Contacts of the strand formed by residues 230 - 235 (chain E) in PDB entry 1QDU
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 PHE 230 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E TYR* 3.7 20.4 - - + -
166E LEU* 4.1 24.9 - - + -
198E PHE* 4.6 0.2 - - - -
218E TYR* 4.2 14.1 - - + -
224E HIS* 4.1 15.5 - + - +
229E CYS* 1.3 79.3 - - - +
231E ILE* 1.3 75.0 + - - +
232E CYS* 4.0 19.3 - - + -
265E PHE* 3.4 45.8 - + - -
273E LEU* 3.9 24.2 - - + -
277E PRO 3.1 6.5 + - - +
278E LYS* 3.5 4.3 - - + -
279E VAL* 2.8 27.4 + - - +
280E PHE* 4.1 13.9 - + - -
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Residues in contact with ILE 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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164E TYR 3.0 8.4 + - - +
165E CYS* 3.2 21.4 - - - -
166E LEU* 2.8 24.4 + - - +
193E PHE* 3.2 37.5 - - + -
198E PHE* 3.5 27.6 - - + -
229E CYS* 4.1 4.5 - - - -
230E PHE* 1.3 85.0 - - - +
232E CYS* 1.3 65.0 + - - +
233E CYS* 4.0 5.4 - - - -
279E VAL* 3.3 10.1 - - + +
281E PHE* 3.9 29.6 - - + -
400F PHE* 4.1 11.7 - - + -
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Residues in contact with CYS 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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166E LEU* 3.7 17.3 - - + -
168E ILE* 5.0 3.1 - - - -
215E LEU* 4.2 14.8 - - + -
230E PHE* 4.0 14.1 - - + -
231E ILE* 1.3 76.7 - - - +
233E CYS* 1.3 66.7 + - - +
234E ILE* 3.8 26.9 + - - +
279E VAL 2.8 9.9 + - - -
280E PHE* 3.2 32.1 - - + +
281E PHE 3.0 22.3 + - - -
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Residues in contact with CYS 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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165E CYS* 4.4 7.2 - - - -
166E LEU 2.8 22.1 + - - +
167E ILE* 3.5 6.9 - - + -
168E ILE* 2.7 28.4 + - - +
189E LEU* 4.3 24.2 - - + -
193E PHE* 4.9 1.8 - - - -
231E ILE* 4.0 10.3 - - - -
232E CYS* 1.3 76.9 - - - +
234E ILE* 1.3 67.2 + - - +
235E LEU* 4.2 11.4 - - + -
281E PHE* 3.7 32.3 - - + +
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Residues in contact with ILE 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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168E ILE* 3.4 30.5 - - + +
211E ILE* 4.8 3.6 - - + -
215E LEU* 5.5 0.9 - - + -
232E CYS* 3.8 20.2 - - - -
233E CYS* 1.3 81.9 - - - +
235E LEU* 1.3 68.7 + - - +
236E SER* 4.1 3.4 - - - -
243E ILE* 4.0 26.9 - - + -
261E LEU* 3.5 33.9 - - + -
280E PHE* 5.6 1.1 - - + -
281E PHE 3.1 5.7 + - - +
282E ILE* 4.5 23.1 - - + +
283E GLN 2.8 31.4 + - - +
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Residues in contact with LEU 235 (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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167E ILE* 4.6 4.5 - - + -
168E ILE 2.9 14.1 + - - +
169E ASN* 4.1 12.6 - - + +
170E ASN 2.9 25.5 + - - -
179E ARG* 3.4 9.9 + - - +
182E THR* 3.5 29.8 - - + -
185E ASP* 3.7 18.4 - - + -
186E ALA* 4.1 10.5 - - - +
189E LEU* 4.3 13.0 - - + -
233E CYS* 4.4 4.5 - - + -
234E ILE* 1.3 89.5 - - - +
236E SER* 1.3 61.7 + - - +
281E PHE 4.5 0.4 - - - +
283E GLN* 3.5 20.4 - - + +
350F ILE* 4.1 14.8 - - + -
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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