Contacts of the strand formed by residues 242 - 246 (chain A) in PDB entry 1OWH
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 GLY 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A CYS* 3.4 4.3 - - - -
197A ALA 3.1 36.6 + - - -
198A ALA* 4.7 0.2 - - - +
205A ASP* 3.9 9.5 + - - -
231A TRP 3.9 1.3 - - - -
240A LYS 3.8 0.4 + - - -
241A PRO* 1.3 76.6 - - - +
243A VAL* 1.3 58.8 + - - +
244A TYR* 3.5 12.6 - - - -
1001A 239 3.5 25.6 - - - -
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 3.4 35.0 - - + -
190A VAL* 4.2 6.5 - - + -
194A MET* 3.8 24.9 - - + -
195A LEU 3.6 6.7 - - - +
196A CYS* 4.3 5.4 - - - -
229A VAL* 4.4 1.0 - - - +
230A SER* 3.0 22.6 + - - -
231A TRP* 2.7 71.5 + - + +
241A PRO 3.8 0.4 - - - +
242A GLY* 1.3 76.2 - - - +
244A TYR* 1.3 70.2 + - - +
1001A 239 5.5 0.2 - - - -
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Residues in contact with TYR 244 (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 ILE* 3.5 31.5 - - + +
172A VAL* 4.8 3.1 - - - +
194A MET* 3.5 5.7 - - - +
195A LEU* 2.9 41.7 + - + +
197A ALA* 4.0 20.2 + - + -
205A ASP* 4.4 5.4 + - - -
206A SER* 3.0 21.5 + - - -
215A LEU* 3.8 32.5 - - + -
227A GLY* 4.2 2.7 - - - -
228A ILE 3.2 14.4 - - - +
229A VAL* 3.5 41.7 - - + -
230A SER* 4.4 2.2 - - - -
242A GLY* 3.5 28.3 - - - -
243A VAL* 1.3 78.7 - - - +
245A THR* 1.3 60.7 + - - +
246A ARG 3.4 0.3 + - - -
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Residues in contact with THR 245 (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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109A ASP* 2.9 40.3 + - - +
110A ILE* 4.2 14.8 - - + -
193A LYS 4.3 3.1 - - - +
194A MET* 5.0 2.7 - - - +
227A GLY* 3.2 21.1 - - - -
228A ILE* 3.0 22.0 + - + +
230A SER* 4.1 5.7 - - - -
244A TYR* 1.3 69.5 - - - +
246A ARG* 1.3 62.6 + - - +
247A VAL* 3.1 10.2 + - + +
250A PHE* 3.5 32.8 - - + -
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Residues in contact with ARG 246 (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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138A TYR* 5.8 1.4 - - - +
140A ASP* 3.5 17.0 + - - +
192A THR* 2.9 34.8 + - - -
193A LYS* 3.1 23.8 + - - +
194A MET 5.2 0.7 - - - -
195A LEU* 3.8 36.3 - - + -
226A THR 4.1 3.4 - - - -
244A TYR 3.4 1.8 + - - -
245A THR* 1.3 69.1 - - - +
247A VAL* 1.3 64.8 + - - +
248A SER* 3.1 26.4 + - - +
249A HIS* 3.1 31.1 + - - +
250A PHE* 3.4 14.1 - - - -
303A SO4 2.8 43.0 + - - -
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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