Contacts of the strand formed by residues 168 - 172 (chain A) in PDB entry 3OEH
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 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ARG 4.0 1.8 + - - -
167A GLU* 1.3 73.2 - - - +
169A ILE* 1.3 63.8 + - - +
170A ILE* 3.8 22.0 - - + -
327A PRO* 3.5 24.5 - - + +
329A ILE* 3.5 28.3 - - + -
344A VAL* 3.9 11.2 - - + -
345A ILE* 3.5 42.6 - - + +
348A THR* 3.8 12.5 + - + +
350A GLY 2.7 19.2 + - - +
351A GLN* 3.9 8.5 - - + -
352A ILE* 2.8 34.7 + - - +
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Residues in contact with ILE 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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167A GLU 3.7 6.3 + - - +
168A LEU* 1.3 77.1 - - - +
170A ILE* 1.3 60.6 + - - +
177A LYS* 3.6 41.5 - - + +
180A VAL* 3.6 29.2 - - + -
181A ALA* 4.1 13.2 - - + +
326A LEU* 4.1 24.5 - - + -
327A PRO 2.9 14.0 + - - +
328A VAL* 3.3 14.4 - - + +
329A ILE 3.0 23.7 + - - -
352A ILE* 3.7 11.4 - - + +
354A LEU* 3.8 15.7 - - + -
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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
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168A LEU* 3.8 16.6 - - + -
169A ILE* 1.3 73.9 - - - +
171A GLY* 1.3 61.6 + - - +
177A LYS* 4.0 4.7 - - - -
329A ILE* 3.5 20.4 - - + +
331A THR* 3.5 26.7 - - + -
336A VAL* 4.2 5.2 - - + -
341A PRO* 4.4 2.9 - - + -
345A ILE* 3.6 30.1 - - + -
351A GLN* 3.8 19.1 - - + -
352A ILE 3.0 13.2 + - - +
353A PHE* 3.5 24.6 - - + -
354A LEU* 3.0 26.5 + - - +
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Residues in contact with GLY 171 (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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170A ILE* 1.3 81.1 - - - +
172A ASP* 1.3 68.6 + - - +
175A THR* 4.2 2.9 - - - -
177A LYS* 3.5 8.3 + - - +
329A ILE 3.3 3.1 + - - +
330A GLU* 3.3 8.0 - - - -
331A THR* 2.9 27.2 + - - -
353A PHE* 4.9 5.8 - - - -
354A LEU 3.7 14.6 - - - -
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Residues in contact with ASP 172 (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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171A GLY* 1.3 72.3 - - - -
173A ARG* 1.3 66.6 + - + +
175A THR* 2.6 37.4 + - + +
177A LYS* 2.7 12.9 + - - -
330A GLU* 4.2 0.2 - - - -
331A THR* 2.6 37.9 + - - +
332A GLN* 4.7 0.2 - - - -
333A GLY* 3.2 15.0 + - - -
334A GLY* 2.8 27.4 + - - -
353A PHE* 5.9 0.2 - - - -
354A LEU 4.4 2.4 + - - +
356A ALA* 5.7 6.4 - - + +
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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