Contacts of the helix formed by residues 471 - 486 (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 GLN 471 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ARG* 3.5 17.9 - - - +
10A ASP* 5.4 0.7 - - - -
13A GLN* 3.1 41.6 + - - +
409B PHE* 3.7 12.1 - - - -
180C ASP* 2.9 35.1 + - - +
470C ALA* 1.3 76.5 - - - +
472C ILE* 1.3 66.3 + - - +
473C PHE* 3.3 26.8 - - + -
474C ILE* 3.0 7.8 + - + +
475C GLN* 2.9 18.7 + - - +
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Residues in contact with ILE 472 (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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470C ALA 3.7 0.4 + - - +
471C GLN* 1.3 74.4 - - - +
473C PHE* 1.3 58.3 + - - +
475C GLN* 3.0 19.3 + - + +
476C LYS* 2.9 53.4 + - + +
501C ASN* 3.6 28.3 - - + +
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Residues in contact with PHE 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 4.6 4.5 - - - -
16A LYS* 5.4 5.2 - - - -
408B SER* 3.9 28.9 - - - -
409B PHE* 4.0 18.2 - + - -
184C ASP* 4.9 0.2 - - - -
471C GLN* 3.3 35.0 - - + -
472C ILE* 1.3 79.3 - - - +
474C ILE* 1.3 84.0 + - + +
476C LYS* 3.7 8.3 + - - +
477C LYS* 3.4 35.5 + - - +
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Residues in contact with ILE 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PHE* 4.2 3.6 - - + -
180C ASP* 3.7 46.7 - - + +
183C TRP* 3.4 43.1 - - + +
184C ASP* 4.1 12.1 - - + +
187C SER* 4.2 3.8 - - - +
467C LEU* 4.6 0.7 - - + -
470C ALA* 4.0 6.5 - - + -
471C GLN 3.0 10.1 + - - +
473C PHE* 1.3 111.0 - - + +
475C GLN* 1.3 64.8 + - - +
477C LYS* 3.3 7.0 + - - +
478C ALA* 2.9 22.5 + - - +
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Residues in contact with GLN 475 (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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467C LEU* 3.6 33.0 - - + +
468C LYS* 3.2 17.7 - - - +
470C ALA 3.1 15.7 - - - +
471C GLN 2.9 15.6 + - - +
472C ILE* 3.3 20.7 - - + +
474C ILE* 1.3 77.6 - - - +
476C LYS* 1.3 60.8 + - + +
478C ALA* 3.3 1.7 + - - +
479C VAL* 2.9 35.1 + - - +
494C GLN* 5.0 4.6 - - - +
497C LEU* 3.4 29.5 - - + +
501C ASN* 3.1 26.3 + - - +
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Residues in contact with LYS 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ILE* 2.9 39.9 + - + +
473C PHE* 4.0 7.6 - - - +
475C GLN* 1.3 79.9 - - + +
477C LYS* 1.3 57.5 + - - +
479C VAL* 3.3 3.9 + - + +
480C LYS* 2.8 29.6 + - - +
494C GLN* 3.8 28.7 - - - +
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Residues in contact with LYS 477 (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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408B SER* 4.1 10.6 + - - -
184C ASP* 5.3 0.7 - - - -
187C SER* 3.9 24.9 - - - +
188C LEU* 3.5 32.6 - - + +
473C PHE* 3.4 29.0 + - - +
474C ILE* 3.3 6.5 + - - +
476C LYS* 1.3 78.6 - - - +
478C ALA* 1.3 61.6 + - - +
480C LYS* 3.3 24.0 + - - +
481C ASN* 3.2 27.9 + - - +
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Residues in contact with ALA 478 (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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183C TRP* 4.2 15.5 - - + -
187C SER* 3.8 11.8 - - - -
467C LEU* 3.8 26.5 - - + -
474C ILE* 2.9 17.7 + - + +
475C GLN 3.6 4.3 - - - +
477C LYS* 1.3 78.9 - - - +
479C VAL* 1.3 60.3 + - - +
481C ASN* 3.2 9.4 + - - +
482C PHE* 3.0 31.6 + - + -
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Residues in contact with VAL 479 (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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467C LEU* 4.8 2.5 - - + -
475C GLN 2.9 21.2 + - - +
476C LYS* 3.8 4.7 - - + +
478C ALA* 1.3 73.8 - - - +
480C LYS* 1.3 66.9 + - - +
482C PHE* 3.2 7.6 + - + +
483C THR* 2.9 35.8 + - - +
490C GLY 3.6 20.4 - - - +
493C ILE* 4.2 15.9 - - + -
494C GLN* 3.8 29.6 - - + +
497C LEU* 3.8 19.5 - - + -
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Residues in contact with LYS 480 (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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476C LYS 2.8 18.5 + - - +
477C LYS* 3.5 23.2 - - - +
478C ALA 3.2 0.2 - - - -
479C VAL* 1.3 77.8 - - - +
481C ASN* 1.3 85.7 + - - +
483C THR* 3.4 7.5 + - - -
484C GLU* 3.2 42.1 + - + +
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Residues in contact with ASN 481 (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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186C TRP 4.2 1.8 + - - -
187C SER* 2.9 40.2 + - - +
190C PRO* 4.1 20.5 - - - +
193C LEU* 3.7 25.5 - - + +
477C LYS 3.2 12.6 + - - -
478C ALA* 3.2 8.7 + - - +
479C VAL 3.1 0.4 - - - -
480C LYS* 1.3 99.4 + - - +
482C PHE* 1.3 63.3 + - - +
484C GLU* 3.2 21.4 + - - +
485C VAL* 3.4 14.9 + - - +
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Residues in contact with PHE 482 (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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183C TRP* 4.1 19.5 - + - -
193C LEU* 3.7 23.8 - - + -
196C VAL* 4.1 18.8 - - + -
197C SER* 4.9 1.8 - - - -
463C ILE* 3.9 24.9 - - + -
467C LEU* 4.8 1.8 - - + -
478C ALA* 3.0 35.9 + - + -
479C VAL* 3.2 8.7 + - + +
481C ASN* 1.3 75.5 - - - +
483C THR* 1.3 62.5 + - - +
485C VAL* 3.2 9.1 + - - +
486C HIS 3.1 21.7 + - - +
489C TYR* 3.6 40.0 - + + +
490C GLY* 3.9 16.8 - - - +
493C ILE* 3.6 20.6 - - + -
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Residues in contact with THR 483 (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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479C VAL* 2.9 26.0 + - - +
480C LYS* 3.6 9.1 - - - -
482C PHE* 1.3 75.8 - - - +
484C GLU* 1.3 64.3 + - + +
486C HIS* 3.3 6.8 + - - -
487C PRO* 3.3 36.6 - - + +
490C GLY* 3.4 16.0 - - - -
491C SER 4.4 0.7 + - - -
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Residues in contact with GLU 484 (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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190C PRO* 6.0 1.7 - - - +
193C LEU* 6.1 0.5 - - - +
440C VAL* 3.9 21.2 - - + +
444C ARG* 3.4 12.5 + - - -
480C LYS* 3.2 41.7 + - + +
481C ASN* 3.2 15.1 + - - +
483C THR* 1.3 75.1 - - + +
485C VAL* 1.3 66.9 + - - +
487C PRO* 5.6 0.5 - - - +
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Residues in contact with VAL 485 (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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193C LEU* 3.7 24.7 - - + -
440C VAL* 3.7 14.6 - - + +
443C VAL* 3.7 22.0 - - + +
444C ARG* 2.9 60.3 + - - +
447C TYR* 5.0 0.9 - - + -
481C ASN 3.5 14.4 - - - +
482C PHE* 3.2 12.1 + - - +
484C GLU* 1.3 77.1 - - - +
486C HIS* 1.3 60.1 + - + +
489C TYR* 3.7 19.5 - - + -
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Residues in contact with HIS 486 (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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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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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