Contacts of the helix formed by residues 440 - 450 (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 VAL 440 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193C LEU* 4.1 7.6 - - + -
438C ASP* 3.4 7.8 + - - +
439C ASN* 1.3 89.7 - - + +
441C THR* 1.3 74.4 + - - +
442C GLN 3.4 2.2 - - - -
443C VAL* 2.8 9.4 + - - +
444C ARG* 2.8 35.5 + - - +
484C GLU* 3.9 21.3 - - + +
485C VAL* 3.7 37.5 - - + +
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Residues in contact with THR 441 (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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294C PHE* 3.4 26.5 - - + -
438C ASP* 2.8 32.9 + - - -
440C VAL* 1.3 80.4 - - - +
442C GLN* 1.3 63.7 + - + +
444C ARG* 3.3 20.1 + - - +
445C ALA* 3.3 18.5 + - - +
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Residues in contact with GLN 442 (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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194C HIS* 3.4 22.5 - - + +
294C PHE* 3.6 37.9 - - + -
301C LYS* 3.2 24.1 - - + +
302C VAL* 2.9 52.1 + - - +
304C PRO* 4.7 8.9 - - - +
438C ASP* 4.6 0.4 + - - -
440C VAL 3.4 0.4 - - - -
441C THR* 1.3 74.2 - - + +
443C VAL* 1.3 60.4 + - + +
445C ALA* 3.4 5.5 + - - -
446C PHE* 3.0 18.5 + - - +
3001C NDP 3.0 24.4 + - - +
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Residues in contact with VAL 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LEU 3.6 9.0 - - - +
194C HIS* 3.7 35.7 - - + +
197C SER* 3.4 28.7 - - - +
439C ASN 3.4 26.2 - - - +
440C VAL* 2.8 8.0 + - - +
442C GLN* 1.3 78.6 - - + +
444C ARG* 1.3 57.5 + - - +
446C PHE* 3.2 4.4 + - + +
447C TYR* 3.0 27.2 + - - +
485C VAL* 3.7 22.9 - - + -
489C TYR* 4.7 2.7 - - + -
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Residues in contact with ARG 444 (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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440C VAL* 2.8 20.8 + - - +
441C THR* 3.7 26.1 + - - +
442C GLN 3.3 0.2 - - - -
443C VAL* 1.3 74.5 - - - +
445C ALA* 1.3 59.6 + - - +
447C TYR* 4.4 2.7 - - - -
448C VAL* 2.9 51.4 + - + +
484C GLU 3.4 14.8 + - - -
485C VAL* 2.9 39.7 + - - +
486C HIS* 4.0 14.8 - - + +
487C PRO* 6.0 1.3 - - - +
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Residues in contact with ALA 445 (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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441C THR* 3.3 11.2 + - + +
442C GLN* 3.6 10.8 - - - +
443C VAL 3.2 0.4 - - - -
444C ARG* 1.3 78.0 - - - +
446C PHE* 1.3 58.1 + - - +
448C VAL* 5.0 0.4 - - - -
449C ASN* 2.8 49.7 + - + +
450C VAL* 3.5 3.4 + - - +
3001C NDP 4.0 16.6 - - - +
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Residues in contact with PHE 446 (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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194C HIS* 4.5 1.1 - + - +
197C SER* 3.7 40.8 - - - -
198C PHE* 3.5 33.2 - + + -
201C SER* 4.4 1.1 - - - -
442C GLN 3.0 8.7 + - - +
443C VAL* 3.2 11.2 + - - +
445C ALA* 1.3 77.4 - - - +
447C TYR* 1.3 65.4 + - + +
450C VAL* 3.2 34.8 + - + +
451C LEU* 3.3 46.6 + - + +
459C LEU* 4.8 1.6 - - + -
3001C NDP 3.1 55.6 + + - +
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Residues in contact with TYR 447 (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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443C VAL 3.0 15.9 + - - +
444C ARG* 3.7 7.2 - - - +
446C PHE* 1.3 84.5 - - + +
448C VAL* 1.3 67.5 + - + +
451C LEU* 3.9 9.4 - - + +
453C GLU* 5.5 0.2 + - - -
456C ARG* 2.9 65.5 + - + +
459C LEU* 4.0 17.7 - - + -
460C CYS* 4.2 9.7 - - - -
485C VAL* 5.0 0.2 - - + -
486C HIS* 4.2 22.4 - + + -
488C ASP* 3.9 10.8 + - + +
489C TYR* 3.5 65.2 - + + -
492C HIS* 4.7 4.9 - - - -
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Residues in contact with VAL 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ARG* 2.9 31.8 + - + +
445C ALA* 5.0 0.2 - - - -
447C TYR* 1.3 81.0 - - + +
449C ASN* 1.3 77.2 + - - +
451C LEU 3.6 0.9 - - - +
456C ARG* 2.7 29.3 + - - +
486C HIS* 3.7 31.9 - - + +
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Residues in contact with ASN 449 (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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445C ALA* 2.8 32.3 + - + +
448C VAL* 1.3 93.9 + - - +
450C VAL* 1.3 66.1 + - + +
451C LEU 4.3 1.8 - - - +
3001C NDP 6.1 1.3 - - - -
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Residues in contact with VAL 450 (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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445C ALA 3.5 1.3 + - - +
446C PHE* 3.2 29.0 + - + +
449C ASN* 1.3 79.7 - - + +
451C LEU* 1.3 61.0 + - + +
455C GLN* 4.0 5.4 - - - +
3001C NDP 3.3 94.6 - - + +
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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