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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138X PHE* 4.4 9.4 - - + -
139X LEU* 4.0 21.3 - - + -
142X TRP* 3.9 44.6 - - + -
159X VAL* 3.8 28.9 - - + -
162X PHE* 4.7 4.3 - - + -
166X GLN 2.9 11.9 + - - +
167X ILE* 3.4 10.3 - - - +
169X LYS* 1.3 77.9 - - - +
171X LEU* 1.3 64.0 + - + +
173X LYS* 3.3 14.2 + - - +
176X LEU* 3.2 30.3 - - + +
180X PRO* 4.0 16.6 - - + -
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Residues in contact with LEU 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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167X ILE* 2.8 41.0 + - + +
168X GLU* 4.0 6.1 - - - +
170X LEU* 1.3 74.5 - - + +
172X ASN* 1.3 67.7 + - - +
173X LYS 3.3 3.3 + - - +
176X LEU* 3.9 11.3 - - + +
179X LYS* 3.8 24.9 - - + -
180X PRO* 3.7 29.6 - - + -
199X TYR* 4.1 7.9 - - - +
203X MLY 4.3 28.7 - - + +
205X ILE* 4.3 3.6 - - + -
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Residues in contact with ASN 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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168X GLU* 2.8 44.2 + - - +
169X LYS* 4.0 4.5 - - - +
171X LEU* 1.3 83.8 - - - +
173X LYS* 1.3 59.3 + - - +
174X PRO* 3.1 15.2 - - - +
203X MLY 5.9 2.4 - - - -
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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