Contacts of the helix formed by residues 352 - 365 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A GLU* 4.1 6.5 - - - +
350A GLU* 2.5 23.1 + - - +
351A ALA* 1.3 76.5 - - - +
353A ALA* 1.3 57.1 + - - +
354A ASP* 3.5 8.5 + - - +
355A LEU* 3.0 23.4 + - - +
356A LEU* 2.7 36.8 + - - +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A GLU* 3.8 13.2 + - - +
254A ARG* 3.7 37.0 - - + +
255A ALA* 3.4 26.4 - - - +
352A THR* 1.3 73.6 - - - +
354A ASP* 1.3 56.8 + - - +
357A ARG* 2.8 36.4 + - - +
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Residues in contact with ASP 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A THR* 3.1 7.1 + - - +
353A ALA* 1.3 80.9 - - - +
355A LEU* 1.3 57.9 + - - +
357A ARG* 3.6 23.3 + - - +
358A GLU* 2.8 31.6 + - - +
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A ARG* 5.9 2.2 - - - +
346A LEU* 3.5 27.1 - - + -
350A GLU* 3.2 32.1 - - + +
352A THR* 3.0 20.2 + - - +
354A ASP* 1.3 75.1 - - - +
356A LEU* 1.3 58.2 + - - +
358A GLU* 4.3 18.8 - - - +
359A THR* 2.6 51.2 + - - +
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Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A PHE* 4.5 8.1 - - + -
251A GLU* 4.2 15.5 - - + +
252A CYS* 3.9 30.3 - - - -
255A ALA* 3.8 12.1 - - + -
256A PHE* 4.3 7.8 - - + -
303A VAL* 4.9 10.1 - - + -
322A ILE* 3.9 26.1 - - + +
324A VAL* 5.0 2.5 - - + -
346A LEU* 3.6 23.3 - - + +
351A ALA* 4.1 17.5 - - + +
352A THR 2.7 22.0 + - - +
355A LEU* 1.3 71.6 - - - +
357A ARG* 1.3 58.5 + - - +
359A THR* 3.7 3.3 - - - -
360A ALA* 2.9 30.7 + - - +
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Residues in contact with ARG 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ARG 5.7 0.6 + - - -
255A ALA* 3.8 15.4 + - - +
256A PHE* 4.5 4.7 - - - -
259A LEU* 3.7 39.7 - - + +
353A ALA* 2.8 20.0 + - - +
354A ASP* 3.6 32.4 + - - +
356A LEU* 1.3 76.1 - - - +
358A GLU* 1.3 63.8 + - - +
360A ALA* 3.2 7.1 + - + +
361A LEU* 2.9 48.6 + - + +
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Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ASP 2.8 23.5 + - - +
355A LEU* 3.8 18.3 - - + +
357A ARG* 1.3 74.9 - - - +
359A THR* 1.3 59.3 + - - +
361A LEU* 3.4 11.0 + - - +
362A ALA* 2.9 31.0 + - + +
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Residues in contact with THR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ILE* 3.8 23.3 - - + -
344A ARG* 3.5 47.9 + - + +
346A LEU* 4.6 4.5 - - + +
355A LEU* 2.6 40.0 + - - +
356A LEU* 3.7 3.8 - - - -
358A GLU* 1.3 74.4 - - - +
360A ALA* 1.3 64.9 + - - +
362A ALA* 3.1 7.8 + - + +
363A LEU* 3.0 26.4 + - + +
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Residues in contact with ALA 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A PHE* 3.5 21.3 - - + -
259A LEU* 6.2 0.2 - - + -
262A TRP* 3.8 8.3 - - + -
301A LEU* 3.4 30.5 - - + -
322A ILE* 3.9 3.3 - - + +
356A LEU 2.9 18.4 + - - +
357A ARG* 3.3 4.7 - - - +
359A THR* 1.3 76.8 - - - +
361A LEU* 1.3 62.8 + - + +
363A LEU* 3.2 1.9 + - - +
364A VAL* 3.1 28.8 + - - +
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU* 4.8 4.5 - - + -
262A TRP* 3.7 32.1 - - + +
357A ARG* 2.9 49.3 + - + +
358A GLU* 3.7 8.1 - - - +
360A ALA* 1.3 76.2 - - - +
362A ALA* 1.3 55.5 + - - +
363A LEU 3.2 1.2 + - - -
364A VAL* 3.6 5.3 + - + +
365A ASP* 2.6 43.1 + - - +
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Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A ARG* 6.2 1.6 - - - +
358A GLU* 2.9 21.7 + - + +
359A THR* 3.1 8.7 + - + +
361A LEU* 1.3 76.3 - - - +
363A LEU* 1.3 63.2 + - + +
365A ASP* 4.2 7.0 - - - +
366A ASP* 4.0 18.2 - - - +
369A VAL* 5.3 0.2 - - - +
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Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LEU* 4.2 7.6 - - + -
320A PRO* 4.2 13.0 - - + +
321A MET 3.3 28.9 - - - +
322A ILE* 3.9 18.4 - - + -
341A GLY 5.6 0.2 - - - +
342A VAL 4.7 1.1 - - - +
343A ALA* 4.4 21.3 - - - +
344A ARG* 4.2 6.3 - - + +
359A THR* 3.0 25.6 + - + +
360A ALA 3.2 3.1 + - - +
362A ALA* 1.3 81.4 - - + +
364A VAL* 1.3 65.7 + - - +
365A ASP 3.2 2.5 + - - -
366A ASP* 3.7 15.3 + - - +
369A VAL* 4.1 33.3 - - + +
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Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LYS* 4.5 29.7 + - + -
262A TRP* 3.6 33.7 - - + -
300A ASP* 3.5 30.5 - - + +
301A LEU* 3.8 15.0 - - + -
320A PRO* 4.9 4.0 - - - -
360A ALA 3.1 20.0 + - - +
361A LEU* 3.8 7.0 - - + +
363A LEU* 1.3 76.1 - - - +
365A ASP* 1.3 67.3 + - - +
366A ASP 3.5 3.0 + - - -
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Residues in contact with ASP 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LYS* 6.1 2.2 - - - +
361A LEU* 2.6 33.1 - - - +
362A ALA* 4.2 6.3 - - - +
363A LEU 3.2 0.8 - - - -
364A VAL* 1.3 84.4 - - + +
366A ASP* 1.3 59.3 + - - +
367A PRO* 4.4 4.5 - - - +
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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