Contacts of the strand formed by residues 186 - 191 (chain B) in PDB entry 1OBZ
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 ILE 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B VAL 3.8 0.5 - - - +
116B ILE* 3.4 2.1 - - - -
117B LEU* 2.8 45.9 + - + +
119B LYS* 4.1 27.6 - - + -
125B ILE* 4.1 24.9 - - + -
161B ILE* 4.1 16.4 - - + -
162B ASN* 3.4 11.9 - - - +
178B LEU* 5.2 3.1 - - + +
181B ALA* 4.1 14.1 - - + -
182B PHE 3.3 24.2 - - - +
183B GLY 4.4 4.9 - - - +
185B LYS* 1.3 72.0 - - - +
187B THR* 1.3 70.1 + - - +
188B MET* 4.0 18.3 + - + +
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Residues in contact with THR 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU* 4.7 11.0 - - - -
115B VAL 3.3 7.0 - - - -
116B ILE* 4.0 19.1 - - + -
161B ILE* 3.4 2.3 - - - +
162B ASN* 2.8 53.2 + - - +
163B GLY 4.0 1.7 + - - -
185B LYS* 4.0 25.8 - - + +
186B ILE* 1.3 75.3 - - - +
188B MET* 1.3 68.3 + - - +
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Residues in contact with MET 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ARG 3.8 0.3 - - - +
114B GLU* 3.4 7.3 - - - +
115B VAL* 2.9 47.5 + - + +
117B LEU* 4.0 13.7 - - + -
125B ILE* 3.6 31.0 - - + -
127B LEU* 3.8 17.5 - - + -
152B LEU* 4.7 1.8 - - - -
158B VAL* 4.6 8.7 - - + -
160B GLN 3.2 8.5 - - - +
161B ILE* 4.1 13.7 - - + -
178B LEU* 3.6 20.0 - - + -
186B ILE* 4.1 13.5 - - + +
187B THR* 1.3 81.2 - - - +
189B THR* 1.3 63.6 + - - +
190B ILE* 3.9 19.5 - - + -
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Residues in contact with THR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PRO* 3.5 30.7 - - + -
113B ARG 3.5 1.3 - - - +
114B GLU* 2.2 31.8 + - + +
158B VAL* 3.8 2.8 - - - -
159B LEU* 2.9 32.2 + - + +
160B GLN* 2.9 44.4 + - - +
188B MET* 1.3 70.6 - - - +
190B ILE* 1.3 60.3 + - - +
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Residues in contact with ILE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASP 4.6 0.2 - - - +
112B PRO* 3.1 6.5 - - - +
113B ARG* 2.8 54.1 + - + +
115B VAL* 4.1 19.5 - - + -
152B LEU* 3.6 35.9 - - + -
156B ASP* 4.1 8.1 - - + -
157B GLN 3.5 3.8 - - - +
158B VAL* 3.9 24.2 - - + -
159B LEU* 4.9 0.2 - - - -
188B MET* 3.9 19.1 - - + -
189B THR* 1.3 81.6 - - - +
191B ARG* 1.3 72.8 + - - +
192B ASP* 3.8 14.1 + - - +
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Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ARG* 3.5 42.6 - - - +
199A ILE* 3.8 22.8 - - - +
230A ASN* 2.8 28.1 + - - +
231A GLY 3.0 20.4 + - - -
233A LEU* 5.2 2.4 - - - +
110B MET 4.6 5.0 + - - +
111B ASP 5.2 0.7 - - - -
112B PRO* 4.5 9.0 - - + +
156B ASP* 3.7 1.4 - - - -
157B GLN* 2.8 73.5 + - + +
159B LEU* 4.1 24.4 - - + +
189B THR 4.3 0.6 + - - -
190B ILE* 1.3 72.6 - - - +
192B ASP* 1.3 73.3 + - - +
194B PRO* 4.0 8.0 - - + +
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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