Contacts of the helix formed by residues 357 - 372 (chain B) in PDB entry 2A72
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 SER 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348B LEU* 4.1 9.4 - - - -
351B LEU* 3.7 23.6 - - - -
352B GLU* 3.2 30.2 + - - -
355B PHE* 3.7 1.7 - - - -
356B SER* 1.3 74.9 + - - +
358B GLU* 1.3 59.6 + - - +
359B ASN 3.3 2.8 + - - -
360B LEU* 3.3 3.8 + - - +
361B ARG* 2.8 53.1 + - - +
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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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356B SER 3.4 2.6 - - - -
357B SER* 1.3 78.3 + - - +
359B ASN* 1.3 54.5 + - - +
361B ARG* 3.7 19.4 - - - +
362B PHE* 2.8 36.0 + - - +
388B PHE* 3.7 3.9 - - - -
395B SER* 3.7 25.4 - - - +
396B ALA 4.0 8.5 - - - +
397B ILE* 3.9 9.2 - - + -
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Residues in contact with ASN 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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426A ILE* 3.4 36.6 - - + +
429A LEU* 3.5 32.3 - - - +
430A MET* 4.0 12.4 - - + +
433A ASP* 5.0 6.7 + - - +
434A SER* 4.6 9.8 + - - +
356B SER 4.7 3.5 + - - +
357B SER 3.3 0.6 - - - -
358B GLU* 1.3 77.2 - - - +
360B LEU* 1.3 57.3 + - - +
362B PHE* 3.3 2.1 + - - +
363B TRP* 3.0 23.9 + - - +
397B ILE* 3.4 23.6 - - - +
398B ASN 4.8 2.3 + - - +
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Residues in contact with LEU 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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430A MET* 3.6 28.9 - - + -
434A SER* 5.4 0.4 + - - -
338B LEU* 3.8 25.8 - - + -
344B ARG* 4.9 2.9 - - + +
347B PHE* 3.9 20.6 - - + -
348B LEU* 3.9 28.3 - - + +
351B LEU* 3.7 31.5 - - + +
356B SER 5.5 0.2 + - - -
357B SER 3.3 5.3 + - - +
359B ASN* 1.3 77.2 - - - +
361B ARG* 1.3 57.8 + - - +
363B TRP* 3.1 11.7 + - + +
364B LEU* 2.8 46.0 + - + +
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Residues in contact with ARG 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 3.8 19.7 - - + -
352B GLU* 4.2 17.5 + - - -
357B SER* 2.8 39.4 + - - +
358B GLU* 3.8 14.2 - - - +
360B LEU* 1.3 72.3 - - - +
362B PHE* 1.3 57.2 + - - +
364B LEU* 3.8 8.9 - - + +
365B ALA* 2.9 28.6 + - - +
387B GLU* 4.2 3.8 + - - +
388B PHE* 3.7 14.5 - - + -
394B PRO 5.5 0.2 + - - -
395B SER* 3.0 40.2 + - - +
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Residues in contact with PHE 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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419A PHE* 4.0 10.1 - + + -
422A ALA* 4.0 19.3 - - + -
423A GLN* 4.0 23.3 - - - -
426A ILE* 3.9 17.3 - - + -
358B GLU 2.8 22.7 + - - +
359B ASN 3.6 2.9 - - - +
361B ARG* 1.3 71.8 - - - +
363B TRP* 1.3 67.0 + - - +
365B ALA* 3.2 2.4 + - - +
366B VAL* 3.1 45.4 + - + +
384B ILE* 3.9 11.2 - - + -
388B PHE* 3.5 39.4 - + + -
389B LEU* 3.8 19.7 - - + -
397B ILE* 3.7 24.5 - - + -
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Residues in contact with TRP 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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423A GLN* 3.4 49.4 + - + +
426A ILE* 4.5 3.1 - - + -
427A TYR* 3.7 31.5 - + + +
430A MET* 3.8 19.1 - - + -
338B LEU* 4.0 27.4 - - + -
344B ARG* 4.2 17.3 - - - -
359B ASN 3.0 13.6 + - - +
360B LEU* 3.1 14.8 + - + +
362B PHE* 1.3 82.7 - - - +
364B LEU* 1.3 88.8 + - + +
366B VAL 3.4 0.5 + - - -
367B GLU* 3.1 47.7 + - + +
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Residues in contact with LEU 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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338B LEU* 5.4 0.2 - - + -
344B ARG* 3.6 41.7 - - + +
348B LEU* 4.6 20.0 - - + -
360B LEU* 2.8 43.0 + - + +
361B ARG* 3.8 9.2 - - + +
363B TRP* 1.3 93.6 - - + +
365B ALA* 1.3 63.4 + - - +
367B GLU* 3.4 4.8 + - + +
368B ASP* 3.0 23.6 + - - +
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Residues in contact with ALA 365 (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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361B ARG 2.9 17.8 + - - +
362B PHE 3.2 5.1 + - - +
364B LEU* 1.3 78.2 - - - +
366B VAL* 1.3 58.3 + - - +
368B ASP* 3.5 8.8 + - - +
369B LEU 3.0 20.8 + - - -
384B ILE* 3.5 25.3 - - + +
388B PHE* 3.8 21.8 - - + -
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Residues in contact with VAL 366 (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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416A ARG 5.5 2.0 - - - +
419A PHE* 3.8 32.3 - - + +
420A GLU* 5.8 0.4 - - - -
423A GLN* 3.5 31.9 - - + +
362B PHE* 3.1 49.9 + - + +
363B TRP 3.8 0.2 - - - +
364B LEU 3.3 0.2 - - - -
365B ALA* 1.3 74.2 - - - +
367B GLU* 1.3 64.8 + - - +
369B LEU* 3.1 19.7 + - + +
370B LYS* 3.2 22.4 + - + +
384B ILE* 4.5 4.0 - - + -
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLN* 2.7 22.5 + - - +
344B ARG* 6.0 2.7 - - - +
363B TRP* 3.1 49.2 + - + +
364B LEU* 3.6 12.1 - - + +
366B VAL* 1.3 76.0 - - - +
368B ASP* 1.3 62.3 + - - +
370B LYS* 2.8 43.4 + - - +
371B LYS* 3.7 16.6 + - - +
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Residues in contact with ASP 368 (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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364B LEU 3.0 14.6 + - - +
365B ALA* 3.5 11.3 - - - +
367B GLU* 1.3 74.4 - - - +
369B LEU* 1.3 64.6 + - - +
371B LYS* 3.0 43.5 + - - +
372B ARG* 2.8 51.5 + - - +
380B ARG* 3.9 10.2 + - - -
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Residues in contact with LEU 369 (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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415A GLY 4.3 2.0 - - - +
416A ARG* 3.0 45.5 + - - +
419A PHE* 3.8 30.7 - - + -
365B ALA 3.0 15.6 + - - +
366B VAL* 3.1 13.8 + - + +
368B ASP* 1.3 75.4 + - - +
370B LYS* 1.3 58.8 + - - +
371B LYS 3.1 1.0 + - - -
372B ARG* 3.2 11.4 + - + +
377B VAL* 4.3 14.6 - - + +
380B ARG* 3.9 31.0 - - + +
381B VAL* 3.9 25.4 - - + +
384B ILE* 3.9 7.0 - - + -
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Residues in contact with LYS 370 (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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416A ARG* 3.3 43.0 + - + +
417A TYR* 4.6 27.8 - - + +
420A GLU* 6.5 1.1 - - - +
423A GLN* 3.1 23.1 + - - -
366B VAL* 3.2 16.4 + - + +
367B GLU* 2.8 37.7 + - - +
368B ASP 3.2 0.4 - - - -
369B LEU* 1.3 76.3 - - - +
371B LYS* 1.3 57.7 + - - +
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Residues in contact with LYS 371 (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* 6.0 1.8 - - - +
367B GLU* 3.7 18.9 + - - +
368B ASP* 3.0 44.3 + - - +
370B LYS* 1.3 78.6 - - - +
372B ARG* 1.3 75.1 + - - +
373B PRO* 3.8 2.1 - - - +
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Residues in contact with ARG 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ARG* 2.8 27.8 + - - +
368B ASP* 2.8 49.9 + - - +
369B LEU* 3.2 13.1 + - + +
371B LYS* 1.3 87.6 - - - +
373B PRO* 1.3 77.3 - - + +
376B GLU* 4.1 9.0 + - + -
377B VAL* 5.1 4.0 - - + -
380B ARG* 3.3 54.8 - - - +
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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