Contacts of the helix formed by residues 486 - 501 (chain C) in PDB entry 1DGH
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 HIS 486 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444C ARG* 4.0 15.0 - - + +
447C TYR* 4.2 15.2 - + + -
448C VAL* 3.7 25.2 - - + +
482C PHE 3.1 5.6 + - - +
483C THR 3.3 3.9 + - - +
485C VAL* 1.3 84.1 - - + +
487C PRO* 1.3 71.8 - - + +
488C ASP* 3.0 55.4 + - + +
489C TYR* 2.8 40.5 + - + +
490C GLY 3.2 1.6 + - - -
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Residues in contact with PRO 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ARG* 6.0 1.3 - - - +
483C THR* 3.3 27.0 + - + +
484C GLU 5.6 0.2 - - - +
485C VAL 4.8 0.2 - - - -
486C HIS* 1.3 97.2 - - + +
488C ASP* 1.3 63.4 + - - +
490C GLY* 4.0 0.6 - - - -
491C SER* 3.1 29.1 + - - -
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Residues in contact with ASP 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C TYR* 3.9 10.8 + - + +
486C HIS* 3.0 25.9 + - + +
487C PRO* 1.3 79.8 - - - +
489C TYR* 1.3 64.4 + - - +
491C SER* 3.5 8.8 + - - -
492C HIS* 3.2 25.6 + - - +
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Residues in contact with TYR 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C SER* 3.1 27.5 + - - -
443C VAL* 4.7 2.2 - - + -
447C TYR* 3.5 39.2 + + + -
459C LEU* 3.5 31.2 - - + +
460C CYS* 4.0 7.0 - - - -
463C ILE* 3.5 16.3 - - + +
482C PHE* 3.6 27.4 - + + +
485C VAL* 3.7 29.2 - - + -
486C HIS* 2.8 18.7 + - + +
488C ASP* 1.3 81.0 - - - +
490C GLY* 1.3 60.7 + - - +
492C HIS* 3.5 1.7 + - - +
493C ILE* 3.3 44.1 + - + +
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Residues in contact with GLY 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C VAL* 3.6 11.0 - - - +
482C PHE* 3.8 11.8 + - - -
483C THR* 3.4 29.8 - - - -
486C HIS 3.2 6.9 + - - -
487C PRO 3.7 0.2 + - - -
489C TYR* 1.3 81.3 - - - +
491C SER* 1.3 55.5 + - - +
493C ILE* 3.4 3.9 + - - +
494C GLN* 3.0 27.9 + - - +
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Residues in contact with SER 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C THR* 4.4 1.2 + - - -
487C PRO 3.1 19.5 + - - -
488C ASP* 3.5 12.8 + - - -
490C GLY* 1.3 72.4 - - - +
492C HIS* 1.3 61.7 + - - +
494C GLN* 3.3 7.8 + - - +
495C ALA* 2.9 29.6 + - - +
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Residues in contact with HIS 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C TYR* 4.7 6.1 - - - -
453C GLU* 5.4 5.6 + - - -
456C ARG* 4.8 1.1 - - + -
457C LYS* 3.9 35.1 - - + +
460C CYS* 3.8 20.4 - - + -
488C ASP 3.2 17.5 + - - +
489C TYR 3.8 4.0 - - - +
490C GLY 3.3 0.2 - - - -
491C SER* 1.3 80.6 + - - +
493C ILE* 1.3 61.5 + - - +
495C ALA* 3.4 7.7 + - - +
496C LEU* 3.2 43.0 + - + +
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Residues in contact with ILE 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C CYS* 3.7 20.9 - - + +
463C ILE* 3.9 26.7 - - + -
464C ALA* 4.5 6.3 - - + -
467C LEU* 4.5 5.6 - - + -
479C VAL* 4.2 13.2 - - + -
482C PHE* 3.6 34.3 - - + -
489C TYR* 3.3 28.8 + - + +
490C GLY* 3.7 6.5 - - - +
491C SER 3.3 0.4 - - - -
492C HIS* 1.3 73.9 - - - +
494C GLN* 1.3 60.0 + - - +
496C LEU* 3.1 10.4 + - - +
497C LEU* 2.9 40.9 + - + +
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Residues in contact with GLN 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475C GLN* 5.0 3.7 - - - +
476C LYS* 3.8 29.0 - - - +
479C VAL* 3.8 27.8 - - + +
490C GLY 3.0 17.2 + - - +
491C SER* 3.7 9.0 - - - +
493C ILE* 1.3 76.6 - - - +
495C ALA* 1.3 57.0 + - - +
497C LEU* 4.0 18.8 - - - +
498C ASP* 2.9 50.9 + - - +
501C ASN* 5.7 0.6 + - - -
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Residues in contact with ALA 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C SER 2.9 16.4 + - - +
492C HIS* 3.6 10.8 - - - +
493C ILE 3.2 0.2 - - - -
494C GLN* 1.3 78.0 - - - +
496C LEU* 1.3 62.4 + - + +
498C ASP* 3.3 19.0 + - - +
499C LYS* 3.4 12.1 + - - +
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Residues in contact with LEU 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C CYS* 3.6 41.3 - - + +
461C GLU* 3.6 20.6 - - + +
464C ALA* 3.6 12.1 - - + -
492C HIS* 3.2 30.3 + - + +
493C ILE* 3.1 6.5 + - - +
495C ALA* 1.3 75.5 - - + +
497C LEU* 1.3 65.7 + - - +
499C LYS* 3.3 20.5 + - + +
500C TYR* 3.3 42.0 + - + +
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Residues in contact with LEU 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ALA* 3.7 32.3 - - - +
467C LEU* 4.1 13.0 - - + -
468C LYS* 3.8 21.5 - - - +
475C GLN* 3.4 34.1 - - + +
479C VAL* 3.8 28.9 - - + -
493C ILE* 2.9 20.2 + - + +
494C GLN* 3.6 13.9 - - - +
496C LEU* 1.3 73.3 - - - +
498C ASP* 1.3 65.8 + - - +
500C TYR* 3.1 5.0 + - - +
501C ASN* 2.9 30.6 + - - -
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Residues in contact with ASP 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C GLN* 2.9 41.5 + - - +
495C ALA* 3.5 13.1 - - - +
497C LEU* 1.3 77.8 - - - +
499C LYS* 1.3 60.8 + - - +
501C ASN* 3.4 22.9 + - - +
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Residues in contact with LYS 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C ALA 3.4 6.0 + - - +
496C LEU* 3.3 23.9 + - + +
497C LEU 3.2 0.6 - - - -
498C ASP* 1.3 75.9 - - - +
500C TYR* 1.3 93.2 + - + +
501C ASN* 3.1 9.9 - - - +
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Residues in contact with TYR 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C GLU* 4.3 14.0 + - - +
464C ALA* 3.6 42.0 - - + -
465C GLY* 3.7 8.6 - - - -
468C LYS* 3.9 35.3 - - + +
496C LEU* 3.3 29.1 + - + +
497C LEU* 3.1 6.8 + - - +
499C LYS* 1.3 107.7 - - + +
501C ASN* 1.3 64.6 + - - +
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Residues in contact with ASN 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C LYS* 4.0 18.4 + - - +
472C ILE* 3.6 16.8 - - + +
475C GLN* 3.1 35.5 + - - -
494C GLN* 5.7 0.3 + - - -
497C LEU* 2.9 20.9 + - - +
498C ASP* 3.5 16.0 - - - +
499C LYS 3.1 14.1 - - - +
500C TYR* 1.3 83.1 + - - +
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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