Contacts of the strand formed by residues 250 - 254 (chain R) in PDB entry 5G04
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 250 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242R ALA* 5.2 0.7 - - + -
243R VAL 3.6 4.5 - - - +
248R ALA 5.2 0.7 - - - +
249R GLU* 1.3 75.0 - - - +
251R GLN* 1.3 61.3 + - - +
263R ASN* 4.1 0.2 - - - -
264R MET* 2.8 55.8 + - + +
266R SER* 5.5 0.7 - - - +
267R HIS* 4.4 4.5 - - + -
271R VAL* 4.1 17.0 - - + -
274R LEU* 3.9 15.3 - - + -
281R LEU* 3.7 29.8 - - + -
283R SER* 4.0 15.7 - - - +
293R HIS* 3.9 25.6 - - + +
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Residues in contact with GLN 251 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220R LEU* 4.5 8.1 - - - +
222R MET* 5.3 5.1 - - - +
241R LEU 3.8 0.2 - - - +
242R ALA* 3.3 5.4 - - - +
243R VAL* 2.8 43.9 + - + +
245R THR* 4.1 14.1 - - - +
249R GLU* 3.1 28.0 + - + -
250R VAL* 1.3 73.6 - - - +
252R LEU* 1.3 60.0 + - - +
253R TRP* 2.9 37.5 + - + +
260R ARG* 4.0 20.4 + - + +
262R ARG 3.5 8.3 - - - +
263R ASN* 3.4 22.4 + - - +
264R MET* 4.9 1.6 - - - -
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Residues in contact with LEU 252 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240R TYR* 4.3 19.7 - - + -
241R LEU 3.5 6.3 - - - +
242R ALA* 4.9 4.7 - - + -
250R VAL 4.2 0.6 + - - -
251R GLN* 1.3 75.0 - - - +
253R TRP* 1.3 63.1 + - - +
260R ARG* 3.8 2.3 - - - +
261R LEU* 2.9 54.0 + - + -
262R ARG* 3.1 41.2 + - + +
264R MET* 4.1 8.3 - - + -
276R TRP* 5.0 11.7 - - + -
281R LEU* 5.5 0.2 - - + -
295R VAL* 3.8 36.8 - - + +
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Residues in contact with TRP 253 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219R LEU* 3.7 44.9 - - + -
220R LEU* 3.5 40.1 - - + +
240R TYR* 3.3 8.4 - - - -
241R LEU 2.8 43.6 + - - +
243R VAL* 4.4 4.7 - - + -
251R GLN* 2.9 38.8 + - + +
252R LEU* 1.3 78.7 - - - +
254R ASP* 1.3 61.7 + - - +
255R VAL* 3.5 3.3 + - - +
258R GLN 4.1 4.5 - - - -
259R LYS* 3.5 15.5 - - - -
260R ARG* 3.5 46.9 - - + +
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Residues in contact with ASP 254 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219R LEU* 4.6 0.7 - - - +
239R ASN 4.0 0.5 - - - +
240R TYR* 3.5 29.8 + - + -
252R LEU 4.2 1.2 + - - -
253R TRP* 1.3 68.4 - - - +
255R VAL* 1.3 58.5 + - - +
256R GLN* 3.2 35.9 + - - +
257R GLN* 2.8 35.9 + - + -
258R GLN* 2.9 22.9 + - - -
259R LYS 2.8 22.4 + - - +
261R LEU* 3.9 20.6 - - + +
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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