Contacts of the helix formed by residues 167 - 182 (chain A) in PDB entry 5LS6
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 3.7 11.7 - - + -
166A ILE* 1.3 78.2 - - - +
168A ASP* 1.3 62.0 + - - +
169A GLU* 3.6 26.0 + - - +
170A ILE* 3.4 21.8 + - + +
171A PHE* 2.6 37.4 + - - +
303B ASP* 4.3 9.4 - - - +
348B SER 4.5 1.9 - - - +
349B ASN* 3.9 6.7 - - - +
350B VAL* 2.6 55.9 + - - +
351B THR* 4.8 0.4 - - - +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASN* 1.3 74.3 + - - +
169A GLU* 1.3 66.3 + - - +
171A PHE* 3.0 10.7 + - - +
172A VAL* 3.0 32.0 + - - +
243A LYS* 4.6 15.6 + - - -
247A LEU* 3.8 31.2 - - + +
303B ASP* 4.7 7.0 + - - +
348B SER* 2.6 37.0 - - - +
349B ASN* 3.4 13.2 - - - +
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LYS* 3.2 13.8 + - - +
34A ARG* 2.7 35.4 + - - -
167A ASN* 3.6 19.0 + - - +
168A ASP* 1.3 78.4 - - - +
170A ILE* 1.3 68.7 + - + +
172A VAL* 3.9 5.0 + - - +
173A GLU* 3.3 32.2 + - - +
335B LYS* 3.8 22.4 - - + +
349B ASN* 3.5 13.8 + - - +
350B VAL 4.0 0.7 - - - +
351B THR* 3.6 18.8 + - - +
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Residues in contact with ILE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 4.8 7.2 - - + -
26A LEU* 4.9 9.4 - - + +
27A ARG* 4.7 24.2 - - + +
30A LYS* 4.3 21.3 - - + +
165A PHE* 4.3 12.1 - - + -
166A ILE* 3.7 19.1 - - + -
167A ASN* 3.4 32.5 + - + +
168A ASP 3.2 0.4 - - - -
169A GLU* 1.3 92.1 - - + +
171A PHE* 1.3 61.7 + - - +
173A GLU* 3.7 10.3 + - - +
174A LEU* 3.2 20.3 + - + +
351B THR* 6.4 1.8 - - - -
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 4.1 18.4 - - + -
167A ASN 2.6 21.3 + - - +
168A ASP* 3.0 11.8 + - - +
170A ILE* 1.3 72.4 - - - +
172A VAL* 1.3 61.4 + - + +
174A LEU* 3.0 24.1 + - + +
175A VAL* 3.1 28.2 + - + +
224A PHE* 4.6 2.2 - + - -
227A ILE* 3.3 34.3 - - + -
240A LEU* 4.1 33.2 - - + -
243A LYS* 4.7 12.6 - - + -
244A TYR* 4.3 17.0 - + + -
247A LEU* 4.2 18.4 - - + -
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP 3.0 16.7 + - - +
169A GLU* 4.5 4.7 - - - +
171A PHE* 1.3 77.1 - - + +
173A GLU* 1.3 56.9 + - + +
175A VAL* 3.4 7.5 + - - +
176A ASN* 3.0 30.3 + - + +
244A TYR* 4.0 25.1 - - + -
247A LEU* 3.4 33.7 - - + -
248A THR* 4.1 11.4 - - + -
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.0 22.2 - - + +
29A LEU* 5.9 2.1 - - - +
30A LYS* 3.5 35.8 + - - +
169A GLU* 3.3 22.7 + - - +
170A ILE* 3.9 8.7 - - - +
171A PHE 3.2 0.4 - - - -
172A VAL* 1.3 78.3 - - + +
174A LEU* 1.3 52.2 + - - +
176A ASN* 4.0 8.0 - - - +
177A ALA* 2.7 37.9 + - - +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 3.9 29.6 - - + +
22A GLU* 4.2 11.2 - - + -
23A TYR* 4.0 35.2 - - + +
26A LEU* 3.8 9.4 - - + +
166A ILE* 4.9 8.3 - - + -
170A ILE* 3.2 14.2 + - + +
171A PHE* 3.0 18.6 + - + +
173A GLU* 1.3 75.0 - - - +
175A VAL* 1.3 59.2 + - + +
178A LEU* 2.9 33.9 + - + +
227A ILE* 4.3 23.1 - - + -
231A PHE* 4.8 11.0 - - + -
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 3.1 42.6 + - + +
172A VAL 3.4 6.5 + - - +
173A GLU 3.3 0.2 - - - -
174A LEU* 1.3 77.5 - - + +
176A ASN* 1.3 58.4 + - - +
178A LEU* 3.5 5.3 + - - +
179A GLY* 3.0 23.6 + - - -
216A ARG* 5.8 1.8 - - + +
220A SER 5.9 1.8 - - - +
223A ILE* 4.2 13.4 - - + +
224A PHE* 4.0 29.6 - - + -
227A ILE* 4.5 5.8 - - + -
244A TYR* 4.1 29.4 - - + +
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Residues in contact with ASN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 3.0 19.3 + - + +
173A GLU* 4.0 7.5 - - - +
175A VAL* 1.3 73.4 - - - +
177A ALA* 1.3 60.0 + - - +
178A LEU 3.2 1.3 - - - -
179A GLY* 3.4 2.0 + - - +
180A GLN* 3.1 28.1 + - - +
244A TYR* 5.9 3.3 - - + +
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLU* 4.4 15.7 - - + +
25A ARG* 5.5 2.8 + - - +
26A LEU* 4.1 28.5 - - + -
173A GLU 2.7 23.2 + - - +
174A LEU 4.6 0.7 - - - +
176A ASN* 1.3 73.3 - - - +
178A LEU* 1.3 56.7 + - - +
179A GLY 3.4 0.2 - - - -
180A GLN* 3.9 7.3 - - - +
181A TYR* 3.1 26.4 + - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 4.0 27.8 - - + -
18A ARG 5.3 0.9 - - - -
19A VAL* 3.5 36.1 - - + +
22A GLU* 5.1 7.1 - - + +
174A LEU* 2.9 26.3 + - + +
175A VAL 3.7 4.5 - - - +
176A ASN 3.2 0.2 - - - -
177A ALA* 1.3 77.9 - - - +
179A GLY* 1.3 56.9 + - - +
181A TYR* 3.9 13.2 - - + -
182A ASN* 3.1 21.3 + - - -
223A ILE* 3.6 43.7 - - + +
227A ILE* 3.9 9.9 - - + -
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A VAL 3.0 14.9 + - - -
176A ASN* 3.4 3.0 + - - -
178A LEU* 1.3 75.5 - - - +
180A GLN* 1.3 65.4 + - - +
182A ASN* 3.7 20.5 - - - +
212A SER* 5.2 5.7 - - - -
214A PRO* 5.6 6.6 - - - +
220A SER 5.9 5.2 - - - -
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Residues in contact with GLN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ASN* 3.1 18.8 + - - +
177A ALA* 3.9 7.4 - - - +
179A GLY* 1.3 76.4 - - - +
181A TYR* 1.3 66.4 + - - +
182A ASN* 4.0 2.8 - - - +
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Residues in contact with TYR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 4.5 8.3 - + - -
18A ARG* 2.8 63.7 + - + +
22A GLU* 3.1 28.9 - - - +
25A ARG* 5.7 1.6 - - - -
177A ALA 3.1 18.4 + - - +
178A LEU* 3.9 11.2 - - + +
179A GLY 3.3 0.2 - - - -
180A GLN* 1.3 82.9 - - - +
182A ASN* 1.3 77.3 + - - +
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Residues in contact with ASN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 3.5 26.2 - - - -
18A ARG* 4.9 3.4 + - - -
178A LEU 3.1 15.5 + - - -
179A GLY* 3.7 16.7 - - - +
180A GLN 3.5 2.7 - - - +
181A TYR* 1.3 103.6 - - - +
211A GLU 3.0 37.1 + - - +
212A SER* 4.1 10.1 - - - -
214A PRO* 4.3 15.1 - - - +
220A SER* 5.1 4.0 + - - -
223A ILE* 6.4 0.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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