Contacts of the helix formed by residues 480 - 494 (chain A) in PDB entry 1O8A
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 ASN 480 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A SER 5.7 1.6 + - - -
476A ILE* 3.7 6.9 - - + +
477A THR* 2.8 25.9 + - - +
479A GLU* 1.3 89.5 - - - +
481A TYR* 1.3 63.0 + - - +
482A ASN 3.4 2.7 - - - -
483A GLN* 3.5 15.5 + - + +
484A GLU* 3.0 40.9 + - + +
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Residues in contact with TYR 481 (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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194A LEU* 3.9 16.6 - - + -
197A TYR* 3.9 20.0 - + + -
198A PRO* 3.5 35.7 - - + +
201A VAL* 4.1 7.6 - - - +
467A TRP* 2.9 36.7 + + + -
471A VAL* 4.0 20.6 - - + +
476A ILE* 3.9 11.2 - - + -
477A THR 3.1 17.9 + - - -
478A LYS* 3.5 40.5 + - + +
479A GLU 3.7 1.4 - - - -
480A ASN* 1.3 79.2 - - - +
482A ASN* 1.3 64.0 + - - +
483A GLN* 4.1 0.4 + - - -
485A TRP* 3.1 6.2 + - - +
505A ASP 5.8 0.7 - - - +
506A PHE* 3.6 27.8 - + + -
508A PRO* 5.3 0.4 - - - -
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Residues in contact with ASN 482 (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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480A ASN 3.4 0.2 - - - -
481A TYR* 1.3 77.2 - - + +
483A GLN* 1.3 75.8 + - + +
485A TRP* 3.2 4.3 + - - +
486A TRP* 3.0 34.1 + - - -
501A ARG* 3.5 28.3 - - - +
502A THR 5.3 1.1 + - - +
505A ASP* 3.6 25.2 - - - +
506A PHE* 3.6 0.7 - - - -
507A ASP* 2.8 50.1 + - - +
508A PRO* 3.4 8.3 - - - +
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Residues in contact with GLN 483 (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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479A GLU 3.4 24.8 + - - +
480A ASN* 3.5 20.2 + - + +
482A ASN* 1.3 83.0 + - - +
484A GLU* 1.3 62.9 + - - +
486A TRP* 3.5 5.1 + - - +
487A SER* 3.0 30.9 + - - +
503A GLN* 6.2 2.4 - - - +
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Residues in contact with GLU 484 (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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467A TRP* 3.9 2.0 - - - -
470A ARG* 2.8 29.9 + - - +
475A SER 5.9 0.2 - - - +
476A ILE* 3.6 37.7 - - + -
480A ASN* 3.0 31.2 + - + +
481A TYR 4.0 1.6 - - - +
483A GLN* 1.3 78.5 - - - +
485A TRP* 1.3 65.9 + - - +
487A SER* 3.4 13.6 + - - -
488A LEU* 3.1 28.4 + - - +
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Residues in contact with TRP 485 (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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279A TRP* 6.1 2.0 - + - -
460A PHE* 4.6 12.6 - + - -
463A LEU* 3.5 26.7 - - + -
464A VAL* 4.3 26.5 - - + -
467A TRP* 3.6 28.6 - + + +
481A TYR 3.1 14.0 + - - +
482A ASN* 3.4 8.3 - - - +
484A GLU* 1.3 77.7 - - - +
486A TRP* 1.3 79.6 + + - +
488A LEU* 3.2 6.3 + - - +
489A ARG* 2.9 53.2 + - + +
507A ASP* 4.2 6.1 - - + +
508A PRO* 3.5 42.8 - - + -
511A LYS* 5.2 10.5 - - + -
514A ILE* 5.2 2.9 - - + -
703A CL 3.3 25.3 - - + +
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Residues in contact with TRP 486 (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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182A TRP* 3.6 31.2 - + - -
272A ALA* 3.9 8.1 - - + -
482A ASN* 3.0 34.2 + - - +
483A GLN* 4.1 5.2 - - - +
485A TRP* 1.3 86.8 - + - +
487A SER* 1.3 64.5 + - - +
489A ARG* 3.5 42.8 - - + +
490A LEU* 2.9 25.1 + - - +
495A LEU* 4.5 1.8 - - + -
496A CYS* 3.8 11.2 - - - -
497A PRO* 3.5 41.7 - - + -
501A ARG* 3.8 11.7 - - + +
507A ASP* 2.7 24.3 + - - -
703A CL 3.5 18.6 - - + -
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Residues in contact with SER 487 (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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483A GLN* 3.0 19.9 + - - +
484A GLU* 3.7 20.0 + - - -
485A TRP 3.3 0.2 - - - -
486A TRP* 1.3 76.0 - - - +
488A LEU* 1.3 59.7 + - - +
490A LEU* 3.6 7.4 + - - +
491A LYS* 2.9 29.7 + - - +
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Residues in contact with LEU 488 (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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463A LEU* 3.5 26.3 - - + +
466A GLN* 4.2 5.6 - - + -
467A TRP* 3.6 44.2 - - + +
470A ARG* 4.0 24.2 - - - +
484A GLU 3.1 15.2 + - - +
485A TRP* 3.5 7.2 - - - +
486A TRP 3.1 0.4 - - - -
487A SER* 1.3 78.7 - - - +
489A ARG* 1.3 59.7 + - - +
490A LEU 3.1 0.4 - - - -
491A LYS* 4.3 10.5 - - + +
492A TYR* 2.8 54.4 + - + +
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Residues in contact with ARG 489 (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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182A TRP* 4.8 0.4 - - - +
186A ARG* 4.2 4.4 - - - +
272A ALA* 4.0 12.9 - - - +
279A TRP* 2.9 32.9 + - - +
460A PHE* 3.8 7.6 - - - -
463A LEU* 3.4 13.9 - - + +
485A TRP* 2.9 55.1 + - + +
486A TRP* 3.5 38.6 - - + +
488A LEU* 1.3 76.0 - - - +
490A LEU* 1.3 58.2 + - - +
493A GLN* 2.7 61.8 + - - +
494A GLY 3.1 6.4 + - - -
495A LEU* 3.3 16.2 + - + +
703A CL 3.2 23.9 - - - +
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Residues in contact with LEU 490 (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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269A PRO* 3.6 32.8 - - + -
486A TRP 2.9 15.5 + - - +
487A SER* 3.8 7.0 - - - +
489A ARG* 1.3 76.0 - - - +
491A LYS* 1.3 67.3 + - - +
494A GLY* 2.9 17.4 + - - -
495A LEU 3.5 11.4 + - - +
496A CYS* 5.5 0.9 - - + -
616A TRP* 3.0 40.4 + - + +
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Residues in contact with LYS 491 (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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237A PHE* 5.7 0.2 - - - -
241A GLN* 5.5 4.3 + - - -
487A SER 2.9 19.6 + - - +
488A LEU* 3.9 12.0 - - + +
490A LEU* 1.3 79.7 - - - +
492A TYR* 1.3 97.2 + - + +
616A TRP* 3.6 15.6 + - - +
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Residues in contact with TYR 492 (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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234A GLU* 4.3 9.2 + - - -
237A PHE* 3.3 33.9 - + - -
238A GLN* 5.6 1.1 - - - -
241A GLN* 4.9 1.9 + - - +
244A TYR* 3.6 11.3 - - - -
459A PRO* 3.3 32.3 - - + +
462A TYR* 3.7 34.0 - + - -
463A LEU* 4.2 15.3 - - + -
466A GLN* 4.6 11.1 + - + +
488A LEU* 2.8 50.5 + - + +
491A LYS* 1.3 108.2 + - + +
493A GLN* 1.3 60.5 + - - +
494A GLY 3.5 0.4 - - - -
616A TRP* 4.2 3.8 - - - -
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Residues in contact with GLN 493 (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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244A TYR* 2.6 28.5 + - - +
248A HIS* 3.4 8.5 + - - -
280A ALA 3.2 26.3 + - - -
283A TRP* 5.0 1.4 - - - +
456A ALA 4.5 4.6 + - - -
459A PRO* 4.0 7.4 - - + -
460A PHE* 3.5 44.3 - - - +
463A LEU* 3.7 5.8 - - + +
489A ARG* 2.7 51.3 + - - +
492A TYR* 1.3 75.0 - - - +
494A GLY* 1.3 62.9 + - - +
495A LEU* 3.6 19.0 - - + +
616A TRP* 4.0 2.9 - - - -
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Residues in contact with GLY 494 (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 HIS* 3.0 12.1 - - - -
269A PRO* 3.1 7.9 - - - +
270A ILE 2.9 21.1 + - - -
489A ARG 3.1 0.2 + - - -
490A LEU* 2.9 21.1 + - - -
493A GLN* 1.3 77.6 - - - +
495A LEU* 1.3 59.2 + - - +
616A TRP* 3.3 30.5 - - - -
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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