Contacts of the helix formed by residues 167 - 179 (chain B) in PDB entry 5L5E
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 ASN 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B SER 4.6 1.0 + - - -
33B THR* 4.6 3.2 + - - +
165B GLY 3.9 0.8 + - - -
166B ALA* 1.3 80.7 + - - +
168B THR* 1.3 59.1 + - - +
169B SER* 3.3 3.8 - - - +
170B ALA* 3.5 10.6 + - + +
171B ALA* 3.0 28.6 + - - +
199B THR* 2.9 38.0 + - - +
200B THR* 5.0 0.6 - - - +
201B ASP* 3.5 28.1 + - - +
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Residues in contact with THR 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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163B SER* 3.6 20.9 + - - +
164B VAL* 3.4 32.3 - - - +
165B GLY 3.3 23.1 + - - +
166B ALA 4.1 1.3 - - - +
167B ASN* 1.3 74.8 - - - +
169B SER* 1.3 59.1 + - - +
171B ALA* 4.1 0.4 - - - -
172B GLN* 2.8 38.1 + - - +
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Residues in contact with SER 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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167B ASN* 5.1 1.1 - - - -
168B THR* 1.3 84.3 + - - +
170B ALA* 1.3 60.8 + - - +
172B GLN* 4.0 3.5 - - - +
173B THR* 2.9 27.4 + - - -
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASN* 3.5 15.0 + - + +
169B SER* 1.3 78.6 - - - +
171B ALA* 1.3 61.7 + - - +
173B THR* 3.3 8.3 + - - -
174B LEU* 3.2 27.2 + - + +
199B THR* 4.2 15.0 - - + -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 4.8 4.3 - - + -
35B ILE* 4.7 4.3 - - + -
163B SER* 3.6 23.8 - - - +
167B ASN 3.0 19.1 + - - +
168B THR* 3.8 0.7 - - - +
170B ALA* 1.3 76.7 - - - +
172B GLN* 1.3 57.8 + - - +
174B LEU* 3.3 3.8 + - - +
175B LEU* 3.0 34.1 + - - +
195B THR* 3.8 14.2 - - + +
199B THR* 3.8 19.0 - - + +
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Residues in contact with GLN 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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159B TRP* 4.2 5.3 - - + -
161B ALA 3.3 24.0 + - - -
162B ILE* 3.5 16.9 - - - +
163B SER* 3.3 28.8 + - - +
168B THR* 2.8 22.7 + - - +
169B SER* 4.0 4.9 - - - +
171B ALA* 1.3 73.1 - - - +
173B THR* 1.3 57.3 + - - +
175B LEU* 3.6 6.9 + - - +
176B GLN* 3.0 39.7 + - - +
51C LYS 4.1 12.6 + - - +
52C LEU* 4.0 11.7 - - - +
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Residues in contact with THR 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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169B SER* 2.9 16.2 + - - -
170B ALA* 3.5 9.3 - - - -
171B ALA 3.2 0.4 - - - -
172B GLN* 1.3 78.6 - - - +
174B LEU* 1.3 63.1 + - + +
176B GLN* 3.3 10.4 + - + +
177B MET* 3.1 34.1 + - + +
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Residues in contact with LEU 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 ALA* 3.2 11.9 + - + +
171B ALA 3.3 5.8 + - - +
173B THR* 1.3 77.8 - - + +
175B LEU* 1.3 61.6 + - - +
177B MET* 3.4 21.6 + - + +
178B ASP* 3.3 28.5 + - - +
191B LEU* 4.5 1.6 - - + +
195B THR* 4.1 18.8 - - + +
198B LYS* 3.7 48.0 - - + +
199B THR* 3.9 28.7 - - + -
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Residues in contact with LEU 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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35B ILE* 4.3 14.8 - - + -
37B ILE* 3.7 31.6 - - + -
161B ALA* 4.4 2.9 - - + -
162B ILE 4.2 25.6 - - - +
163B SER* 4.5 4.0 - - - +
171B ALA 3.0 22.6 + - - +
172B GLN* 3.9 19.1 - - - +
174B LEU* 1.3 74.1 - - - +
176B GLN* 1.3 60.8 + - - +
179B TYR* 3.0 36.9 + - - +
191B LEU* 4.1 10.5 - - + -
195B THR* 3.7 22.0 - - + +
52C LEU* 3.7 14.4 - - + -
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Residues in contact with GLN 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 GLN* 3.0 27.8 + - - +
173B THR* 3.3 9.3 + - - +
175B LEU* 1.3 76.4 - - - +
177B MET* 1.3 61.6 + - - +
179B TYR 4.5 5.5 + - - +
49C THR 5.6 2.8 + - - -
51C LYS* 4.4 27.7 + - + +
52C LEU* 3.6 28.0 - - + +
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Residues in contact with MET 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 THR* 3.1 24.2 + - + +
174B LEU* 3.5 26.0 - - + +
175B LEU 3.1 0.2 - - - -
176B GLN* 1.3 80.9 - - - +
178B ASP* 1.3 73.7 + - - +
179B TYR 3.8 2.6 + - - +
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Residues in contact with ASP 178 (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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174B LEU* 3.3 17.0 + - - +
177B MET* 1.3 94.6 - - - +
179B TYR* 1.3 63.9 + - - +
180B LYS* 3.6 8.1 + - - +
183B MET* 4.3 10.6 - - - +
191B LEU* 4.1 24.4 - - + +
194B LYS* 6.1 0.9 - - - +
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Residues in contact with TYR 179 (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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37B ILE* 3.9 19.1 - - + -
38B MET* 2.7 32.7 + - - +
39B ALA* 4.9 1.0 - - - -
160B LYS* 3.6 35.3 - - + +
161B ALA* 4.2 7.0 - - + -
175B LEU* 3.0 21.5 + - - +
176B GLN* 4.6 4.7 - - - +
177B MET 3.6 4.4 - - - +
178B ASP* 1.3 78.0 - - - +
180B LYS* 1.3 82.8 + - - +
181B ASP* 3.9 19.7 + - - -
183B MET* 4.0 16.8 - - + +
191B LEU* 4.2 8.9 - - + +
52C LEU* 4.2 25.7 - - + +
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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