Contacts of the strand formed by residues 230 - 234 (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 LYS 230 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226E ILE* 3.7 0.9 - - - -
227E GLU* 2.7 67.4 + - + +
229E ASP* 1.3 100.3 - - - +
231E VAL* 1.3 64.2 + - - +
232E ILE* 4.4 10.5 - - + -
242E GLU* 2.8 43.1 + - + +
243E VAL 3.2 17.7 - - - +
244E PRO* 4.6 0.9 - - + -
245E ALA* 4.0 3.7 + - - +
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Residues in contact with VAL 231 (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 17.0 - - + -
185E ILE* 4.1 20.2 - - + -
223E VAL* 4.0 13.5 - - + -
225E ALA 3.6 4.3 - - - +
226E ILE* 3.7 26.0 - - + -
230E LYS* 1.3 76.2 - - - +
232E ILE* 1.3 66.8 + - - +
233E TYR* 4.1 1.1 + - - +
242E GLU* 3.3 4.5 - - - +
243E VAL* 2.9 42.4 + - + +
248E THR* 3.6 30.3 - - + -
250E PHE* 4.2 4.3 - - + -
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Residues in contact with ILE 232 (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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223E VAL* 3.6 3.1 - - - +
224E LYS* 2.8 40.0 + - + -
225E ALA* 2.8 32.8 + - + +
227E GLU* 3.4 29.6 - - + +
230E LYS* 4.4 11.2 - - + -
231E VAL* 1.3 77.7 - - - +
233E TYR* 1.3 59.9 + - - +
240E THR* 3.3 24.2 - - - +
241E HIS 3.3 4.7 - - - +
242E GLU* 4.2 17.0 - - + +
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Residues in contact with TYR 233 (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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185E ILE* 4.1 16.8 - - + -
218E ILE* 3.6 42.2 - - + +
221E VAL* 3.7 31.9 - - + -
222E ALA 3.2 12.8 - - - +
223E VAL* 4.0 13.2 - - + -
224E LYS* 4.1 2.7 - - - +
231E VAL* 4.6 4.9 - - + -
232E ILE* 1.3 76.8 - - - +
234E GLU* 1.3 60.6 + - - +
239E ASN 4.0 0.2 - - - +
240E THR* 3.5 2.8 + - - -
241E HIS* 2.7 85.3 + + + +
242E GLU 4.5 4.5 - - - -
243E VAL* 4.8 7.4 - - + -
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Residues in contact with GLU 234 (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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221E VAL* 3.5 4.1 - - - +
222E ALA* 2.7 36.5 + - + +
224E LYS* 3.5 39.7 + - + +
233E TYR* 1.3 75.0 - - - +
235E ASP* 1.3 72.6 - - - +
238E GLY* 3.7 33.0 - - - +
239E ASN 3.4 6.1 - - - +
240E THR* 4.7 6.6 - - - +
306E ILE* 4.9 0.5 - - - +
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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