Contacts of the helix formed by residues 342 - 348 (chain f) in PDB entry 5T0J
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 LEU 342 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338f VAL 4.0 10.6 + - - +
339f LEU 3.7 5.3 + - - +
340f THR 3.4 0.2 - - - -
341f LEU* 1.3 77.6 - - - +
343f LEU* 1.3 64.0 + - - +
344f PRO 3.5 0.4 - - - -
345f VAL* 3.3 28.2 - - + +
346f MET* 3.8 26.7 + - + +
363f CYS* 4.0 28.5 - - + -
378f THR* 3.7 26.0 - - + +
379f ILE* 5.0 3.4 - - + -
382f THR* 3.5 34.3 - - + +
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Residues in contact with LEU 343 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339f LEU 4.0 4.6 + - - +
340f THR* 3.5 28.6 + - + +
342f LEU* 1.3 77.4 - - - +
344f PRO* 1.3 77.2 - - + +
345f VAL 3.1 1.0 + - - -
346f MET* 3.7 9.0 + - + +
347f GLY* 3.2 18.8 + - - -
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Residues in contact with PRO 344 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319f ARG* 4.9 10.3 - - - +
323f ILE* 5.8 2.9 - - + -
326f LEU* 5.2 11.4 - - + -
340f THR 3.3 16.4 - - - +
341f LEU 3.4 11.0 - - - +
343f LEU* 1.3 98.6 - - + +
345f VAL* 1.3 62.8 + - - +
347f GLY* 3.7 4.7 - - - +
348f ASP* 3.1 25.0 + - + +
359f THR* 3.4 24.1 - - + +
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Residues in contact with VAL 345 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342f LEU* 3.3 33.4 - - + +
343f LEU 3.1 0.8 - - - -
344f PRO* 1.3 81.2 - - - +
346f MET* 1.3 62.8 + - - +
348f ASP 3.3 14.4 - - - +
356f ALA* 4.1 7.9 - - - +
359f THR* 3.3 39.2 + - - +
360f ALA* 3.7 12.6 - - + -
363f CYS* 5.8 1.1 - - + -
382f THR* 3.7 11.4 - - + -
386f LYS* 3.4 40.9 - - + +
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Residues in contact with MET 346 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342f LEU* 3.8 29.4 - - + +
343f LEU* 3.9 11.2 - - + +
345f VAL* 1.3 80.5 - - + +
347f GLY* 1.3 61.9 + - - +
348f ASP 3.4 4.0 + - - +
382f THR* 5.0 9.6 - - + +
385f GLU* 4.8 21.6 - - + +
386f LYS* 6.3 0.7 - - - -
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Residues in contact with GLY 347 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343f LEU* 3.2 18.6 + - - -
344f PRO* 3.9 3.4 - - - -
345f VAL 3.2 1.2 - - - -
346f MET* 1.3 80.0 - - - +
348f ASP* 1.3 57.9 + - - +
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Residues in contact with ASP 348 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314f ASN* 4.4 3.9 + - - +
319f ARG* 2.5 40.4 + - - +
344f PRO* 3.1 18.4 + - + +
345f VAL 3.3 12.3 - - - +
346f MET* 4.3 3.7 - - - +
347f GLY* 1.3 79.2 - - - +
349f SER 3.1 23.1 - - - +
350f LYS 4.2 2.4 - - - +
355f VAL* 3.5 22.9 - - - +
356f ALA* 3.4 19.4 - - + +
359f THR* 5.3 0.4 - - + -
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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