Contacts of the strand formed by residues 189 - 195 (chain A) in PDB entry 4O61
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 SER 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A PHE 3.6 4.9 - - - -
137A GLU* 3.8 10.3 + - - +
164A ILE* 4.4 0.2 - - - -
187A VAL* 3.4 8.3 - - - +
188A ASN* 1.3 83.1 - - - +
190A ALA* 1.3 59.0 + - - +
191A VAL* 4.2 6.9 - - - +
211A PHE* 3.7 27.7 - - - -
281A ILE 3.5 0.6 - - - +
282A LEU* 3.5 1.0 - - - -
283A ARG* 3.0 36.3 + - - +
285A THR* 4.5 0.7 - - - -
308A UNX 2.5 21.4 - - - -
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Residues in contact with ALA 190 (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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133A TYR 3.7 1.2 - - - +
135A PHE* 2.9 45.4 + - + +
164A ILE* 4.1 18.2 - - + +
168A VAL* 4.0 20.4 - - + -
187A VAL* 5.1 0.2 - - + -
189A SER* 1.3 74.3 + - - +
191A VAL* 1.3 62.7 + - - +
192A ILE* 6.0 0.9 - - + -
280A ILE* 4.8 4.0 - - + -
281A ILE 3.3 4.9 - - - -
282A LEU* 3.7 19.1 - - + -
308A UNX 3.7 0.2 - - - -
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Residues in contact with VAL 191 (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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132A LYS* 3.6 32.1 - - + +
133A TYR 3.2 8.3 - - - +
134A PHE* 3.6 20.2 - - + -
139A TYR* 5.4 0.2 - - + -
189A SER* 4.2 1.1 - - - +
190A ALA* 1.3 73.7 - - - +
192A ILE* 1.3 64.8 + - - +
193A ASN* 3.7 14.1 - - - +
211A PHE* 5.6 0.2 - - + -
279A VAL 3.5 1.2 - - - +
280A ILE* 3.3 4.0 - - - +
281A ILE* 2.7 41.8 + - + +
283A ARG* 3.5 28.9 - - - +
308A UNX 3.3 21.1 - - - -
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Residues in contact with ILE 192 (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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107A ILE* 4.3 29.2 - - + -
110A VAL* 4.2 13.0 - - + -
132A LYS* 3.4 2.6 - - - -
133A TYR* 2.8 53.4 + - + -
135A PHE* 4.0 26.9 - - + -
167A TRP* 3.9 31.9 - - + -
168A VAL* 5.2 2.2 - - + -
190A ALA* 5.4 1.1 - - + +
191A VAL* 1.3 76.6 - - - +
193A ASN* 1.3 69.3 + - - +
194A ASP* 4.8 1.3 - - + +
278A ALA* 4.9 1.8 - - + -
279A VAL 3.2 8.7 - - - +
280A ILE* 4.2 16.2 - - + -
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Residues in contact with ASN 193 (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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130A ARG* 4.1 6.4 - - - -
131A ASN 3.4 4.3 - - - +
132A LYS* 2.7 38.0 + - - +
191A VAL* 3.7 3.7 - - - +
192A ILE* 1.3 73.1 - - - +
194A ASP* 1.3 60.0 + - - +
195A TYR* 3.6 36.0 + - + +
278A ALA* 3.2 5.0 - - - +
279A VAL* 2.9 47.3 + - + +
281A ILE* 4.2 4.8 - - - +
302A CIT 3.0 30.1 + - - +
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Residues in contact with ASP 194 (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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107A ILE* 5.0 1.1 - - - -
111A VAL* 3.6 16.3 - - + +
130A ARG* 3.3 3.6 - - - -
131A ASN* 2.8 38.4 + - + +
133A TYR* 4.3 14.6 + - + -
192A ILE* 4.1 4.2 + - + -
193A ASN* 1.3 72.3 - - - +
195A TYR* 1.3 65.0 + - - +
196A GLN* 4.0 1.8 + - - +
276A ARG* 2.9 50.2 + - - +
277A ARG 3.8 3.4 - - - +
278A ALA* 4.0 8.8 - - + +
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Residues in contact with TYR 195 (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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129A LEU 3.6 4.5 - - - +
130A ARG* 3.4 28.3 + - + +
193A ASN* 3.6 40.0 + - + -
194A ASP* 1.3 74.9 + - - +
196A GLN* 1.3 68.6 + - - +
200A CYS 3.7 25.4 - - - -
201A ILE* 3.2 30.8 - - + +
268A ILE* 4.9 1.1 - - + -
273A ILE* 3.8 25.6 - - + -
276A ARG* 3.5 10.9 - - - +
277A ARG* 2.8 67.9 + - - +
279A VAL* 4.2 4.5 - - + -
306A UNX 4.0 1.6 - - - -
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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