Contacts of the strand formed by residues 289 - 293 (chain A) in PDB entry 1OY6
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 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A VAL* 3.1 7.4 - - - +
140A VAL* 3.0 36.2 + - + +
142A VAL* 5.7 2.0 - - + -
158A VAL* 3.8 21.3 - - + -
162A MET* 4.2 27.4 - - + -
163A LYS* 3.9 20.4 - - + +
166A ILE* 4.6 15.5 - - + -
175A VAL* 3.4 28.3 - - + -
176A GLN 3.6 6.7 - - - +
177A LEU* 4.3 3.1 - - + -
178A PHE* 3.9 2.9 - - - -
288A GLY* 1.3 76.0 - - - +
290A GLY* 1.3 59.8 + - - +
291A ILE* 3.6 18.7 - - + +
310A LEU* 5.0 7.2 - - + -
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Residues in contact with GLY 290 (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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136A PHE* 3.2 25.9 - - - -
138A MET 4.2 0.2 - - - -
139A VAL* 4.1 14.6 - - - -
174A ASP 3.8 0.3 - - - +
176A GLN* 3.2 26.2 + - - +
178A PHE* 3.3 25.1 - - - -
289A LEU* 1.3 69.0 - - - +
291A ILE* 1.3 60.1 + - - -
292A LYS 3.5 1.4 + - - -
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Residues in contact with ILE 291 (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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136A PHE* 3.4 3.4 - - - -
137A LEU* 3.3 33.3 + - + +
138A MET* 3.2 27.1 + - + +
140A VAL* 4.3 9.9 - - + -
166A ILE* 3.7 21.3 - - + -
172A VAL* 3.5 29.6 - - + -
174A ASP 4.4 3.1 - - - -
175A VAL* 4.4 7.2 - - + +
289A LEU* 3.6 24.5 - - + +
290A GLY* 1.3 70.8 - - - -
292A LYS* 1.3 65.3 + - - +
293A LEU* 5.8 0.9 - - + -
302A THR* 5.7 2.2 - - + -
306A ILE* 3.6 35.9 - - + -
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Residues in contact with LYS 292 (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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131A LYS 4.5 0.4 - - - +
132A SER* 4.4 8.3 - - - -
133A SER* 3.7 19.1 - - - +
134A SER* 3.7 9.2 - - - +
135A SER 3.5 34.5 - - - +
136A PHE* 3.8 25.2 - - + -
137A LEU* 4.4 1.1 - - - -
172A VAL* 4.6 0.2 - - - -
173A GLY 3.2 20.4 + - - -
174A ASP* 3.4 47.8 + - + +
176A GLN* 6.1 0.9 - - - -
290A GLY 3.5 0.2 + - - -
291A ILE* 1.3 81.7 - - - +
293A LEU* 1.3 67.3 + - - +
617A PHE* 5.3 4.0 - - - -
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Residues in contact with LEU 293 (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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131A LYS 3.3 12.5 - - - +
133A SER* 2.7 36.7 + - - +
135A SER* 4.0 1.1 + - - +
137A LEU* 3.8 27.5 - - + +
171A GLY 5.2 0.7 - - - +
172A VAL* 6.0 0.2 - - - -
173A GLY* 3.8 1.8 - - - +
291A ILE* 6.2 1.1 - - + -
292A LYS* 1.3 79.3 - - - +
294A ALA* 1.3 56.9 - - - +
296A GLY 5.8 0.7 - - - +
297A ALA* 3.5 35.4 - - + +
299A ALA* 3.8 29.8 - - + +
302A THR* 3.9 29.2 - - + +
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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
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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