Contacts of the helix formed by residues 352 - 364 (chain B) in PDB entry 4M83
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 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B GLU* 3.5 14.1 - - + +
349B GLU 4.7 4.0 - - - +
350B GLU* 3.6 20.4 + - + -
351B ALA* 1.3 77.7 - - - +
353B ALA* 1.3 67.4 + - - +
354B ASP* 3.0 8.1 + - - +
355B LEU* 3.1 19.5 + - - +
356B LEU* 2.9 25.1 + - - +
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Residues in contact with ALA 353 (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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251B GLU* 3.0 28.5 + - - +
254B ARG* 3.9 21.3 - - + +
255B ALA* 3.4 25.1 - - - +
352B THR* 1.3 71.4 - - - +
354B ASP* 1.3 62.9 + - - +
357B ARG* 3.0 30.5 + - - +
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Residues in contact with ASP 354 (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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352B THR* 3.2 6.4 + - - +
353B ALA* 1.3 78.7 + - - +
355B LEU* 1.3 60.3 + - - +
357B ARG* 3.1 7.5 + - - +
358B GLU* 2.7 40.7 + - + +
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Residues in contact with LEU 355 (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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344B ARG* 6.2 0.4 - - + -
346B LEU* 3.8 30.5 - - + +
350B GLU* 3.4 29.8 - - - +
352B THR* 3.1 18.6 + - - +
354B ASP* 1.3 77.4 - - - +
356B LEU* 1.3 58.2 + - - +
358B GLU* 4.6 16.2 - - - +
359B THR* 2.3 44.6 + - - +
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Residues in contact with LEU 356 (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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248B PHE* 4.0 18.4 - - + -
251B GLU 3.9 23.1 - - - +
252B CYS* 4.3 6.5 - - - -
255B ALA* 3.9 12.6 - - + -
256B PHE* 4.6 7.4 - - + -
303B VAL* 5.0 4.5 - - + -
322B ILE* 3.7 24.8 - - + +
324B VAL* 4.8 2.0 - - + -
346B LEU* 4.0 13.7 - - + -
351B ALA* 3.5 43.7 - - + +
352B THR 2.9 16.6 + - - +
355B LEU* 1.3 78.6 - - - +
357B ARG* 1.3 57.2 + - - +
359B THR* 3.5 5.1 - - - -
360B ALA* 3.0 26.9 + - - +
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Residues in contact with ARG 357 (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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254B ARG 5.2 2.0 - - - -
255B ALA* 3.2 27.5 - - - +
256B PHE* 4.8 2.5 - - + -
259B LEU* 4.0 30.7 - - + +
353B ALA 3.0 20.4 + - - +
354B ASP* 3.1 8.2 + - - +
356B LEU* 1.3 72.7 - - - +
358B GLU* 1.3 62.1 + - - +
360B ALA* 2.9 27.5 + - - +
361B LEU* 3.1 18.9 + - + +
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Residues in contact with GLU 358 (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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354B ASP* 2.7 22.6 + - + +
355B LEU* 4.3 15.7 - - - +
357B ARG* 1.3 73.7 - - - +
359B THR* 1.3 68.6 + - - +
360B ALA 3.1 0.9 + - - -
361B LEU* 3.4 7.5 + - - +
362B ALA* 3.1 29.3 + - + +
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Residues in contact with THR 359 (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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322B ILE* 3.9 13.2 - - + -
344B ARG* 4.1 23.8 - - + +
346B LEU* 4.7 3.0 - - + +
355B LEU* 2.3 39.7 + - - +
356B LEU* 3.5 5.6 - - - -
358B GLU* 1.3 81.1 + - - +
360B ALA* 1.3 56.6 + - - +
362B ALA* 3.8 4.7 - - - +
363B LEU* 2.9 53.8 + - + +
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Residues in contact with ALA 360 (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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256B PHE* 3.6 17.5 - - + -
262B TRP* 3.7 10.8 - - + -
301B LEU* 3.4 30.7 - - + -
322B ILE* 4.6 0.9 - - - -
356B LEU 3.0 12.7 + - - +
357B ARG 2.9 13.3 + - - +
359B THR* 1.3 72.3 - - - +
361B LEU* 1.3 66.5 + - + +
362B ALA 3.1 1.3 - - - -
363B LEU* 3.1 2.5 + - - +
364B VAL* 3.0 29.5 + - - +
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Residues in contact with LEU 361 (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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259B LEU* 3.7 25.8 - - + -
262B TRP* 3.5 25.1 - - + +
357B ARG* 3.1 27.0 + - + +
358B GLU* 4.1 7.4 - - - +
360B ALA* 1.3 77.8 - - - +
362B ALA* 1.3 60.1 - - - +
364B VAL* 3.5 18.7 - - - +
365B ASP* 3.6 20.4 + - - +
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Residues in contact with ALA 362 (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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358B GLU* 3.1 21.6 + - + +
359B THR* 4.1 4.9 - - - +
360B ALA 3.1 1.2 - - - -
361B LEU* 1.3 75.2 - - + +
363B LEU* 1.3 62.1 + - - +
365B ASP* 4.2 2.8 - - - +
366B ASP* 3.8 19.1 + - - +
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Residues in contact with LEU 363 (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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301B LEU* 4.1 15.3 - - + -
320B PRO* 4.6 8.5 - - + +
321B MET 3.7 22.0 - - - +
322B ILE* 3.9 11.0 - - + -
343B ALA* 4.7 14.8 - - - +
344B ARG* 4.6 4.7 - - + +
359B THR* 2.9 41.0 + - + +
360B ALA 3.7 2.7 - - - +
362B ALA* 1.3 77.6 - - - +
364B VAL* 1.3 62.4 + - - +
365B ASP 3.1 5.4 + - - -
366B ASP* 3.3 18.4 + - - +
369B VAL* 4.2 35.9 - - + +
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Residues in contact with VAL 364 (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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232B LYS* 3.5 40.1 - - + -
262B TRP* 4.2 8.1 - - + -
300B ASP* 3.4 29.6 - - + +
301B LEU* 4.1 15.5 - - + -
320B PRO* 5.0 4.9 - - + -
360B ALA 3.0 23.7 + - - +
361B LEU* 3.5 14.6 - - - +
363B LEU* 1.3 75.8 - - - +
365B ASP* 1.3 70.5 + - - +
366B ASP 3.5 1.2 - - - +
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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