Contacts of the strand formed by residues 182 - 185 (chain E) in PDB entry 3HYW
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 MET 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E VAL* 3.4 13.0 - - + -
148E ILE* 4.1 22.7 - - + -
164E ALA* 3.3 29.6 - - + +
167E LEU* 4.1 10.5 - - + -
168E HIS* 3.8 24.7 - - + +
171E LEU* 3.9 10.5 - - + -
177E ARG* 3.4 37.3 - - - +
180E VAL* 3.9 3.1 - - + +
181E PRO* 1.3 77.8 - - - +
183E THR* 1.3 64.6 + - - +
214E ASN 4.3 1.2 + - - +
215E ILE* 3.9 17.6 - - + -
216E ASP* 3.0 31.0 + - - +
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Residues in contact with THR 183 (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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146E VAL* 3.0 10.7 + - - +
147E VAL* 3.1 12.5 - - - +
148E ILE* 2.9 26.5 + - - +
181E PRO* 5.2 3.1 - - - +
182E MET* 1.3 78.1 + - - +
184E PHE* 1.3 62.6 + - - +
185E ILE* 4.1 11.7 - - + -
215E ILE* 4.8 2.0 - - - -
216E ASP* 3.2 24.0 + - + +
218E ILE* 4.1 28.9 - - + -
243E VAL* 4.3 16.1 - - + +
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Residues in contact with PHE 184 (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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148E ILE* 3.1 17.0 - - + -
149E GLY* 4.1 7.4 - - - -
150E ALA* 5.9 0.7 - - + -
157E PHE* 6.0 1.1 - + - -
160E ALA* 3.6 38.8 - - + -
161E TYR* 3.5 46.0 - + - -
164E ALA* 4.1 12.1 - - + -
183E THR* 1.3 72.5 - - - +
185E ILE* 1.3 62.0 + - - +
186E THR* 3.8 26.0 - - + -
188E GLU* 4.8 0.4 - - - -
191E LEU* 4.3 4.0 - - + -
210E PHE* 3.5 35.2 - + + -
215E ILE* 4.2 4.2 - - + +
216E ASP 2.7 11.5 + - - +
217E TRP* 3.2 4.0 - - + +
218E ILE 2.8 27.2 + - - +
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Residues in contact with ILE 185 (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 VAL* 3.6 26.0 - - + -
148E ILE 2.8 9.7 + - - -
149E GLY* 3.0 5.8 - - - -
150E ALA 2.9 24.9 + - - +
183E THR* 4.1 4.9 - - + -
184E PHE* 1.3 77.2 - - - +
186E THR* 1.3 64.8 + - - +
218E ILE* 3.3 22.2 - - + +
221E VAL* 3.4 28.3 - - + -
223E VAL* 3.7 20.4 - - + -
231E VAL* 4.1 9.0 - - + -
233E TYR* 4.1 17.3 - - + -
243E VAL* 3.8 21.3 - - + -
250E PHE* 3.9 4.8 - - + -
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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