Contacts of the helix formed by residues 487 - 501 (chain C) in PDB entry 1DQ8
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 THR 487 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482C GLU* 5.5 1.3 - - - +
485C ILE* 3.4 12.7 - - - +
486C GLU* 1.3 87.9 + - - +
488C HIS* 1.3 67.3 + - + +
489C GLU* 3.6 19.7 - - + +
490C ARG* 3.8 19.1 - - + +
491C GLY* 3.1 17.0 + - - -
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Residues in contact with HIS 488 (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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482C GLU* 3.9 18.8 - - + +
487C THR* 1.3 73.2 - - - +
489C GLU* 1.3 59.5 - - - +
491C GLY* 2.8 19.9 + - - -
492C VAL* 3.0 15.8 + - - +
519C TYR* 3.7 25.1 + - + +
520C SER* 3.7 32.0 + - - +
523C MET* 3.4 31.4 + - + +
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Residues in contact with GLU 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C THR* 3.4 11.9 - - + +
488C HIS* 1.3 77.6 - - - +
490C ARG* 1.3 58.2 + - - +
492C VAL* 3.0 11.9 + - - +
493C SER* 2.8 26.7 + - - -
514C TYR* 3.8 24.7 + - + +
515C ARG* 3.8 25.6 + - - +
516C ASP* 3.5 24.4 + - - +
517C TYR 5.1 2.1 + - - +
519C TYR* 4.5 9.7 - - + -
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Residues in contact with ARG 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ASP* 2.5 56.0 - - - +
467C ILE* 3.6 15.6 - - - +
485C ILE* 3.8 19.5 - - + +
486C GLU* 4.3 21.8 + - - +
487C THR* 3.4 22.1 + - + +
488C HIS 3.2 0.6 - - - -
489C GLU* 1.3 79.0 - - - +
491C GLY* 1.3 63.0 + - - +
493C SER* 3.1 7.6 + - - -
494C ILE* 2.9 31.0 + - + +
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Residues in contact with GLY 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C LEU* 3.6 13.5 - - - +
482C GLU* 3.5 17.4 - - - +
485C ILE* 3.5 23.3 - - - +
487C THR 3.1 9.2 + - - -
488C HIS 2.8 9.5 + - - -
490C ARG* 1.3 77.8 - - - +
492C VAL* 1.3 61.1 + - - +
494C ILE 3.4 0.2 + - - -
495C ARG* 3.1 18.7 + - - +
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Residues in contact with VAL 492 (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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488C HIS 3.0 11.6 + - - +
489C GLU 3.0 7.7 + - - +
491C GLY* 1.3 75.1 - - - +
493C SER* 1.3 57.6 + - - +
495C ARG* 3.2 5.2 + - - +
496C ARG* 2.9 38.2 + - - +
514C TYR* 4.0 14.6 - - + -
519C TYR* 4.0 21.5 - - + +
523C MET* 3.6 27.1 - - + -
530C VAL 3.5 11.9 - - - +
531C ILE 3.5 33.9 - - - +
532C GLY* 3.7 3.1 - - - +
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Residues in contact with SER 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ASP* 4.0 10.8 + - - -
489C GLU* 2.8 13.8 + - - -
490C ARG* 3.1 13.4 + - - -
492C VAL* 1.3 77.3 - - - +
494C ILE* 1.3 62.5 + - - +
496C ARG* 3.2 9.3 + - - +
497C GLN* 3.0 39.0 + - - +
514C TYR* 3.9 27.2 + - - -
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Residues in contact with ILE 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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464C ASP* 3.9 30.3 - - - +
467C ILE* 3.8 31.2 - - + -
468C ILE* 4.4 13.4 - - + +
471C VAL* 5.2 0.4 - - + -
481C LEU* 3.8 21.1 - - + -
485C ILE* 3.6 24.2 - - + -
490C ARG* 2.9 25.2 + - + +
491C GLY 3.8 4.0 - - - +
493C SER* 1.3 74.7 - - - +
495C ARG* 1.3 57.6 + - - +
497C GLN* 3.2 8.6 + - - +
498C LEU* 2.8 40.1 + - + +
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Residues in contact with ARG 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C ALA* 2.8 39.6 + - + -
479C TYR* 3.8 7.1 + - - +
481C LEU* 3.7 14.6 - - + +
482C GLU* 2.6 44.0 + - - -
491C GLY 3.1 10.2 + - - +
492C VAL* 3.2 11.6 + - - +
494C ILE* 1.3 77.6 - - - +
496C ARG* 1.3 54.1 + - - +
498C LEU* 3.3 5.5 + - + +
499C LEU* 2.8 38.0 + - + +
523C MET* 3.8 4.8 - - - +
529C ASN* 3.0 35.5 + - - +
530C VAL 2.9 36.4 + - - +
531C ILE* 4.0 12.8 - - + -
540D VAL* 4.9 4.9 - - + -
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Residues in contact with ARG 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C VAL* 2.9 21.2 + - - +
493C SER* 3.2 9.4 + - - +
495C ARG* 1.3 78.5 - - - +
497C GLN* 1.3 57.2 + - + +
499C LEU* 3.4 2.6 + - - -
500C SER* 2.8 29.5 + - - -
509C LEU* 2.7 52.2 + - + +
510C GLN* 4.8 3.6 + - - +
512C LEU* 2.7 33.9 + - - +
514C TYR* 3.4 40.6 - - - +
531C ILE* 2.9 42.6 + - + +
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Residues in contact with GLN 497 (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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464C ASP* 3.0 43.2 + - - +
468C ILE* 3.4 22.3 - - + +
493C SER* 3.0 34.2 + - - +
494C ILE* 3.6 8.7 - - - +
496C ARG* 1.3 74.1 - - + +
498C LEU* 1.3 66.7 + - - +
500C SER* 3.3 19.0 - - - -
501C LYS* 3.6 14.4 + - - +
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Residues in contact with LEU 498 (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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468C ILE* 3.7 30.3 - - + -
471C VAL* 3.8 30.3 - - + -
472C ASN* 4.0 14.1 - - - +
478C ALA* 4.6 12.6 - - + -
481C LEU* 4.2 13.2 - - + -
494C ILE* 2.8 35.9 + - + +
495C ARG* 3.6 5.2 - - - +
497C GLN* 1.3 79.8 - - - +
499C LEU* 1.3 63.4 + - - +
500C SER 3.4 0.2 + - - -
501C LYS* 3.4 20.6 + - + +
502C LYS* 4.0 17.2 + - - +
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Residues in contact with LEU 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ARG* 2.8 22.9 + - + +
496C ARG 3.6 3.6 - - - +
498C LEU* 1.3 74.2 - - - +
500C SER* 1.3 63.4 + - - +
502C LYS* 2.9 21.7 + - + +
503C LEU* 3.4 15.7 + - + +
509C LEU* 4.1 21.5 - - + -
531C ILE* 4.0 36.1 - - + -
540D VAL* 4.4 13.9 - - + -
552D GLN* 3.6 42.4 - - + +
820D MET* 4.5 7.4 - - - -
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Residues in contact with SER 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C ARG 2.8 18.6 + - - -
497C GLN* 3.3 12.6 - - - -
499C LEU* 1.3 75.8 - - - +
501C LYS* 1.3 63.1 + - - +
503C LEU* 3.0 29.8 + - - +
506C PRO* 2.9 39.1 + - - +
509C LEU* 4.4 4.2 - - - +
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Residues in contact with LYS 501 (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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468C ILE* 4.0 31.4 - - + +
472C ASN* 4.9 7.8 - - - +
497C GLN* 3.9 13.2 - - - +
498C LEU* 3.4 13.3 + - + +
499C LEU 3.3 0.8 - - - -
500C SER* 1.3 76.9 - - - +
502C LYS* 1.3 61.8 + - + +
503C LEU 3.3 3.6 + - - +
506C PRO* 5.6 3.0 - - - +
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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