Contacts of the strand formed by residues 177 - 184 (chain A) in PDB entry 1O6L
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 TYR 177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 3.6 29.1 - - + +
168A LEU* 4.2 12.1 - - + -
169A VAL 3.3 14.4 - - - +
170A ARG* 2.9 38.5 + - + -
175A GLY 3.5 19.5 - - - -
176A ARG* 1.3 74.5 - - - +
178A TYR* 1.3 72.3 + - - +
231A TYR* 4.1 11.7 + - + +
433A GLU* 3.7 51.2 + - + +
434A VAL* 4.3 17.7 - - + +
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Residues in contact with TYR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 4.6 4.0 - + - -
168A LEU* 3.6 7.3 - - - +
169A VAL* 2.9 37.3 + - + +
171A GLU* 3.6 29.1 + - + -
176A ARG* 3.7 46.9 + - + +
177A TYR* 1.3 77.9 - - - +
179A ALA* 1.3 60.4 + - - +
216A LYS* 3.5 46.0 + - + +
217A TYR* 5.0 0.2 - + - -
228A VAL* 3.7 24.9 - - + -
229A MET 3.3 20.6 - - - +
230A GLU* 4.2 5.8 - - + -
231A TYR* 3.9 9.6 - - - -
479A TRP* 4.8 11.5 - + - -
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Residues in contact with ALA 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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158A LEU* 4.0 17.3 - - + -
166A VAL* 4.1 5.8 - - + -
167A ILE 3.6 4.9 - - - -
178A TYR* 1.3 74.0 - - - +
180A MET* 1.3 59.7 + - - +
227A PHE 3.4 2.1 - - - +
228A VAL* 4.7 0.2 - - - -
229A MET* 2.9 38.6 + - + +
231A TYR* 4.0 5.5 - - - +
1480A ANP 3.5 40.2 - - + +
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Residues in contact with MET 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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149A MET* 4.5 0.2 - - - +
152A PHE* 3.6 31.4 - - + -
154A TYR* 3.5 35.9 - - + +
165A LYS 3.6 1.7 - - - +
166A VAL* 3.3 3.8 - - - -
167A ILE* 2.8 36.7 + - + +
169A VAL* 3.9 18.8 - - + -
178A TYR 4.0 1.0 + - - -
179A ALA* 1.3 71.3 - - - +
181A LYS* 1.3 61.5 + - - +
182A ILE* 3.7 27.5 + - + +
219A PHE* 3.9 11.7 - - + -
226A CYS* 4.0 20.0 - - + -
227A PHE 3.2 9.9 - - - +
228A VAL* 4.0 12.6 - - + +
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Residues in contact with LYS 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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164A GLY* 5.7 1.3 - - - -
165A LYS 3.4 6.3 - - - +
166A VAL* 4.0 13.5 - - + -
179A ALA 3.9 1.4 + - - -
180A MET* 1.3 70.4 - - - +
182A ILE* 1.3 62.8 + - - +
183A LEU* 4.0 24.5 - - + -
200A GLU* 2.8 33.9 + - - +
225A LEU 3.5 1.9 - - - +
226A CYS* 3.4 4.5 - - - -
227A PHE* 2.9 50.6 + - + -
229A MET* 3.9 21.7 - - + +
293A ASP* 3.4 6.6 + - - +
1480A ANP 2.8 54.4 + - - +
1482A MN 4.3 0.4 + - - -
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Residues in contact with ILE 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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149A MET* 5.1 4.9 - - - -
154A TYR* 4.4 9.0 - - + -
164A GLY* 3.5 5.2 - - - -
165A LYS* 2.8 39.5 + - + +
167A ILE* 3.9 28.0 - - + -
180A MET* 3.8 33.7 - - + +
181A LYS* 1.3 75.0 - - - +
183A LEU* 1.3 64.8 + - - +
184A ARG* 5.8 2.7 - - + +
224A ARG* 3.8 45.8 - - + +
225A LEU 3.5 3.6 - - - +
226A CYS* 4.2 6.3 - - - -
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Residues in contact with LEU 183 (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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163A PHE* 3.3 25.4 - - + +
164A GLY* 3.8 7.9 - - - -
181A LYS* 4.0 20.0 - - + -
182A ILE* 1.3 80.5 - - - +
184A ARG* 1.3 63.2 + - - +
185A LYS 3.8 0.2 + - - -
188A ILE* 3.6 18.6 - - + -
197A THR* 3.7 30.5 - - + +
200A GLU* 4.4 8.3 - - - +
224A ARG* 3.4 5.5 - - - +
225A LEU* 2.8 38.6 + - + +
227A PHE* 3.8 24.2 - - + -
1480A ANP 5.5 1.1 - - - +
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Residues in contact with ARG 184 (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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163A PHE 4.6 5.1 + - - -
165A LYS* 5.7 8.7 - - - +
182A ILE* 5.8 2.5 - - + +
183A LEU* 1.3 73.8 - - - +
185A LYS* 1.3 65.8 + - - +
186A GLU* 4.7 3.1 - - + +
187A VAL* 3.3 35.6 + - + +
188A ILE* 3.3 16.8 + - - +
223A ASP 3.7 7.6 - - - +
224A ARG* 4.2 32.6 - - + +
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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