Contacts of the strand formed by residues 171 - 177 (chain A) in PDB entry 1OBA
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 171 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 3.7 5.4 - - - +
150A ILE* 4.3 20.4 - - + +
165A PHE* 4.1 10.8 - - + -
166A PRO* 3.3 36.8 - - + +
168A MET* 3.4 37.4 + - + +
169A ASP 3.2 2.6 - - - +
170A GLY* 1.3 74.8 - - - +
172A ARG* 1.3 60.6 + - - +
173A TRP 3.5 22.2 - - - +
174A TRP* 4.8 1.6 - - + -
187A LEU* 3.7 32.3 - - + +
188A LEU* 3.8 12.1 - - - +
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 3.6 30.3 + - - -
123A ILE* 3.9 21.4 - - + +
145A PRO 5.0 1.6 + - - -
146A ASN* 2.8 43.9 + - - +
147A SER 4.7 0.7 - - - -
148A LEU 2.6 17.0 + - - +
170A GLY 3.3 1.8 + - - -
171A ILE* 1.3 74.1 - - - +
173A TRP* 1.3 81.4 + - + +
187A LEU* 2.9 28.7 + - - +
188A LEU* 3.7 27.3 + - + +
189A ASP 3.0 23.6 + - - -
190A ASP* 3.8 2.2 + - - +
191A GLU* 3.1 33.2 + - - +
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Residues in contact with TRP 173 (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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2A VAL* 4.2 5.5 - - + +
8A PHE* 3.5 23.6 - + + -
32A ILE* 3.4 25.1 - - + -
56A ILE* 4.5 9.6 - - + -
88A TYR* 3.5 54.1 - + + -
90A VAL* 4.1 5.2 - - + -
123A ILE* 3.9 20.2 - - + -
148A LEU 3.1 2.8 + - - -
149A TRP* 3.3 34.6 - + + -
150A ILE 3.1 24.3 + - - -
171A ILE* 3.5 9.3 - - - +
172A ARG* 1.3 107.1 - - + +
174A TRP* 1.3 61.7 + - - +
185A ILE 3.7 3.1 - - - +
186A VAL* 3.6 34.9 - - + +
187A LEU* 4.2 0.4 - - - -
190A ASP* 4.9 2.1 + - - -
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Residues in contact with TRP 174 (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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150A ILE 3.5 10.1 - - - -
152A GLY 3.0 25.6 + - - -
153A TYR 6.0 0.4 - - - -
160A ALA* 4.2 7.0 - - + -
161A ASN 3.8 37.2 - - - -
162A PHE* 4.1 7.4 - + - -
164A TYR* 4.4 1.6 - - + -
165A PHE* 3.5 36.1 - + + -
166A PRO* 3.4 20.3 - - + +
171A ILE* 4.8 1.8 - - + -
173A TRP* 1.3 73.8 - - - +
175A GLN* 1.3 70.3 + - - +
176A TYR* 3.1 30.7 + - + -
184A ASN* 4.1 1.8 - - - -
185A ILE* 2.9 55.7 + - + +
187A LEU* 3.8 13.2 - - + -
338A VAL* 3.7 24.9 - - + -
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Residues in contact with GLN 175 (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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10A ASP* 2.8 29.9 + - - +
125A TYR* 2.9 25.3 + - + -
149A TRP* 3.7 14.4 - - + +
150A ILE 3.1 7.2 + - - +
151A ALA* 3.3 12.1 - - + +
152A GLY 3.2 23.4 + - - -
153A TYR* 2.7 29.6 + - + -
174A TRP* 1.3 71.6 - - - +
176A TYR* 1.3 59.1 + - - +
177A SER 4.0 9.9 - - - +
182A ASP* 3.3 17.9 + - - -
183A LYS 3.2 10.8 - - - +
184A ASN* 2.9 20.8 + - - +
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Residues in contact with TYR 176 (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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7A LEU* 4.2 11.9 - - + +
26A MET* 3.6 21.1 - - - +
152A GLY 3.8 1.1 - - - +
153A TYR* 3.6 23.0 - - - +
156A ASN* 5.1 0.5 - - - -
158A GLY 4.1 3.3 + - - -
159A THR* 3.6 22.6 - - - +
160A ALA* 3.8 28.3 - - + -
174A TRP* 3.1 47.8 + - + +
175A GLN* 1.3 72.3 - - - +
177A SER* 1.3 67.2 + - - +
183A LYS* 3.0 33.5 + - + +
184A ASN 3.9 20.0 - - - -
185A ILE* 3.9 18.4 - - + -
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Residues in contact with SER 177 (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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153A TYR* 3.7 7.4 - - - -
156A ASN* 2.8 19.0 + - - +
158A GLY* 3.2 29.3 - - - -
159A THR 4.3 0.7 - - - -
175A GLN* 3.4 7.1 + - - +
176A TYR* 1.3 97.4 - - - +
178A SER* 1.3 69.5 + - - +
179A ASN* 3.1 8.1 + - - +
181A PHE 4.0 0.9 - - - -
182A ASP* 3.5 2.8 - - - -
183A LYS* 2.9 32.9 + - - +
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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