Contacts of the strand formed by residues 148 - 153 (chain E) in PDB entry 4OMC
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 VAL 148 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E GLY 4.6 0.7 - - - +
147E ILE* 1.3 77.2 - - - +
149E VAL* 1.3 63.9 + - - +
168E ASP* 3.8 9.2 - - - +
171E ALA* 3.5 31.2 - - + -
220E ARG* 3.6 28.9 - - + +
246E HIS* 3.5 36.6 - - + +
247E ILE* 3.9 12.7 - - + +
248E HIS* 2.7 43.6 + - + +
249E ILE 3.1 7.3 + - - -
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Residues in contact with VAL 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E ILE* 4.6 2.0 - - + -
148E VAL* 1.3 81.2 - - - +
150E SER* 1.3 68.1 + - - +
151E ILE* 4.3 7.6 - - + -
171E ALA* 4.3 1.4 - - - +
202E VAL* 4.0 24.5 - - + -
219E ALA* 4.9 5.8 - - + -
220E ARG 3.0 9.3 + - - +
221E ILE* 3.5 18.2 - - + +
222E GLY* 2.8 24.9 + - - -
247E ILE* 4.5 0.4 - - - -
249E ILE* 3.3 35.2 - - + +
251E SER* 4.8 1.3 - - - -
375E ALA* 4.5 11.9 - - + +
379E ALA* 4.1 16.2 - - + -
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Residues in contact with SER 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E VAL* 1.3 76.0 - - - +
151E ILE* 1.3 64.3 + - - +
152E LEU* 3.7 7.5 + - - +
171E ALA 2.8 26.2 + - - -
222E GLY 3.5 4.6 + - - -
224E VAL* 3.5 20.6 - - - +
247E ILE* 3.7 26.1 - - - +
249E ILE 2.8 7.7 + - - +
250E TYR* 3.5 4.4 - - - -
251E SER* 2.9 26.0 + - - -
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Residues in contact with ILE 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E VAL* 4.3 2.0 - - + -
150E SER* 1.3 73.4 + - - +
152E LEU* 1.3 59.0 + - - +
153E ASP* 3.3 25.4 + - + +
155E GLY 5.8 1.5 - - - +
156E ILE* 5.7 1.6 - - + -
195E GLY* 4.0 8.3 - - - +
198E CYS* 4.0 23.1 - - + +
199E ALA* 3.8 24.0 - - + -
202E VAL* 3.9 28.3 - - + -
221E ILE* 4.0 9.2 - - + -
222E GLY 3.0 17.8 + - - +
223E GLY* 3.4 3.9 - - - -
224E VAL 2.9 22.9 + - - +
251E SER* 3.8 25.6 - - - +
253E SER* 6.3 0.9 - - - +
372E PRO* 5.3 0.2 - - + -
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Residues in contact with LEU 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E SER* 3.9 10.5 - - - +
151E ILE* 1.3 69.5 - - - +
153E ASP* 1.3 62.7 + - - +
224E VAL* 3.4 33.7 - - + -
226E MET* 3.9 11.7 - - + -
239E SER* 4.0 26.0 - - - +
240E LEU* 3.6 33.0 - - + +
250E TYR* 4.1 20.2 - - + -
251E SER 3.0 17.0 + - - +
252E ALA* 4.3 4.3 - - + -
254E TRP* 2.8 43.1 + - + +
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Residues in contact with ASP 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E ILE* 3.3 13.3 + - + +
152E LEU* 1.3 77.0 - - - +
154E ASP* 1.3 69.8 + - - +
155E GLY 3.3 6.1 - - - +
194E HIS* 2.8 39.8 + - - -
195E GLY* 3.0 28.6 + - - -
198E CYS* 4.3 3.3 - - - -
224E VAL 3.0 8.3 + - - +
226E MET* 2.8 33.0 + - - -
227E LEU* 2.9 27.7 + - - +
253E SER* 4.1 10.7 + - - +
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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