Contacts of the strand formed by residues 174 - 180 (chain A) in PDB entry 2O1S
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 MSE 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ILE* 4.1 7.2 - - + +
130A GLY* 3.8 18.4 - - - +
131A ILE* 3.7 29.2 - - - +
134A ALA* 4.1 8.5 - - + -
146A THR* 3.6 14.6 - - + +
148A CYS* 3.7 29.8 - - - -
167A ALA* 4.6 8.1 - - - -
172A PRO* 3.2 20.0 + - - +
173A ASP* 1.3 76.3 - - - +
175A LEU* 1.3 62.9 + - - +
176A VAL* 4.2 21.3 - - + -
248A PHE* 4.9 1.1 - - + -
272A LEU 5.8 0.4 + - - -
274A GLY 3.6 2.9 + - - +
275A PRO* 4.5 7.6 - - + -
276A GLN* 2.8 30.7 + - - +
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Residues in contact with LEU 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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67A TYR* 3.3 26.9 - - - +
146A THR 3.1 10.3 + - - +
147A VAL* 3.2 6.0 - - + -
148A CYS* 2.8 27.9 + - - +
174A MSE 1.3 76.5 - - - +
176A VAL* 1.3 75.3 + - - +
177A ILE* 3.7 17.3 - - + -
266A LEU* 3.6 28.7 - - + -
269A MSE 3.9 23.6 - - + +
270A ARG* 5.3 0.4 - - - +
276A GLN* 3.5 26.9 - - + +
278A LEU* 3.9 12.8 - - + +
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Residues in contact with VAL 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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127A ILE* 4.0 23.6 - - + -
148A CYS* 3.7 7.6 - - + +
150A ILE* 3.9 24.2 - - + -
174A MSE 4.2 17.5 - - + -
175A LEU* 1.3 75.7 - - - +
177A ILE* 1.3 62.9 + - - +
178A LEU 4.0 0.3 + - - -
248A PHE* 3.4 29.8 - - + -
276A GLN 2.8 10.5 + - - +
277A PHE* 3.3 27.4 - - + -
278A LEU 2.9 25.8 + - - +
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Residues in contact with ILE 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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59A LEU* 4.2 18.6 - - + -
63A LEU* 3.8 12.3 - - + -
147A VAL* 3.8 13.2 - - + -
148A CYS 2.7 16.1 + - - +
149A VAL* 3.4 8.4 - - + -
150A ILE* 2.8 31.8 + - - +
175A LEU* 3.7 22.0 - - + -
176A VAL* 1.3 75.2 - - - +
178A LEU* 1.3 63.4 + - - +
179A ASN 3.4 0.9 + - - +
266A LEU* 3.7 27.6 - - + -
278A LEU* 3.3 12.6 - - + +
280A ILE* 4.2 32.1 - - + -
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Residues in contact with LEU 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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150A ILE* 3.3 17.0 - - + +
151A GLY 3.8 2.9 - - - +
152A ASP* 3.6 28.7 - - + +
155A ILE* 4.5 12.3 - - + -
176A VAL 4.0 1.8 + - - -
177A ILE* 1.3 69.2 - - - +
179A ASN* 1.3 64.2 + - - +
180A ASP* 3.1 9.6 + - + +
243A PHE* 4.4 10.8 - - + -
277A PHE* 3.6 32.3 - - + -
278A LEU 2.8 10.8 + - - +
279A HIS* 3.5 39.3 - - + +
280A ILE* 3.0 27.2 + - - +
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Residues in contact with ASN 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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52A SER 5.7 0.4 + - - -
55A GLY 5.5 0.4 - - - -
56A THR* 3.5 27.1 - - - +
59A LEU* 4.9 0.4 - - - -
81A GLN* 4.6 10.7 - - - +
149A VAL* 4.1 17.6 - - + +
150A ILE 2.7 18.3 + - - +
151A GLY* 3.5 5.8 - - - +
152A ASP* 3.4 19.8 + - - +
177A ILE* 3.4 1.6 + - - -
178A LEU* 1.3 70.7 - - - +
180A ASP* 1.3 58.1 + - - +
181A ASN* 3.6 9.7 + - - +
280A ILE* 3.9 11.8 - - + +
282A THR* 2.7 39.1 + - - +
3001A TPP 4.9 0.2 + - - -
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Residues in contact with ASP 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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152A ASP* 3.7 20.8 - - - +
178A LEU* 3.1 6.1 + - + +
179A ASN* 1.3 70.8 + - - +
181A ASN* 1.3 62.9 + - - +
182A GLU* 3.3 21.7 + - - +
279A HIS* 2.6 35.0 + - + +
280A ILE 3.1 19.9 + - - +
281A MSE 3.0 14.2 - - + +
282A THR 3.0 20.6 + - - +
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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