Contacts of the strand formed by residues 175 - 179 (chain A) in PDB entry 1O69
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 PHE 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA* 3.9 34.8 - - + -
66A VAL* 3.3 30.7 - - + -
67A ALA* 4.2 12.6 - - + -
151A VAL* 4.4 1.1 - - + -
152A LEU 3.5 2.8 + - - +
153A ILE* 3.5 19.6 - - + -
154A GLU* 2.9 23.3 + - - +
170A GLY 4.1 4.9 - - - +
173A GLY* 3.9 6.6 - - - -
174A GLU* 1.3 104.1 - - + +
176A GLY* 1.3 59.3 + - - +
194A LEU* 4.0 13.2 - - + -
195A ILE 3.4 3.6 - - - +
196A GLY* 4.2 0.7 - - - -
198A ASN* 6.2 0.7 - - + -
201A LYS* 3.8 28.5 - - + -
202A ILE* 3.8 30.5 - - + -
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Residues in contact with GLY 176 (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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154A GLU* 3.4 8.5 - - - -
170A GLY* 3.4 25.5 + - - -
175A PHE* 1.3 75.1 - - - +
177A VAL* 1.3 69.6 + - - +
194A LEU* 3.6 1.4 - - - +
195A ILE* 2.8 39.6 + - - +
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Residues in contact with VAL 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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56A ALA* 3.4 40.4 - - + +
59A ALA* 3.6 24.7 - - + -
60A LEU* 3.7 31.6 - - + +
153A ILE* 5.0 2.9 - - + -
154A GLU 3.0 11.1 + - - +
155A ASP* 4.8 3.1 - - - +
156A ALA* 2.9 35.6 + - - +
157A ALA* 3.3 1.0 + - - -
170A GLY* 5.1 0.2 - - - -
176A GLY* 1.3 81.0 - - - +
178A TYR* 1.3 65.4 + - - +
193A MET 3.2 3.6 - - - -
194A LEU* 3.8 10.5 - - + -
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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
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41A VAL* 3.8 29.4 - - + -
44A TYR* 6.0 0.2 - - - -
45A SER* 3.5 20.9 - - - -
56A ALA* 3.9 6.0 - - - +
156A ALA* 3.5 29.4 - - + +
157A ALA* 4.1 1.6 - - - -
159A ALA 4.6 0.9 - - - -
160A LEU* 3.9 42.7 - - + +
161A GLY 5.5 0.2 - - - -
168A ALA* 4.1 3.3 - - - +
169A LEU 2.7 29.2 + - - -
170A GLY* 4.5 1.1 - - - -
171A THR* 4.4 0.2 - - - +
177A VAL* 1.3 76.8 - - - +
179A SER* 1.3 59.5 + - - +
180A TYR* 3.9 18.8 - - + +
192A GLY* 3.3 3.5 - - - -
193A MET* 2.8 36.7 + - + -
195A ILE* 3.6 26.0 - - + +
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Residues in contact with SER 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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56A ALA* 3.6 10.5 - - - -
157A ALA* 3.2 26.5 + - - +
160A LEU* 5.3 4.2 - - - +
178A TYR* 1.3 75.1 - - - +
180A TYR* 1.3 72.5 + - - +
181A ASN* 3.1 11.2 + - - +
184A LYS* 3.5 29.2 - - - +
185A ILE* 6.0 1.0 - - - +
186A ILE* 4.2 1.2 - - - +
191A GLY 3.6 4.3 - - - -
402A X04 2.8 28.4 + - - -
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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