Contacts of the strand formed by residues 175 - 183 (chain A) in PDB entry 2O3B
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 GLU 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLN* 3.3 23.1 + - + -
83A LEU 3.6 8.7 - - - +
84A ASN* 3.3 20.2 + - + +
174A LYS* 1.3 76.8 - - - +
176A LEU* 1.3 71.0 + - - +
177A TYR* 3.8 17.8 + - + -
205A VAL 3.8 0.3 - - - +
207A LEU* 3.0 51.7 + - + +
210A PRO* 3.6 20.0 - - + +
211A GLY* 2.9 32.1 + - - -
212A SER 4.4 0.2 + - - -
213A GLY 4.7 0.5 + - - -
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Residues in contact with LEU 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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82A GLN* 3.5 5.7 - - - +
83A LEU* 2.7 47.3 + - + +
166A CYS* 3.4 46.7 - - + +
169A LEU* 4.3 11.2 - - + -
170A VAL* 4.1 13.7 - - + -
174A LYS* 4.8 0.4 - - + -
175A GLU* 1.3 84.3 - - - +
177A TYR* 1.3 67.1 + - - +
178A ILE* 4.0 11.9 - - + -
204A VAL* 3.8 12.8 - - + -
205A VAL 3.3 4.5 - - - +
206A VAL* 3.6 37.9 - - + -
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Residues in contact with TYR 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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38A VAL* 3.4 26.1 + - - +
39A HIS 5.0 6.1 - - - -
41A LEU* 3.3 34.4 - - + +
42A LEU* 3.4 35.9 - - + +
81A TRP 3.7 2.5 - - - -
82A GLN* 3.0 41.4 + - + -
175A GLU* 3.8 13.7 + - + -
176A LEU* 1.3 76.7 - - - +
178A ILE* 1.3 60.9 + - - +
179A VAL* 5.8 0.2 - - - +
203A ILE 3.8 1.4 - - - +
204A VAL* 3.8 1.0 - - - -
205A VAL* 3.0 36.8 + - + +
207A LEU* 3.6 33.7 - - + -
213A GLY* 4.9 2.3 - - - -
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Residues in contact with ILE 178 (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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42A LEU* 6.2 0.7 - - - -
80A ALA* 3.0 4.3 - - - +
81A TRP* 2.7 92.3 + - + +
83A LEU* 4.1 26.0 - - + -
130A ASP* 4.3 1.3 - - - +
166A CYS* 4.4 10.5 - - + -
176A LEU* 4.2 18.6 - - + -
177A TYR* 1.3 78.9 - - - +
179A VAL* 1.3 65.1 + - - +
202A LYS* 4.0 21.1 - - + +
203A ILE 3.4 10.5 - - - +
204A VAL* 4.3 8.1 - - + -
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Residues in contact with VAL 179 (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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42A LEU* 6.0 4.5 - - + -
45A PRO* 4.1 24.7 - - + -
78A TRP* 4.2 7.4 - - + -
79A VAL 3.3 9.9 - - - +
80A ALA* 4.1 12.8 - - + -
177A TYR 5.8 0.2 - - - +
178A ILE* 1.3 76.9 - - - +
180A ALA* 1.3 64.8 + - - +
201A TRP* 3.6 16.1 - - + -
202A LYS* 3.5 0.9 - - - +
203A ILE* 2.8 52.4 + - + +
256A PHE* 4.0 18.2 - - + -
257A LEU* 5.8 4.5 - - + -
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Residues in contact with ALA 180 (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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78A TRP* 3.2 1.7 - - - -
79A VAL 2.8 31.6 + - - +
81A TRP* 4.2 4.7 - - + -
125A ILE* 3.6 17.0 - - + +
159A TRP* 3.8 7.6 - - + -
179A VAL* 1.3 77.2 - - - +
181A GLY* 1.3 60.3 + - - +
201A TRP* 3.3 25.4 - - - +
202A LYS* 3.8 26.5 - - + -
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Residues in contact with GLY 181 (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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77A ASN 4.0 2.5 - - - -
78A TRP* 4.2 1.1 - - - -
125A ILE* 4.4 8.3 - - - +
148A MET* 4.2 7.3 - - - +
159A TRP* 4.8 1.0 - - - -
180A ALA* 1.3 79.8 - - - +
182A PRO* 1.3 68.0 - - - +
200A THR* 3.6 3.8 - - - -
201A TRP* 3.0 48.4 + - - +
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Residues in contact with PRO 182 (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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73A LYS* 4.7 13.5 + - + +
75A THR* 3.9 13.9 - - - +
76A ALA 3.2 29.8 - - - +
77A ASN* 4.0 10.7 - - - +
125A ILE* 4.6 4.5 - - + -
148A MET* 3.9 20.0 - - + -
181A GLY* 1.3 86.4 - - - +
183A ASN* 1.3 63.2 + - - +
184A GLY 5.8 0.2 - - - +
197A PRO* 3.3 25.4 - - + -
199A SER 3.5 6.3 - - - +
201A TRP* 3.0 12.9 + - - -
252A THR* 5.4 0.5 - - - +
254A TYR* 5.9 0.7 - - - -
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Residues in contact with ASN 183 (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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73A LYS* 4.6 5.7 - - - +
182A PRO* 1.3 79.4 + - - +
184A GLY* 1.3 70.2 + - - +
198A LYS* 2.8 29.5 + - - +
199A SER* 3.0 27.4 + - - +
201A TRP* 4.0 11.2 - - + -
251A LEU* 3.6 48.2 + - + +
252A THR* 4.0 13.3 - - - +
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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