Contacts of the helix formed by residues 163 - 176 (chain B) in PDB entry 5LUB
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 VAL 163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B GLY* 2.9 32.0 + - - +
162B HIS* 1.3 72.6 - - - +
164B LYS* 1.3 57.6 + - + +
166B LEU* 3.3 3.4 + - + +
167B ASN* 2.8 39.4 + - + +
193B SER 3.8 6.5 - - - +
194B MET* 3.6 50.6 - - + +
197B HIS* 6.5 1.3 - - + -
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Residues in contact with LYS 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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162B HIS* 3.2 6.4 - - + +
163B VAL* 1.3 84.9 - - + +
165B ASP* 1.3 64.5 + - - +
167B ASN* 3.3 8.8 - - + +
168B GLU* 3.0 50.0 + - + +
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Residues in contact with ASP 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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114B LEU* 3.7 21.2 - - + +
161B LEU* 4.6 3.4 - - + -
162B HIS* 3.1 33.6 + - - +
164B LYS* 1.3 82.0 - - - +
166B LEU* 1.3 59.0 + - - +
168B GLU* 3.7 15.0 + - - +
169B THR* 2.7 34.2 + - - -
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Residues in contact with LEU 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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113B PHE* 4.4 9.9 - - + -
114B LEU* 4.1 13.8 - - + +
117B LEU* 4.2 24.7 - - + -
154B LEU* 5.0 4.9 - - + -
161B LEU* 4.6 10.7 - - + +
162B HIS 3.2 11.2 + - - +
163B VAL* 3.7 8.1 - - + +
165B ASP* 1.3 73.9 - - - +
167B ASN* 1.3 56.5 + - - +
169B THR* 3.2 2.1 + - - -
170B ILE* 2.8 54.6 + - + +
184B PHE* 4.5 8.5 - - + -
186B ILE* 5.3 1.3 - - + -
194B MET* 3.9 28.5 - - + +
195B MET* 3.7 26.5 - - + -
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Residues in contact with ASN 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 VAL* 2.8 25.0 + - + +
164B LYS* 3.3 11.2 - - - +
166B LEU* 1.3 73.9 - - - +
168B GLU* 1.3 70.1 + - - +
170B ILE* 3.2 9.3 + - - +
171B HIS* 3.1 24.9 + - - +
197B HIS* 5.0 14.6 + - - +
198B LEU* 6.1 0.6 - - - +
199B PRO* 5.9 3.6 - - - +
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Residues in contact with GLU 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 LYS* 3.0 46.9 + - + +
165B ASP* 4.1 13.8 - - - +
167B ASN* 1.3 83.4 - - - +
169B THR* 1.3 57.5 + - - +
171B HIS* 3.5 8.4 + - - +
172B TYR* 3.0 26.7 + - - +
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Residues in contact with THR 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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114B LEU* 3.4 30.1 - - + +
117B LEU* 3.8 35.2 - - + -
118B ARG* 3.9 24.6 + - + +
165B ASP 2.7 22.1 + - - -
166B LEU 3.2 4.9 + - - -
168B GLU* 1.3 75.0 - - - +
170B ILE* 1.3 65.5 + - - +
172B TYR* 3.3 7.4 + - - +
173B MET* 3.0 24.2 + - + +
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Residues in contact with ILE 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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117B LEU* 5.6 0.4 - - + -
166B LEU* 2.8 43.5 + - + +
167B ASN* 3.7 7.9 - - - +
169B THR* 1.3 71.8 - - + +
171B HIS* 1.3 62.8 + - - +
173B MET* 3.3 14.8 + - + +
174B TYR* 3.1 20.8 + - - +
179B TYR* 4.4 2.9 + - + +
182B MET* 5.5 2.5 - - - -
184B PHE* 4.0 31.0 - - + -
195B MET* 4.2 11.2 - - + -
198B LEU* 4.2 13.7 - - + -
202B ILE* 3.7 28.0 - - + -
204B VAL* 4.3 13.2 - - + -
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Residues in contact with HIS 171 (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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167B ASN* 3.1 15.4 + - - +
168B GLU* 3.6 12.0 + - - +
170B ILE* 1.3 75.1 - - - +
172B TYR* 1.3 60.9 + - - +
174B TYR* 3.2 16.3 + + - +
175B LYS* 2.9 50.5 + - + +
202B ILE* 5.8 5.8 - - + -
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Residues in contact with TYR 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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118B ARG* 3.7 54.4 + - + -
168B GLU 3.0 14.9 + - - +
169B THR* 3.5 11.2 - - - +
171B HIS* 1.3 78.1 + - - +
173B MET* 1.3 62.0 + - - +
175B LYS* 3.3 4.3 + - - -
176B HIS* 3.0 77.2 + + - +
178B MET* 4.2 5.6 - - - -
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Residues in contact with MET 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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117B LEU* 3.2 52.9 - - + +
118B ARG* 4.7 2.5 - - - +
133B LEU* 3.9 19.7 - - + -
135B SER* 4.9 3.1 - - - +
141B VAL* 4.8 0.2 - - + -
169B THR* 3.0 20.5 + - + +
170B ILE* 3.5 12.1 - - - +
171B HIS 3.3 0.2 - - - -
172B TYR* 1.3 78.5 - - - +
174B TYR* 1.3 60.4 + - - +
176B HIS 3.6 0.2 + - - -
177B LYS 3.3 3.1 + - - -
178B MET* 3.0 48.7 + - + +
179B TYR* 3.7 13.0 - - + -
182B MET* 3.2 37.7 - - + +
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Residues in contact with TYR 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 ILE 3.1 10.7 + - - +
171B HIS* 3.5 19.3 - + - +
173B MET* 1.3 74.5 - - - +
175B LYS* 1.3 71.9 + - + +
177B LYS* 3.1 27.0 + - - +
179B TYR* 3.5 20.1 - + - +
201B ASN 3.9 9.9 + - - -
202B ILE* 3.6 55.0 - - + -
203B ASN* 4.5 11.2 - - - -
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Residues in contact with LYS 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 HIS* 2.9 38.7 + - + +
172B TYR* 3.7 6.1 - - - +
174B TYR* 1.3 83.2 - - + +
176B HIS* 1.3 74.3 + - + +
177B LYS* 3.3 19.6 + - - +
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Residues in contact with HIS 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 TYR* 3.0 72.3 + + + +
175B LYS* 1.3 97.7 - - + +
177B LYS* 1.3 71.7 + - - +
178B MET* 3.3 17.9 + - + +
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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