Contacts of the strand formed by residues 166 - 170 (chain A) in PDB entry 3LX9
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 LEU 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 4.0 2.9 - - + -
88A TYR* 3.9 20.4 - - + -
90A CYS* 4.1 19.5 - - + -
131A LEU 3.2 2.4 + - - -
132A GLY* 3.8 11.4 - - - -
133A ILE 2.9 26.2 + - - +
164A VAL* 3.2 12.1 - - - +
165A ASP* 1.3 81.4 - - - +
167A LEU* 1.3 76.7 + - - +
168A LYS* 3.6 11.2 - - + +
198A ILE* 3.8 1.1 - - - -
199A VAL* 3.2 36.6 - - + +
201A SER* 4.8 4.7 - - - -
225A HIS* 4.6 2.5 - - + +
295A PHE* 3.9 27.1 - - + -
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Residues in contact with LEU 167 (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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133A ILE* 3.5 15.0 - - + +
135A ALA* 3.8 13.7 - - + +
159A PHE* 3.7 30.3 - - + -
164A VAL* 5.2 1.1 - - + -
166A LEU* 1.3 77.7 - - - +
168A LYS* 1.3 74.6 + - - +
169A PHE* 3.9 19.7 - - + -
187A MET* 3.9 25.8 - - + -
191A LEU* 4.0 15.5 - - + -
198A ILE* 3.7 12.7 - - + +
199A VAL 2.8 10.5 + - - +
200A TYR* 3.7 7.7 - - + -
201A SER* 2.9 26.9 + - - +
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Residues in contact with LYS 168 (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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45A LEU* 4.0 22.8 - - + +
47A TRP* 5.2 0.8 - - - +
90A CYS* 6.6 0.2 - - + -
91A ILE 5.5 1.1 - - - +
92A ASP* 2.7 28.5 + - - +
133A ILE 2.8 14.7 + - - +
134A TYR* 3.3 16.1 - - + -
135A ALA 3.0 26.7 + - - +
166A LEU* 3.6 8.5 - - + +
167A LEU* 1.3 72.1 - - - +
169A PHE* 1.3 63.2 + - - +
170A ASP* 4.9 0.2 - - - -
201A SER* 3.7 20.4 - - - +
203A SER* 4.6 5.4 - - - +
227A ARG* 4.2 10.2 - - + +
266A ASP* 5.2 0.4 + - - -
267A MET* 5.2 1.6 - - - +
1000A A2G 2.6 53.9 + - - -
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Residues in contact with PHE 169 (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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135A ALA* 3.6 23.8 - - + -
136A ASP 3.5 19.7 - - - -
137A VAL* 3.5 34.1 - - + -
148A SER* 4.0 2.0 - - - -
152A TYR* 3.8 8.5 - + - -
167A LEU* 3.9 9.4 - - + -
168A LYS* 1.3 74.2 - - - +
170A ASP* 1.3 55.8 + - - +
183A GLY 3.9 3.8 - - - -
184A TYR* 2.6 39.4 + + + -
187A MET* 3.5 45.1 - - + -
200A TYR* 3.3 31.6 - + + -
201A SER 2.8 15.3 + - - +
203A SER* 3.2 13.1 + - - -
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Residues in contact with ASP 170 (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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134A TYR* 2.6 41.4 + - + +
135A ALA 2.8 8.0 + - - +
136A ASP* 3.2 9.3 - - - +
137A VAL* 2.8 29.5 + - - +
142A CYS* 3.1 4.1 - - - -
168A LYS* 4.0 0.6 + - - -
169A PHE* 1.3 70.2 - - - +
171A GLY* 1.3 59.7 + - - +
184A TYR* 3.0 9.1 + - - -
203A SER* 4.0 3.1 - - - -
207A TYR* 2.6 28.0 + - - -
1000A A2G 2.9 43.7 - - - +
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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