Contacts of the strand formed by residues 196 - 201 (chain A) in PDB entry 2OB1
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 THR 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.4 1.1 - - - -
100A GLN* 2.6 42.3 + - + +
102A VAL* 4.0 11.4 - - + -
194A ILE 2.8 8.9 + - - -
195A PRO* 1.3 70.9 - - - +
197A ILE* 1.3 75.6 + - - +
198A VAL* 3.9 6.2 + - + -
223A PHE* 3.4 39.8 - - + -
225A HIS 3.1 6.8 + - - -
226A GLY* 3.0 4.9 - - - -
227A LEU 2.8 25.5 + - - +
328A TRP* 4.5 2.5 - - - -
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Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.9 18.8 - - + +
92A PHE* 3.5 31.0 - - + -
93A LEU* 3.5 36.1 - - + -
99A VAL* 4.1 4.9 - - + +
100A GLN 2.8 9.5 + - - +
101A VAL* 3.3 15.7 - - + +
102A VAL 2.7 31.7 + - - +
196A THR* 1.3 73.4 - - - +
198A VAL* 1.3 63.4 + - - +
199A ILE* 4.0 12.1 - - + -
227A LEU* 3.1 12.6 - - + +
229A ILE* 3.7 24.7 - - + -
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Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 3.4 11.2 - - + +
104A LEU* 3.5 31.6 - - + -
196A THR* 4.1 15.3 - - + -
197A ILE* 1.3 78.5 - - - +
199A ILE* 1.3 61.1 + - - +
219A ILE* 3.8 23.3 - - + -
223A PHE* 5.0 0.9 - - + -
227A LEU 2.8 7.8 + - - +
228A TRP* 3.3 35.5 - - + +
229A ILE* 2.7 33.1 + - - +
328A TRP* 4.5 10.5 - - + -
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 4.5 15.3 - - + -
89A ILE* 3.6 28.0 - - + -
101A VAL* 3.6 25.1 - - + -
102A VAL 2.8 12.4 + - - +
103A ASN* 3.9 23.5 - - - +
104A LEU* 2.9 32.1 + - - +
111A ARG* 4.1 13.7 - - - +
124A TYR* 4.2 0.9 - - + +
197A ILE* 4.0 13.2 - - + -
198A VAL* 1.3 79.2 - - - +
200A SER* 1.3 64.4 + - - +
201A GLU* 4.2 20.2 - - + +
229A ILE* 3.4 10.1 - - + +
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Residues in contact with SER 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.0 6.1 - - - -
198A VAL 4.2 0.2 - - - -
199A ILE* 1.3 73.8 - - - +
201A GLU* 1.3 60.2 + - - +
202A CYS 3.8 0.4 - - - -
203A LEU* 4.1 26.0 + - - -
204A LEU* 3.8 11.9 - - - +
228A TRP* 2.8 28.3 + - - -
229A ILE 3.0 7.0 + - - -
230A SER* 2.8 27.5 + - - -
231A TYR 2.9 24.0 + - - +
232A ASP* 5.1 0.3 - - - +
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Residues in contact with GLU 201 (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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16A LYS* 5.3 5.4 + - - -
81A ARG* 2.7 46.0 + - - +
82A THR* 5.2 2.8 + - - -
85A ILE* 3.5 24.8 - - + +
103A ASN* 5.3 2.2 + - - +
104A LEU 4.5 3.6 + - - -
105A GLY 4.7 8.9 + - - +
109A ASP* 3.9 6.1 - - - +
111A ARG* 2.8 31.9 + - - -
199A ILE* 4.0 9.8 - - + +
200A SER* 1.3 73.0 - - - +
202A CYS* 1.3 67.4 + - - +
203A LEU* 3.3 4.2 + - - +
231A TYR* 3.7 9.4 - - + -
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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