Contacts of the helix formed by residues 352 - 368 (chain A) in PDB entry 2O8F
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 ASP 352 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A GLN 5.1 0.2 + - - -
350A LEU* 4.6 2.1 - - + +
351A MET* 1.3 76.3 - - - +
353A LYS* 1.3 63.6 + - - +
354A ASN* 3.8 21.5 + - - +
355A ARG* 2.9 45.9 + - + +
356A ILE* 3.1 14.9 + - - +
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Residues in contact with LYS 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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351A MET 3.4 4.8 + - - -
352A ASP* 1.3 76.1 + - - +
354A ASN* 1.3 76.8 + - - +
356A ILE* 4.0 5.8 - - - -
357A GLU* 3.3 35.5 + - - +
624A ILE* 4.4 12.1 - - + +
625A LEU 4.9 0.4 - - - -
626A GLU* 3.8 45.6 + - + +
627A LYS 5.1 0.9 - - - +
704A ILE* 3.7 20.0 - - + -
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Residues in contact with ASN 354 (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 18.2 + - - +
353A LYS* 1.3 98.2 + - - +
355A ARG* 1.3 60.1 + - + +
357A GLU* 4.1 5.5 - - - +
358A GLU* 3.2 28.6 + - - +
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Residues in contact with ARG 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 3.7 27.7 - - + +
352A ASP* 2.9 28.7 + - + +
354A ASN* 1.3 78.3 - - + +
356A ILE* 1.3 64.6 + - - +
358A GLU* 3.5 28.4 + - - +
359A ARG* 3.3 30.2 + - - +
601A GLN* 5.8 4.4 - - - +
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Residues in contact with ILE 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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350A LEU* 3.6 40.8 - - + +
352A ASP 3.1 17.0 + - - +
353A LYS* 4.4 2.2 - - - +
354A ASN 3.4 0.2 - - - -
355A ARG* 1.3 75.5 - - - +
357A GLU* 1.3 58.1 + - - +
359A ARG* 3.2 5.7 + - - +
360A LEU* 3.0 30.4 + - + +
624A ILE* 3.5 16.6 - - + -
689A ALA 3.3 25.4 - - - +
690A GLN* 4.0 21.8 - - + +
692A GLY* 4.1 8.4 - - - -
704A ILE* 4.0 29.4 - - + -
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Residues in contact with GLU 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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353A LYS* 3.3 24.4 + - - +
354A ASN* 4.3 5.3 - - - +
356A ILE* 1.3 74.2 - - - +
358A GLU* 1.3 63.0 + - - +
360A LEU* 3.8 12.5 - - + +
361A ASN* 3.2 31.0 + - - +
621A ARG* 5.0 4.7 - - - +
624A ILE* 3.3 47.8 + - + +
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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 ASN 3.2 20.1 + - - +
355A ARG* 3.6 38.0 + - - +
356A ILE 3.1 0.2 - - - -
357A GLU* 1.3 77.0 - - - +
359A ARG* 1.3 64.6 + - + +
361A ASN* 3.3 9.9 + - - +
362A LEU* 3.2 35.1 + - + +
432A LEU* 5.5 10.8 - - + +
435A VAL* 4.4 18.0 - - - +
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Residues in contact with ARG 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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345A TRP* 3.1 67.7 - - + +
348A GLN 5.5 1.2 + - - -
350A LEU* 3.4 34.9 - - - +
355A ARG* 3.3 25.4 + - - +
356A ILE* 3.2 6.3 + - - +
358A GLU* 1.3 80.0 - - + +
360A LEU* 1.3 63.5 + - - +
362A LEU* 3.9 19.7 - - + +
363A VAL* 3.3 27.5 + - - +
605A VAL* 5.3 4.8 - - + +
691A ILE* 2.3 30.2 + - - +
692A GLY* 3.6 12.5 + - - +
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Residues in contact with LEU 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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356A ILE 3.0 16.1 + - - +
357A GLU* 3.8 8.3 - - + +
358A GLU 3.2 0.2 - - - -
359A ARG* 1.3 75.7 - - - +
361A ASN* 1.3 54.5 + - - +
363A VAL* 3.3 5.3 + - - +
364A GLU* 2.8 33.5 + - - +
621A ARG* 3.5 33.7 - - + +
622A PRO* 3.6 31.0 - - + +
624A ILE* 3.7 23.3 - - + -
689A ALA 4.6 4.5 - - - +
692A GLY* 3.7 5.6 - - - -
693A CYS 3.6 40.2 - - - +
694A PHE* 3.7 6.8 - - + +
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Residues in contact with ASN 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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357A GLU* 3.2 12.7 + - - +
358A GLU* 3.3 10.0 + - - +
360A LEU* 1.3 76.0 - - - +
362A LEU* 1.3 59.7 + - - +
364A GLU* 3.5 8.1 - - - +
365A ALA* 2.9 23.6 + - - +
429A GLN* 3.0 35.7 - - - +
432A LEU* 3.8 22.4 - - + +
621A ARG* 2.9 32.4 + - - -
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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
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358A GLU* 3.2 29.2 + - + +
359A ARG* 3.9 21.1 - - + +
360A LEU 3.3 0.2 - - - -
361A ASN* 1.3 75.0 - - - +
363A VAL* 1.3 61.2 + - - +
365A ALA* 3.3 9.5 + - + +
366A PHE* 3.0 27.2 - - + -
432A LEU* 3.8 30.3 - - + +
433A LEU* 4.4 9.4 - - + -
435A VAL* 5.8 5.2 - - + -
436A PHE* 3.7 35.7 - - + -
601A GLN* 5.9 1.3 - - - +
605A VAL* 3.6 23.1 - - + -
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Residues in contact with VAL 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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359A ARG 3.3 15.0 + - - +
360A LEU 3.3 7.7 + - - +
362A LEU* 1.3 73.2 - - - +
364A GLU* 1.3 64.2 + - - +
366A PHE* 3.0 12.7 + - - -
367A VAL* 3.1 17.0 + - + +
605A VAL* 3.6 30.7 - - + +
608A PHE* 3.9 17.7 - - + +
609A ALA* 3.7 29.8 - - + +
692A GLY 3.7 15.0 - - - +
694A PHE* 3.7 24.5 - - + +
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Residues in contact with GLU 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 LEU 2.8 16.8 + - - +
361A ASN* 3.5 22.6 - - - +
363A VAL* 1.3 76.9 - - - +
365A ALA* 1.3 60.6 + - - +
367A VAL* 3.2 16.1 + - + +
368A GLU* 3.8 8.5 + - + +
428A HIS* 5.1 8.4 - - + -
429A GLN* 3.9 17.3 + - - +
621A ARG* 3.6 23.2 + - - -
694A PHE* 3.7 23.3 - - + -
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Residues in contact with ALA 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 ASN 2.9 17.9 + - - +
362A LEU* 3.4 11.2 - - + +
363A VAL 3.2 0.4 - - - -
364A GLU* 1.3 76.4 - - - +
366A PHE* 1.3 65.7 + - + +
369A ASP* 3.3 25.2 - - - +
372A LEU* 3.6 8.4 - - + +
424A HIS* 5.8 3.9 - - + -
428A HIS* 5.9 3.8 - - - +
429A GLN* 4.3 18.6 + - + +
433A LEU* 5.4 12.6 - - + -
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Residues in contact with PHE 366 (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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362A LEU* 3.0 25.8 - - + -
363A VAL* 3.0 8.7 + - - +
365A ALA* 1.3 85.6 - - + +
367A VAL* 1.3 54.7 + - - +
368A GLU 3.8 0.2 - - - -
369A ASP* 4.3 2.7 - - - -
370A ALA 4.1 5.7 + - - -
372A LEU* 3.5 34.3 - - + +
373A ARG* 2.7 40.0 + - + +
376A LEU* 3.7 18.4 - - + -
421A LEU* 4.2 15.9 - - + -
433A LEU* 5.0 13.9 - - + -
436A PHE* 5.6 8.1 - + - -
602A LEU* 4.9 7.9 - - + -
605A VAL* 3.7 20.0 - - + -
606A VAL* 3.7 27.1 - - + -
609A ALA* 3.7 14.4 - - + -
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Residues in contact with VAL 367 (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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363A VAL 3.1 19.9 + - - +
364A GLU* 3.2 9.0 + - + +
366A PHE* 1.3 77.7 - - - +
368A GLU* 1.3 73.7 + - + +
369A ASP 3.3 1.2 + - - -
370A ALA* 3.7 1.2 + - - +
373A ARG* 3.1 28.3 + - - +
609A ALA* 3.8 14.4 - - + +
612A SER* 3.9 18.4 - - - +
613A ASN* 4.5 18.8 - - + +
618A PRO* 6.4 1.6 - - + -
619A TYR 5.9 1.8 - - - +
694A PHE* 4.1 23.6 - - + -
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Residues in contact with GLU 368 (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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364A GLU* 3.8 8.1 + - + +
367A VAL* 1.3 88.6 - - + +
369A ASP* 1.3 61.8 + - - +
370A ALA* 3.3 4.4 - - - +
425A GLU* 4.1 5.2 - - - +
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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