Contacts of the strand formed by residues 229 - 233 (chain C) in PDB entry 1TYG
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 229 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ILE* 3.6 18.8 - - + -
199C VAL* 3.6 12.6 - - + -
219C SER* 3.4 27.1 - - - +
222C LEU* 4.0 20.4 - - + -
223C LEU* 3.8 27.4 - - + -
227C PHE* 4.0 7.4 - - + +
228C ILE* 1.3 73.9 - - - +
230C LEU* 1.3 74.1 + - - +
231C PRO* 3.7 2.9 - - + -
248C VAL* 3.7 16.2 - - + +
249C HIS* 3.7 26.3 + - + -
250C ALA 4.0 1.9 - - - +
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Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ILE* 3.6 27.6 - - + -
116C LEU* 5.0 2.7 - - + -
169C LEU* 4.1 9.2 - - + -
196C MET* 3.7 26.7 - - + -
197C ILE 2.7 18.9 + - - +
198C LYS* 3.2 14.6 - - - +
199C VAL 3.1 16.2 + - - -
228C ILE* 4.0 10.8 - - + +
229C VAL* 1.3 80.7 - - - +
231C PRO* 1.3 67.6 - - - +
249C HIS 5.0 0.4 - - - +
250C ALA* 3.3 24.9 - - + +
252C MET* 3.5 32.3 - - + +
282C ILE* 4.8 5.4 - - + -
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Residues in contact with PRO 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C VAL* 3.3 23.5 - - + +
215C THR* 4.1 7.4 - - + -
219C SER* 3.8 11.2 - - - +
229C VAL* 3.7 12.3 - - + -
230C LEU* 1.3 86.3 - - - +
232C TYR* 1.3 55.0 + - - +
233C THR* 3.9 0.6 + - - -
243C LEU* 3.6 32.5 - - + -
248C VAL* 3.8 13.0 - - + -
250C ALA 3.6 11.4 - - - +
251C ILE* 4.4 5.4 - - + -
252C MET* 2.6 39.6 + - - +
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Residues in contact with TYR 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C LYS* 4.1 11.4 - - - -
199C VAL 2.4 23.6 + - - +
200C GLU* 3.7 27.9 - - + -
201C VAL 5.9 0.2 - - - -
202C ILE* 6.1 0.4 - - + -
208C LEU 4.0 4.9 + - - -
209C LEU* 3.4 22.6 - - + +
210C PRO* 3.1 32.5 - - + +
215C THR* 3.2 21.4 - - - +
231C PRO* 1.3 71.4 - - - +
233C THR* 1.3 80.6 + - - +
252C MET* 3.3 7.2 - - - -
254C GLY* 4.2 9.4 - - - -
256C SER 4.0 1.7 + - - -
258C ILE* 3.6 31.7 + - + +
284C ASP* 3.7 15.9 - - - +
285C ALA* 3.2 24.2 - - + +
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Residues in contact with THR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C PRO* 3.5 9.8 - - - +
215C THR* 5.3 2.3 - - - +
231C PRO 3.9 0.9 + - - -
232C TYR* 1.3 95.9 + - - +
234C SER* 1.3 73.0 + - - +
235C ASP* 4.3 2.0 - - - +
239C LEU* 3.1 29.1 - - - +
240C ALA* 4.6 20.9 - - + +
243C LEU* 3.5 26.9 - - + +
251C ILE* 4.7 5.2 - - + -
252C MET 3.0 10.3 + - - -
253C PRO* 3.9 19.3 - - + -
254C GLY* 3.2 10.3 + - - -
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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