Contacts of the helix formed by residues 249 - 253 (chain X) in PDB entry 1T6B
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 PRO 249 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247X VAL 3.5 2.4 - - - +
248X SER* 1.3 86.3 - - - +
250X GLU* 1.3 71.6 + - - +
252X ARG* 3.1 32.4 + - - +
253X HIS* 4.3 0.9 + - - +
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Residues in contact with GLU 250 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248X SER* 3.7 11.1 - - - -
249X PRO* 1.3 94.3 - - - +
251X ALA* 1.3 57.8 + - - +
252X ARG 3.1 4.3 + - - -
253X HIS* 3.1 23.0 + - - +
256X VAL* 3.6 14.4 - - + +
371X THR* 4.6 1.3 - - + -
503X ARG* 2.7 41.1 + - - +
529X ILE 3.5 20.4 - - - +
530X ALA 3.8 18.0 - - - +
531X PHE 6.4 0.2 - - - -
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Residues in contact with ALA 251 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238X LYS* 3.3 28.8 + - - +
247X VAL* 3.9 7.2 - - + +
248X SER 2.9 11.8 + - - +
250X GLU* 1.3 75.8 - - - +
252X ARG* 1.3 56.7 + - - +
253X HIS 3.2 6.1 - - - -
256X VAL* 3.9 10.8 - - + -
257X ALA 3.8 12.6 - - - +
258X ALA* 3.8 13.2 - - + -
371X THR* 3.6 30.3 - - + -
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Residues in contact with ARG 252 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219X TYR* 5.2 1.1 - - - -
238X LYS* 3.3 43.8 - - - +
239X VAL* 3.9 8.3 - - - +
241X GLY* 4.9 7.2 + - - -
243X ILE* 3.8 26.6 + - + +
244X ASP 3.3 7.9 + - - -
245X LYS* 3.0 35.0 + - - +
247X VAL* 2.6 38.0 + - + +
248X SER 3.3 3.5 + - - +
249X PRO* 3.1 22.2 + - - +
250X GLU 3.1 1.6 - - - -
251X ALA* 1.3 77.9 - - - +
253X HIS* 1.3 59.9 + - - +
254X PRO 3.8 0.7 - - - -
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Residues in contact with HIS 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217X THR* 5.0 6.7 + - + -
218X LYS 4.6 8.8 + - - -
219X TYR* 3.6 33.1 - + + -
220X LYS 4.8 3.6 - - - -
238X LYS* 3.8 0.6 + - - -
249X PRO 4.3 0.8 + - - -
250X GLU* 3.1 15.2 + - - +
251X ALA 3.8 1.7 - - - +
252X ARG* 1.3 78.5 - - - +
254X PRO* 1.3 73.2 - - + +
255X LEU* 3.0 48.4 + - + +
256X VAL* 3.0 29.4 + - + +
525X GLU* 5.5 1.8 + - + +
529X ILE* 3.7 40.0 - - + +
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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