Contacts of the helix formed by residues 413 - 422 (chain A) in PDB entry 2O8C
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 GLN 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A LEU* 4.0 12.2 - - + +
383A ARG* 2.7 57.2 + - + +
384A PHE* 4.1 5.3 - - + -
409A GLN* 3.1 27.0 + - - +
410A GLY* 3.5 4.9 - - - +
412A ASN* 1.3 85.8 - - + +
414A LEU* 1.3 62.3 + - - +
415A PRO 3.5 1.6 - - - -
416A ASN* 3.5 18.0 + - + +
417A VAL* 3.3 25.3 + - - +
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Residues in contact with LEU 414 (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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384A PHE* 4.1 20.2 - - + -
410A GLY 2.9 13.8 + - - +
411A ILE* 3.4 20.4 - - + +
413A GLN* 1.3 75.7 - - - +
415A PRO* 1.4 67.6 - - + +
417A VAL* 3.3 18.9 + - + +
418A ILE* 3.5 9.4 + - - +
440A LEU* 3.9 36.3 - - + +
443A LEU 4.4 5.8 - - - +
444A ARG* 4.4 26.7 - - + +
447A PHE* 5.1 0.9 - - + -
595A LEU* 4.0 31.6 - - + -
599A LEU* 4.5 4.0 - - + -
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Residues in contact with PRO 415 (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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411A ILE 3.3 14.1 - - - +
412A ASN* 3.4 13.9 - - - +
414A LEU* 1.4 92.3 - - + +
416A ASN* 1.3 59.4 + - + +
417A VAL 3.2 0.2 - - - -
418A ILE* 3.2 26.5 - - + +
419A GLN* 3.2 25.5 + - - +
444A ARG* 3.5 37.0 - - - +
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Residues in contact with ASN 416 (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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380A LEU* 3.6 29.8 - - + +
383A ARG* 5.2 2.6 - - - +
412A ASN 5.0 1.3 - - - +
413A GLN* 3.6 29.2 + - + +
414A LEU 3.2 0.8 - - - -
415A PRO* 1.3 80.2 - - + +
417A VAL* 1.3 62.5 + - - +
419A GLN* 3.6 22.1 - - - +
420A ALA* 3.8 4.7 + - - +
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Residues in contact with VAL 417 (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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376A LEU* 4.1 17.4 - - + +
380A LEU* 3.9 24.0 - - + +
381A LEU* 6.2 1.1 - - + -
384A PHE* 3.6 30.7 - - + -
413A GLN 3.3 15.7 - - - +
414A LEU* 3.3 10.1 + - + +
415A PRO 3.2 0.2 - - - -
416A ASN* 1.3 78.6 - - - +
418A ILE* 1.3 62.2 + - - +
419A GLN 3.1 1.1 - - - -
420A ALA* 3.1 15.1 + - - +
421A LEU* 3.2 27.7 + - + +
440A LEU* 4.7 11.4 - - + -
599A LEU* 5.6 3.4 - - + -
602A LEU* 5.0 6.7 - - + -
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Residues in contact with ILE 418 (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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414A LEU 3.5 8.2 + - - +
415A PRO* 3.2 28.7 - - + +
417A VAL* 1.3 72.6 - - + +
419A GLN* 1.3 64.0 + - + +
420A ALA 3.3 0.2 - - - -
421A LEU* 3.7 18.6 - - + +
422A GLU* 3.1 45.2 + - + +
437A VAL* 4.8 7.6 - - + +
440A LEU* 3.9 34.8 - - + +
441A THR* 4.0 29.2 - - - +
444A ARG* 5.0 7.0 - - + -
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Residues in contact with GLN 419 (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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415A PRO* 3.2 23.8 + - - +
416A ASN* 3.6 20.4 - - - +
417A VAL 3.1 1.0 - - - -
418A ILE* 1.3 81.2 - - - +
420A ALA* 1.3 60.6 + - - +
422A GLU* 3.8 9.0 + - - +
423A LYS* 3.4 31.7 - - - +
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Residues in contact with ALA 420 (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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372A LEU* 3.3 23.8 - - + +
375A THR* 4.2 25.1 - - + +
376A LEU* 5.5 4.7 - - + -
380A LEU* 4.8 9.0 - - + -
416A ASN 3.8 6.8 + - - +
417A VAL 3.1 9.9 + - - +
419A GLN* 1.3 76.8 - - - +
421A LEU* 1.3 64.1 + - + +
422A GLU 3.6 0.3 + - - -
423A LYS* 3.6 20.8 + - - +
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Residues in contact with LEU 421 (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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366A PHE* 5.0 11.4 - - + -
372A LEU* 4.9 10.6 - - + +
376A LEU* 4.8 19.5 - - + -
417A VAL* 3.2 26.6 + - + +
418A ILE* 3.8 29.4 - - + +
419A GLN 3.3 0.2 - - - -
420A ALA* 1.3 79.3 - - + +
422A GLU* 1.3 56.0 + - + +
423A LYS 3.2 3.9 + - - -
424A HIS* 3.1 30.8 + - + -
433A LEU* 6.4 1.8 - - + -
436A PHE* 4.7 7.4 - - + +
437A VAL* 4.3 25.0 - - + +
440A LEU* 4.2 14.1 - - + -
602A LEU* 4.6 11.2 - - + -
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Residues in contact with GLU 422 (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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418A ILE* 3.1 31.8 + - + +
419A GLN* 3.8 7.4 + - - +
420A ALA 3.3 0.8 - - - -
421A LEU* 1.3 75.5 - - - +
423A LYS* 1.3 63.1 + - - +
424A HIS* 4.2 8.5 - - - -
437A VAL* 4.2 25.4 - - + +
441A THR* 5.3 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