Contacts of the strand formed by residues 236 - 241 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226H LEU* 3.1 9.3 - - - +
227H ILE* 3.1 38.8 + - + +
229H PRO* 3.2 39.2 - - + +
233H VAL* 4.3 10.8 - - + -
234H LYS* 3.4 28.0 - - - +
235H PRO* 1.3 77.0 - - - +
237H ARG* 1.3 74.8 + - - +
238H VAL* 4.3 8.3 - - + -
294H LEU* 4.7 8.3 - - + +
298H LYS* 4.0 55.5 + - + +
301H GLN* 4.6 5.0 + - - -
302H LEU* 5.0 4.5 - - - +
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Residues in contact with ARG 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H CYS 4.8 0.2 + - - -
203H ILE* 3.7 25.1 - - + +
224H MET* 3.2 43.1 - - + +
225H TYR 3.8 6.1 - - - +
226H LEU* 4.2 13.3 - - + +
236H TYR* 1.3 84.3 - - - +
238H VAL* 1.3 67.1 + - - +
276H VAL* 4.0 19.3 - - + +
294H LEU* 4.0 8.7 - - - +
298H LYS* 5.8 0.2 + - - -
141I ASP* 4.0 9.3 + - - -
143I VAL* 3.2 35.7 + - - +
144I GLN* 5.1 0.2 - - - +
145I ILE* 4.7 13.1 - - - +
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Residues in contact with VAL 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211H CYS* 3.6 20.6 - - - -
224H MET* 3.8 2.1 - - - +
225H TYR 2.9 26.5 + - - +
227H ILE* 4.0 27.6 - - + -
236H TYR* 4.3 4.9 - - + +
237H ARG* 1.3 76.2 - - - +
239H TYR* 1.3 70.1 + - - +
240H CYS* 4.3 1.1 - - - -
250H THR* 3.9 18.6 - - + -
251H VAL 4.1 4.7 - - - +
276H VAL* 3.6 12.0 - - - +
292H TYR* 4.4 0.7 - - - +
294H LEU* 3.7 33.7 - - + -
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Residues in contact with TYR 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211H CYS* 3.4 7.8 - - - -
222H SER* 3.4 18.4 + - - -
223H GLU* 3.6 28.3 - - - -
224H MET* 3.9 5.4 - - - +
238H VAL* 1.3 75.3 - - - +
240H CYS* 1.3 85.8 + - - +
241H ASP* 3.7 9.9 - - + -
251H VAL* 3.1 44.1 + - + -
276H VAL* 3.8 16.1 - - - +
277H ALA* 4.3 1.8 - - + -
287H GLY 2.7 23.3 + - - -
288H LEU 3.9 2.9 - - - -
289H PRO* 3.5 49.7 - - + +
292H TYR* 3.5 13.9 + - + +
453H LYS* 6.0 0.4 - - - -
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Residues in contact with CYS 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211H CYS* 2.0 50.7 - - + -
214H ILE* 4.8 1.8 - - - -
222H SER* 3.4 18.7 - - - -
223H GLU 3.4 11.2 + - - -
225H TYR* 3.6 32.8 - - + -
238H VAL* 4.3 0.2 - - - -
239H TYR* 1.3 80.3 - - - +
241H ASP* 1.3 60.4 + - - +
242H MET* 3.3 23.3 + - - +
249H TRP 3.1 8.7 - - - +
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Residues in contact with ASP 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H SER* 3.6 5.9 + - - -
239H TYR* 3.7 13.2 - - + -
240H CYS* 1.3 70.3 - - - +
242H MET* 1.3 59.0 + - - +
243H ASN* 2.6 34.7 + - - +
244H THR* 2.6 46.8 + - - +
247H GLY* 3.5 3.3 - - - -
248H GLY 3.4 2.1 + - - -
249H TRP* 3.2 36.0 + - + +
251H VAL* 4.4 2.9 - - + +
453H LYS* 3.1 29.4 + - - +
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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