Contacts of the helix formed by residues 294 - 302 (chain M) in PDB entry 3J8B
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 PHE 294 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292M ILE 3.5 2.3 + - - -
293M SER* 1.3 71.6 - - - +
295M ASP* 1.3 63.9 + - - +
297M MET* 3.3 7.6 + - - +
298M GLN* 2.9 25.0 + - - +
305M ALA* 5.6 11.1 - - + +
308M VAL* 5.7 6.9 - - + +
330M ARG* 2.9 36.1 + - + +
331M LYS* 4.2 1.3 - - - +
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Residues in contact with ASP 295 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293M SER* 3.2 5.2 - - - -
294M PHE* 1.3 78.8 - - - +
296M THR* 1.3 62.2 - - - +
298M GLN* 3.4 6.4 + - - +
299M GLN* 3.2 21.7 + - - +
330M ARG* 5.9 0.2 - - - +
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Residues in contact with THR 296 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292M ILE* 6.0 1.6 - - - -
293M SER* 3.2 21.6 + - - -
295M ASP* 1.3 75.6 - - - +
297M MET* 1.3 65.6 + - - +
299M GLN* 3.3 6.2 + - - +
300M GLU* 3.0 24.5 + - - +
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Residues in contact with MET 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292M ILE* 5.6 7.1 - - + +
293M SER 3.1 10.2 + - - +
294M PHE* 3.6 11.2 - - - +
296M THR* 1.3 80.2 - - - +
298M GLN* 1.3 50.5 + - - +
300M GLU* 3.9 4.7 - - - +
301M LEU* 2.3 46.3 + - + +
308M VAL* 5.8 6.7 - - + -
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Residues in contact with GLN 298 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294M PHE 2.9 16.7 + - - +
295M ASP* 3.8 7.4 - - - +
297M MET* 1.3 75.6 - - - +
299M GLN* 1.3 54.2 + - - +
301M LEU* 3.7 6.3 - - - -
302M GLN* 2.4 36.4 + - - -
303M ILE 3.3 19.7 + - - +
305M ALA* 5.0 14.6 - - + +
308M VAL* 5.6 4.4 - - + +
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Residues in contact with GLN 299 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295M ASP 3.2 11.0 + - - +
296M THR* 3.8 8.5 - - - +
298M GLN* 1.3 77.7 - - - +
300M GLU* 1.3 65.3 + - - +
302M GLN* 3.4 10.5 + - - +
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Residues in contact with GLU 300 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249M LEU* 4.1 20.3 - - - +
250M ALA* 5.3 4.6 + - - -
278M ARG* 6.1 0.5 - - - +
281M THR* 5.3 14.0 - - - -
296M THR 3.0 16.1 + - - +
297M MET* 3.9 4.5 - - - +
299M GLN* 1.3 78.4 - - - +
301M LEU* 1.3 62.1 + - - +
302M GLN* 4.4 2.1 - - - +
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Residues in contact with LEU 301 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278M ARG* 5.4 11.5 - - - +
297M MET* 2.3 41.3 + - + +
298M GLN* 3.6 6.1 - - - +
300M GLU* 1.3 69.2 - - - +
302M GLN* 1.3 70.7 + - - +
303M ILE* 3.3 17.3 + - + +
308M VAL* 5.9 4.9 - - + -
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Residues in contact with GLN 302 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249M LEU* 6.4 0.7 - - + -
298M GLN 2.4 23.9 + - - -
299M GLN* 3.4 9.1 + - - +
300M GLU 3.3 4.3 - - - +
301M LEU* 1.3 73.7 - - - +
303M ILE* 1.3 55.2 + - - +
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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