Contacts of the strand formed by residues 236 - 240 (chain F) in PDB entry 3CB4
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 ARG 236 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308E GLU* 4.4 7.9 - - - +
311E ARG* 4.4 16.5 - - - +
312E ASP* 2.9 43.4 + - - -
204F LEU* 3.8 19.4 - - - +
219F LYS* 4.4 11.4 - - - +
234F ALA 3.4 0.9 - - - -
235F ASP* 1.3 87.2 - - + +
237F LEU* 1.3 62.2 + - - +
244F GLN* 4.3 7.7 + - - -
246F ASP* 2.7 42.0 + - - +
257F TRP* 3.8 13.8 - - + -
258F LEU* 3.7 4.1 - - - +
259F VAL* 2.7 45.9 + - + +
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Residues in contact with LEU 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F LEU* 4.0 31.4 - - + +
218F ARG 4.2 17.5 - - - +
219F LYS* 4.5 7.5 - - + +
234F ALA* 4.7 2.2 - - + -
236F ARG* 1.3 77.2 - - - +
238F GLY* 1.3 53.2 + - - +
246F ASP* 3.5 7.1 + - - +
247F ARG* 2.7 51.3 + - + +
248F THR 4.1 1.8 - - - +
249F GLU* 3.7 28.7 - - - +
250F LEU* 3.8 12.8 - - + +
257F TRP* 3.2 24.7 - - - +
258F LEU* 4.1 15.0 - - + -
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Residues in contact with GLY 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F LEU* 1.3 78.3 - - - +
239F ILE* 1.3 61.0 + - - +
245F VAL 3.2 13.0 - - - -
247F ARG* 3.7 15.0 - - - -
250F LEU* 4.2 3.9 - - - +
256F GLY* 3.1 6.4 - - - -
257F TRP* 2.8 45.9 + - - -
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Residues in contact with ILE 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F THR* 3.9 34.1 - - + +
72F GLN* 5.4 6.7 - - - +
238F GLY* 1.3 77.9 - - - +
240F PHE* 1.3 58.5 + - - +
241F THR* 3.8 19.1 - - - +
243F LYS 3.6 0.3 - - - +
244F GLN* 3.8 0.5 - - - -
245F VAL* 3.0 32.3 + - + +
247F ARG* 3.9 37.7 - - + +
250F LEU* 4.2 11.4 - - + -
254F GLU* 5.6 2.2 - - + +
255F VAL 3.6 19.7 - - - +
256F GLY* 4.4 3.6 - - - -
257F TRP* 3.1 17.2 + - - -
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Residues in contact with PHE 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F GLN* 6.0 1.6 - - - -
58F SER* 3.3 28.3 - - - +
59F VAL* 4.6 0.2 - - - -
60F THR* 2.8 34.7 + - - +
199F TRP* 4.0 23.1 - + - -
207F VAL* 5.4 0.2 - - + -
209F LEU* 3.8 24.9 - - + -
239F ILE* 1.3 75.3 - - - +
241F THR* 1.3 62.4 + - - +
242F PRO* 3.5 18.6 - - - +
243F LYS 3.4 1.3 - - - -
244F GLN* 3.6 37.9 - - + -
255F VAL 5.5 0.2 + - - -
256F GLY* 5.4 1.0 - - - -
257F TRP* 3.6 34.1 - + + -
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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