Contacts of the strand formed by residues 223 - 227 (chain K) in PDB entry 3GHG
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 GLU 223 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202K ASN 4.8 0.9 - - - +
204K PRO* 3.2 27.9 - - - +
221K THR* 3.4 20.1 + - - +
222K SER* 1.3 77.1 - - - +
224K MET* 1.3 69.4 + - - +
225K TYR* 3.0 26.8 + - + -
239K TYR* 3.3 23.2 - - - -
240K CYS 3.1 23.9 + - - -
285K TYR* 3.9 17.8 - - + +
286K CYS 3.6 11.7 + - - +
287K GLY* 3.7 7.6 - - - -
217L HIS* 2.9 29.6 + - - -
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Residues in contact with MET 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201K CYS* 3.3 40.6 - - + +
202K ASN 5.3 0.6 - - - +
203K ILE* 4.2 13.9 - - + -
204K PRO* 3.3 22.3 - - - +
223K GLU* 1.3 78.5 - - - +
225K TYR* 1.3 67.6 + - - +
226K LEU* 6.0 0.7 - - - -
237K ARG* 3.4 52.3 - - + +
238K VAL 3.8 6.5 - - - +
239K TYR* 4.0 1.9 - - - -
276K VAL* 4.7 8.3 - - + -
277K ALA* 3.6 23.6 - - + +
286K CYS* 3.0 21.1 + - + +
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Residues in contact with TYR 225 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203K ILE* 5.8 0.2 - - - -
204K PRO* 4.0 15.5 - - + -
206K VAL* 3.8 32.3 - - + +
214K ILE* 3.7 20.6 - - + -
219K GLY* 3.6 7.7 - - - -
220K GLU 3.5 10.7 + - - -
221K THR* 2.6 42.8 + - - -
223K GLU* 3.0 31.7 + - + -
224K MET* 1.3 80.9 - - - +
226K LEU* 1.3 63.1 + - - +
237K ARG* 3.8 0.3 - - - -
238K VAL* 2.8 31.0 + - - +
240K CYS* 3.6 27.4 - - + -
242K MET* 3.7 22.0 - - + -
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Residues in contact with LEU 226 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203K ILE* 3.9 41.3 - - + -
204K PRO* 5.0 0.9 - - - +
206K VAL 4.8 4.2 + - - +
207K SER* 2.7 30.2 + - - +
214K ILE* 3.1 15.6 - - - +
224K MET* 6.0 0.7 - - - -
225K TYR* 1.3 76.5 - - - +
227K ILE* 1.3 65.5 + - - +
235K PRO* 4.2 9.4 - - + -
236K TYR* 2.8 49.1 - - - +
237K ARG* 3.7 10.8 - - + +
145L ILE* 4.4 13.5 - - + -
168L PHE* 4.8 8.1 - - + -
179L LEU* 4.6 6.3 - - + -
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Residues in contact with ILE 227 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207K SER* 3.6 3.4 - - - -
208K GLY 3.1 11.9 - - - +
209K LYS 3.8 9.2 - - - +
210K GLU* 3.7 24.9 - - + -
211K CYS* 4.0 2.5 - - - +
214K ILE* 3.6 18.4 - - + -
226K LEU* 1.3 84.2 - - - +
228K GLN* 1.3 62.3 + - - +
229K PRO* 4.5 0.7 - - + +
235K PRO* 3.3 5.7 - - - +
236K TYR* 3.2 61.1 + - + +
238K VAL* 3.8 28.9 - - + -
250K THR* 4.6 9.0 - - + -
302K LEU* 5.0 2.7 - - + -
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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
------------------------------------------------------------
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