Contacts of the helix formed by residues 345 - 351 (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 THR 345 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344X ARG* 1.3 80.1 + - - +
346X TRP* 1.3 66.2 + - - +
347X ALA* 4.3 7.2 - - + +
348X GLU* 2.8 35.6 + - - +
349X THR* 3.1 11.5 + - - -
440X LEU* 5.7 0.9 - - + -
443X GLU* 2.5 36.6 - - - +
660X TYR* 6.0 0.9 - - - -
709X ASN* 5.2 2.5 - - - +
710X PRO* 5.6 12.4 - - + +
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Residues in contact with TRP 346 (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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269X ILE* 6.2 0.2 - - + -
271X LEU* 3.6 30.5 - - + -
289X ILE* 3.5 34.0 - - + +
291X LYS* 4.1 19.0 - - + +
334X ILE* 3.9 30.1 - - + -
335X ASP 4.7 0.9 - - - -
343X GLU* 4.7 10.0 + - - -
344X ARG 4.9 2.9 - - - -
345X THR* 1.3 70.8 - - - +
347X ALA* 1.3 62.7 + - - +
349X THR* 3.2 6.7 + - - -
350X MET* 3.1 19.4 + - - +
439X PHE* 3.7 18.8 - + + -
442X LEU* 3.9 11.0 - - + -
443X GLU* 2.7 52.1 + - + +
446X LYS* 3.6 40.2 - - + +
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Residues in contact with ALA 347 (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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345X THR* 3.2 9.3 - - + -
346X TRP* 1.3 78.6 - - - +
348X GLU* 1.3 62.5 + - + +
350X MET 3.4 0.7 + - - -
351X GLY* 3.2 18.9 + - - -
352X LEU* 3.3 28.1 + - + +
436X TYR* 5.0 7.9 - - + +
439X PHE* 3.7 18.1 - - + -
440X LEU* 4.5 18.2 - - + -
443X GLU* 4.3 1.4 + - - +
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Residues in contact with GLU 348 (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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344X ARG* 3.4 30.4 + - + -
345X THR* 2.8 40.8 + - - +
347X ALA* 1.3 71.1 - - + +
349X THR* 1.3 64.5 + - - +
350X MET 3.2 0.7 + - - -
351X GLY* 3.4 10.5 + - - +
158Y TYR* 4.1 17.6 + - - +
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Residues in contact with THR 349 (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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288X THR 4.7 14.7 + - - +
289X ILE* 4.2 20.1 - - + +
340X LEU* 6.1 3.6 - - + -
343X GLU* 4.2 23.3 + - + +
344X ARG* 4.4 4.4 + - - +
345X THR 3.1 11.9 + - - -
346X TRP* 3.5 10.4 - - - -
348X GLU* 1.3 78.4 - - - +
350X MET* 1.3 59.4 + - - +
154Y LEU* 4.7 18.3 - - + +
158Y TYR* 4.7 5.5 + - - -
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Residues in contact with MET 350 (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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271X LEU 4.1 3.1 - - - +
272X SER* 3.6 20.0 - - - +
273X LYS* 3.2 39.8 - - + +
288X THR 4.6 15.4 + - - +
289X ILE* 3.4 25.1 - - + -
346X TRP 3.1 9.5 + - - +
347X ALA 3.9 3.6 - - - +
348X GLU 3.1 0.4 - - - -
349X THR* 1.3 80.8 - - - +
351X GLY* 1.3 59.2 + - - +
352X LEU* 3.3 38.8 - - + +
358X ALA* 4.3 4.3 - - + -
439X PHE* 3.6 25.6 - - - -
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Residues in contact with GLY 351 (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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273X LYS* 3.1 23.3 + - - -
347X ALA 3.2 6.5 + - - -
348X GLU* 3.4 8.2 + - - -
350X MET* 1.3 77.4 - - - +
352X LEU* 1.3 62.5 + - - +
353X ASN* 3.3 5.2 + - - +
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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