Contacts of the strand formed by residues 236 - 241 (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 TYR 236 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K LEU* 2.8 24.0 - - - +
227K ILE* 3.2 38.9 + - + +
229K PRO* 3.5 33.4 - - + +
233K VAL* 4.9 9.0 - - + -
234K LYS 4.2 8.5 - - - +
235K PRO* 1.3 78.1 - - + +
237K ARG* 1.3 70.2 + - - +
238K VAL* 3.8 2.6 + - + -
294K LEU* 4.0 20.4 - - + -
298K LYS* 3.3 52.8 + - + +
301K GLN* 4.4 2.3 + - - -
302K LEU* 3.6 20.3 - - + +
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Residues in contact with ARG 237 (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* 3.8 16.6 - - - +
224K MET* 3.4 37.6 - - + +
225K TYR 3.8 4.9 - - - -
226K LEU* 4.0 11.7 - - + -
236K TYR* 1.3 84.9 - - - +
238K VAL* 1.3 63.1 + - - +
276K VAL* 4.2 17.7 - - + +
294K LEU* 4.0 8.0 - - - +
298K LYS* 4.7 2.1 + - - -
141L ASP* 4.4 7.2 + - - +
143L VAL* 3.1 35.1 + - - +
144L GLN* 4.5 3.6 - - - +
145L ILE* 4.0 20.0 - - - +
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Residues in contact with VAL 238 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211K CYS* 3.4 33.2 - - - -
224K MET* 3.8 2.6 - - - -
225K TYR* 2.8 32.4 + - - +
227K ILE* 3.8 29.6 - - + -
236K TYR* 3.8 4.0 + - + +
237K ARG* 1.3 71.6 - - - +
239K TYR* 1.3 65.1 + - - +
240K CYS* 3.7 2.4 + - - -
250K THR* 4.1 8.5 - - + -
251K VAL 4.1 12.8 - - - +
276K VAL* 3.7 10.4 - - - +
292K TYR* 4.5 0.4 - - - +
294K LEU* 3.6 30.1 - - + -
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Residues in contact with TYR 239 (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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222K SER* 3.3 26.3 + - - -
223K GLU* 3.3 29.1 - - - -
224K MET* 4.0 2.2 - - - +
238K VAL* 1.3 79.2 - - - +
240K CYS* 1.3 92.3 + - - +
241K ASP* 3.9 5.4 - - + -
250K THR* 4.0 0.2 - - - -
251K VAL* 3.1 38.5 + - + +
276K VAL* 3.6 18.3 - - - +
277K ALA* 4.0 1.6 - - + -
287K GLY 3.7 10.0 + - - -
288K LEU* 3.3 11.7 + - - -
289K PRO* 3.3 43.9 - - + +
292K TYR* 3.6 21.3 + - + +
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Residues in contact with CYS 240 (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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211K CYS* 2.0 47.3 - - + -
214K ILE* 4.5 3.1 - - - -
222K SER* 3.1 25.3 - - - -
223K GLU 3.1 7.0 + - - -
225K TYR* 3.6 28.9 - - + -
238K VAL* 3.7 9.6 - - - -
239K TYR* 1.3 77.6 - - - +
241K ASP* 1.3 61.8 + - - +
242K MET* 3.3 21.9 + - + +
249K TRP 3.1 4.0 - - - -
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Residues in contact with ASP 241 (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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222K SER* 3.3 6.9 + - - -
239K TYR* 3.9 8.8 + - + -
240K CYS* 1.3 69.2 - - - +
242K MET* 1.3 60.9 + - - +
243K ASN* 2.5 37.4 + - - +
244K THR* 2.4 41.1 + - - +
247K GLY* 3.6 0.9 - - - -
248K GLY 3.4 1.0 + - - -
249K TRP* 2.8 53.8 + - + +
251K VAL* 4.4 6.3 - - + +
453K LYS* 3.0 23.5 + - + +
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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