Contacts of the helix formed by residues 350 - 369 (chain A) in PDB entry 4D2Y
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 350 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A LYS* 1.3 58.5 + - - +
352A ASP* 3.4 9.1 + - - +
353A GLN* 2.4 69.3 + - - +
354A LEU* 2.9 31.5 + - - +
392A SER 5.5 3.6 - - - -
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A THR* 1.3 74.4 - - - +
352A ASP* 1.3 68.8 + - - +
354A LEU* 3.5 1.5 + - - -
355A PHE* 3.5 20.6 + - - +
388A ILE* 3.5 24.7 + - + +
389A GLU* 2.4 42.9 + - - +
390A SER 4.1 4.9 + - - -
391A THR 4.9 0.2 - - - -
392A SER* 3.5 42.7 + - - +
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Residues in contact with ASP 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A THR* 3.2 7.3 + - - +
351A LYS* 1.3 84.0 + - - +
353A GLN* 1.3 64.8 + - - +
354A LEU 3.2 0.4 - - - -
355A PHE* 5.9 0.2 - - - -
356A PRO* 3.1 21.0 - - - +
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Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A THR* 2.4 58.5 + - - +
352A ASP* 1.3 77.7 - - + +
354A LEU* 1.3 63.2 + - - +
356A PRO* 3.4 10.3 - - - +
357A LEU* 3.2 28.1 - - + +
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A THR 2.9 17.4 + - - +
351A LYS* 3.9 5.8 - - - +
352A ASP 3.2 0.6 - - - -
353A GLN* 1.3 76.3 - - - +
355A PHE* 1.3 62.0 + - - +
357A LEU* 3.0 9.1 + - + +
358A ALA* 2.9 23.9 + - - +
388A ILE* 3.9 14.8 - - + -
392A SER 3.8 9.9 - - - +
393A THR* 3.7 30.7 - - - -
394A TYR* 4.0 14.4 - - + -
575A GLY 3.7 20.2 - - - +
576A GLY* 3.7 23.1 - - - +
577A LEU* 4.2 7.4 - - + +
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Residues in contact with PHE 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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351A LYS 3.5 10.8 + - - +
352A ASP* 5.9 0.2 - - - -
354A LEU* 1.3 77.7 - - - +
356A PRO* 1.3 66.4 - - + +
358A ALA* 4.2 6.5 - - + -
359A LYS* 2.8 45.9 + - + +
381A LEU* 3.6 33.7 - - + -
384A VAL* 4.5 5.6 - - + -
385A ASN* 3.1 56.1 - - + +
388A ILE* 3.7 26.4 - - + +
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Residues in contact with PRO 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ASP 3.1 20.4 - - - +
353A GLN* 3.4 15.5 - - - +
355A PHE* 1.3 96.1 - - + +
357A LEU* 1.3 57.8 + - + +
359A LYS* 3.6 8.2 - - + +
360A GLU* 2.9 29.8 + - - +
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A THR* 5.9 4.5 - - + -
353A GLN* 3.2 26.7 - - + +
354A LEU* 3.0 9.9 + - + +
356A PRO* 1.3 76.7 - - + +
358A ALA* 1.3 65.9 + - - +
360A GLU* 3.4 20.7 + - - +
361A PHE* 3.2 22.3 + - - +
573A GLU* 4.7 14.1 - - - +
575A GLY* 3.7 6.0 - - - -
576A GLY* 3.7 29.6 - - - +
701A THR* 5.6 4.3 - - + -
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Residues in contact with ALA 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 LEU 2.9 12.2 + - - +
355A PHE* 3.3 9.6 + - + +
357A LEU* 1.3 75.4 - - - +
359A LYS* 1.3 57.2 + - - +
361A PHE* 3.1 3.8 + - - +
362A LEU* 2.9 36.7 + - + +
384A VAL* 3.9 17.9 - - + -
388A ILE* 4.2 4.9 - - + -
394A TYR* 3.7 38.4 - - + +
575A GLY* 3.7 2.1 + - - -
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Residues in contact with LYS 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 2.8 37.5 + - + +
356A PRO* 3.6 9.0 - - + +
358A ALA* 1.3 76.6 - - - +
360A GLU* 1.3 63.1 + - - +
362A LEU* 3.3 0.3 + - - +
363A ASP* 2.9 52.2 + - - +
381A LEU* 4.0 32.5 - - + -
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Residues in contact with GLU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LYS 5.0 5.9 - - - +
321A THR* 4.4 15.3 + - - +
356A PRO 2.9 18.5 + - - +
357A LEU* 3.7 21.3 - - - +
359A LYS* 1.3 73.9 - - - +
361A PHE* 1.3 64.1 + - - +
363A ASP* 3.7 7.6 - - - +
364A GLN* 3.2 35.2 + - - +
701A THR* 3.2 32.8 + - - +
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Residues in contact with PHE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU 3.2 2.5 + - - +
358A ALA 3.1 8.1 + - - +
360A GLU* 1.3 81.0 - - - +
362A LEU* 1.3 74.7 + - + +
364A GLN* 3.1 11.9 - - + +
365A TYR* 2.8 29.1 + - + +
394A TYR* 4.8 1.3 - - - -
396A LEU* 3.9 15.3 - - + -
400A GLU* 3.3 45.1 - - + -
403A TYR* 3.5 31.0 - + - -
404A GLY* 3.9 1.6 - - - -
574A ILE* 3.6 17.9 - - + -
575A GLY* 3.6 28.3 - - - +
701A THR* 6.4 2.2 - - + -
702A PRO* 3.9 25.1 - - + -
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 5.8 0.2 - - + -
358A ALA* 2.9 27.0 + - + +
361A PHE* 1.3 84.4 - - + +
363A ASP* 1.3 58.1 + - - +
365A TYR* 4.1 2.9 - - + -
366A TYR* 2.7 49.8 + - + +
377A HIS* 4.1 2.5 - - - +
380A ARG* 4.3 12.8 - - + +
381A LEU* 3.7 29.2 - - + -
384A VAL* 3.8 33.2 - - + -
394A TYR* 5.4 2.5 - - + +
396A LEU* 5.6 1.3 - - + -
400A GLU* 3.6 33.7 - - + +
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Residues in contact with ASP 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LYS* 2.9 52.6 + - - +
360A GLU* 3.7 7.4 + - - +
362A LEU* 1.3 77.0 - - - +
364A GLN* 1.3 56.8 + - - +
366A TYR* 3.8 0.3 - - - -
367A SER* 2.9 30.6 + - - -
372A PHE* 3.6 21.2 - - + -
377A HIS* 2.8 30.5 + - - -
381A LEU* 4.0 10.6 - - - +
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Residues in contact with GLN 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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360A GLU* 3.2 26.2 + - - +
361A PHE* 3.1 22.5 - - - +
363A ASP* 1.3 76.0 - - - +
365A TYR* 1.3 60.6 + - - +
367A SER* 3.6 7.2 + - - -
368A SER* 2.8 31.2 + - - -
403A TYR* 3.4 24.8 + - + +
407A HIS* 4.8 6.5 - - - -
669A ARG* 5.3 5.1 - - - +
701A THR* 3.5 16.3 + - - +
702A PRO* 3.8 21.8 - - - +
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Residues in contact with TYR 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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361A PHE* 2.8 23.2 + - + +
362A LEU* 3.6 6.7 - - + +
364A GLN* 1.3 77.1 - - - +
366A TYR* 1.3 86.6 + + - +
368A SER* 2.5 28.2 + - - -
369A ILE* 3.3 41.5 + - + +
399A THR* 3.1 45.3 + - - +
400A GLU* 3.9 21.8 - - + -
403A TYR* 3.6 37.5 - + + -
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Residues in contact with TYR 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU* 2.7 34.9 + - + +
363A ASP 4.2 0.7 - - - +
365A TYR* 1.3 90.8 - + - +
367A SER* 1.3 61.2 + - - +
369A ILE* 3.4 27.7 - - + +
371A ARG* 2.8 43.0 + - + +
372A PHE 3.1 2.9 + - - -
376A ALA* 3.6 15.7 + - + +
377A HIS* 3.6 50.9 - + + +
380A ARG* 3.3 43.1 - - + +
400A GLU* 4.6 2.9 + - - -
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Residues in contact with SER 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ASP 2.9 19.6 + - - -
364A GLN* 3.6 8.7 - - - -
366A TYR* 1.3 76.5 - - - +
368A SER* 1.3 63.4 + - - +
370A LYS* 3.2 14.4 + - - +
372A PHE* 3.9 24.8 - - - +
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLN 2.8 15.1 + - - -
365A TYR 2.5 18.4 + - - -
367A SER* 1.3 78.9 + - - +
369A ILE* 1.3 63.2 + - - +
370A LYS* 3.4 8.3 + - - +
403A TYR* 3.1 33.7 - - - -
407A HIS* 5.5 1.1 - - - -
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Residues in contact with ILE 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TYR* 3.8 38.4 - - + +
366A TYR* 3.4 38.6 - - + +
367A SER 3.2 0.2 - - - -
368A SER* 1.3 87.7 + - - +
370A LYS* 1.3 80.2 + - - +
371A ARG* 3.8 26.4 + - + -
403A TYR* 6.1 0.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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