Contacts of the strand formed by residues 159 - 163 (chain A) in PDB entry 1OIK
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 TRP 159 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASP 5.7 1.2 + - - -
157A LYS 3.8 11.9 + - - -
158A LEU* 1.3 79.9 + - - +
160A ALA* 1.3 61.2 + - - +
195A GLU* 3.5 28.5 - - + -
196A HIS 3.4 20.6 - - - -
197A PRO* 3.7 27.7 - - + +
198A VAL* 4.1 3.1 - - - +
219A ILE* 3.5 7.9 - - - +
220A LYS* 3.0 43.8 + - + +
289A GLY* 5.6 0.2 - - - -
291A ASP* 5.1 5.8 + - - -
293A GLN* 3.7 38.2 + - + -
294A LEU 3.4 29.4 - - - -
295A SER* 4.0 0.2 - - - -
296A ARG* 3.8 19.5 - - - -
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Residues in contact with ALA 160 (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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159A TRP* 1.3 74.8 - - - +
161A VAL* 1.3 64.2 - - - +
162A HIS* 3.5 19.5 - - - +
195A GLU* 3.4 4.8 - - - -
196A HIS 2.8 35.7 + - - +
198A VAL* 4.1 10.7 - - + +
211A GLN 5.1 0.2 - - - +
212A LEU* 4.9 1.3 - - + -
216A VAL* 4.1 12.1 - - + -
218A ARG 3.5 11.0 - - - +
219A ILE* 4.0 16.8 - - + -
220A LYS* 4.4 1.3 - - - +
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Residues in contact with VAL 161 (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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160A ALA* 1.3 71.4 - - - +
162A HIS* 1.3 67.0 + - - +
193A GLU* 4.1 30.1 - - + +
194A THR 3.5 7.2 - - - +
195A GLU* 4.3 13.7 - - + +
216A VAL* 3.5 2.6 - - - -
217A LYS* 2.7 39.1 + - + +
218A ARG* 2.9 42.0 + - + +
220A LYS* 3.9 25.6 - - + -
298A THR* 5.7 1.1 - - - +
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Residues in contact with HIS 162 (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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112A THR* 2.9 52.0 + - + +
113A PHE* 3.9 7.0 - - - +
160A ALA* 3.5 21.2 - - - +
161A VAL* 1.3 76.1 - - - +
163A SER* 1.3 62.3 + - - +
192A TYR 4.0 0.2 - - - +
193A GLU* 3.2 5.4 - - - +
194A THR 2.7 37.8 + - - +
196A HIS* 3.6 24.3 - + + +
211A GLN* 3.7 19.1 + - + -
212A LEU 3.8 10.3 - - - -
215A PHE 3.3 7.0 - - - +
216A VAL* 3.4 31.1 + - + +
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Residues in contact with SER 163 (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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113A PHE* 3.6 8.4 - - - +
161A VAL* 4.2 0.6 + - - -
162A HIS* 1.3 76.4 - - - +
164A ASN* 1.3 59.0 + - - +
165A ARG* 3.1 30.0 + - - +
192A TYR 3.3 14.3 + - - -
193A GLU* 3.8 21.8 + - - +
215A PHE* 2.9 30.4 + - - +
217A LYS* 4.6 13.0 - - - -
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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