Contacts of the helix formed by residues 383 - 393 (chain B) in PDB entry 3RL8
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 383 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B GLY* 4.1 1.1 - - - -
337B VAL* 3.8 27.8 - - + +
382B VAL* 1.3 79.8 - - - +
384B HIS* 1.3 65.5 + - - +
385B GLU* 3.6 9.3 + - - +
386B GLU* 2.9 45.8 + - - +
387B ALA* 3.1 19.2 + - - +
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Residues in contact with HIS 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ILE* 3.7 41.2 - - + +
334B ALA* 4.3 5.8 - - - -
335B GLY 3.2 27.3 + - - +
336B GLY* 3.9 6.0 - - - -
337B VAL 4.4 2.4 + - - -
339B ASN* 3.8 23.0 + - + +
348B ILE* 5.7 0.8 - - - +
383B THR* 1.3 72.5 - - - +
385B GLU* 1.3 58.6 + - - +
387B ALA* 3.2 7.1 + - - +
388B VAL* 2.9 46.0 + - + +
2841F THR* 3.6 20.5 + - - +
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Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B THR* 3.8 8.7 + - - +
384B HIS* 1.3 81.4 - - - +
386B GLU* 1.3 54.0 + - + +
388B VAL* 3.4 7.3 + - - +
389B THR* 2.8 40.7 + - - +
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LEU* 5.3 0.4 - - - -
382B VAL* 3.4 23.2 - - + +
383B THR* 2.9 46.0 + - - +
385B GLU* 1.3 72.7 - - + +
387B ALA* 1.3 60.8 + - - +
389B THR* 3.7 5.0 - - - -
390B ALA* 2.8 31.8 + - - +
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Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ILE* 4.3 9.2 - - + -
348B ILE* 3.5 33.4 - - + -
379B LEU* 4.0 17.2 - - + +
382B VAL* 4.0 6.6 - - + +
383B THR 3.1 9.9 + - - +
384B HIS 3.5 8.3 - - - +
386B GLU* 1.3 76.7 - - - +
388B VAL* 1.3 56.5 + - - +
390B ALA* 3.2 2.1 + - - +
391B LEU* 2.8 37.1 + - + +
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ILE* 4.1 11.4 - - + -
384B HIS* 2.9 46.5 + - + +
385B GLU* 3.7 7.0 - - - +
387B ALA* 1.3 74.9 - - - +
389B THR* 1.3 67.0 + - - +
391B LEU* 3.2 5.1 + - - +
392B LYS* 3.0 53.4 + - + +
2841F THR* 3.7 19.3 - - + -
2843F VAL* 4.8 3.1 - - + -
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Residues in contact with THR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B GLU* 2.8 26.5 + - - +
386B GLU* 3.8 5.2 - - - -
388B VAL* 1.3 79.3 - - - +
390B ALA* 1.3 62.2 + - - +
392B LYS* 4.9 1.8 - - - -
393B ASN* 3.0 56.3 + - - +
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Residues in contact with ALA 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B VAL* 4.0 15.0 - - + +
377B VAL* 3.8 31.7 - - + +
379B LEU* 4.1 6.5 - - + -
386B GLU 2.8 21.1 + - - +
387B ALA 3.7 4.0 - - - +
389B THR* 1.3 74.6 - - - +
391B LEU* 1.3 57.8 + - - +
392B LYS 3.6 0.2 + - - -
393B ASN* 3.8 5.2 + - - +
394B THR* 3.1 24.8 - - - +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B LYS* 3.6 5.4 + - - -
329B LEU* 4.1 16.5 - - + +
331B PHE* 4.1 13.5 - - + -
333B ILE* 3.9 25.6 - - + -
371B LEU* 3.9 20.4 - - + -
374B VAL* 3.9 31.0 - - + -
379B LEU* 4.6 6.1 - - + -
387B ALA* 2.8 24.2 + - + +
388B VAL 3.2 3.1 + - - +
390B ALA* 1.3 78.4 - - - +
392B LYS* 1.3 59.7 + - - +
394B THR* 3.5 16.3 + - - +
400B LEU* 4.0 15.7 - - + -
2843F VAL* 4.1 25.1 - - + +
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Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B LYS* 3.3 14.4 + - - +
388B VAL* 3.0 38.9 + - + +
389B THR* 4.9 0.7 - - - -
391B LEU* 1.3 77.3 - - - +
393B ASN* 1.3 66.4 + - - +
394B THR 3.0 12.3 + - - +
2841F THR* 5.8 3.1 - - - +
2842F SER 3.9 21.6 + - - -
2843F VAL* 4.3 16.6 - - + +
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Residues in contact with ASN 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B THR* 3.0 40.8 + - + +
390B ALA* 4.1 3.6 - - - +
391B LEU 3.6 0.2 - - - -
392B LYS* 1.3 80.9 - - - +
394B THR* 1.3 63.3 + - - +
338C GLY 4.2 10.1 - - - +
339C ASN* 5.8 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