Contacts of the helix formed by residues 440 - 449 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LEU* 4.2 7.6 - - + -
438B ASP* 3.2 4.0 + - - +
439B ASN* 1.3 89.3 - - + +
441B THR* 1.3 73.5 + - - +
442B GLN 3.5 1.6 - - - -
443B VAL* 3.0 10.2 + - - +
444B ARG* 2.9 42.0 + - - +
484B GLU* 4.0 41.1 - - + +
485B VAL* 3.9 22.0 - - + +
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Residues in contact with THR 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 3.8 20.1 - - + -
438B ASP* 2.6 37.4 + - - -
440B VAL* 1.3 78.1 - - - +
442B GLN* 1.3 63.5 + - + +
443B VAL 3.3 0.2 + - - -
444B ARG* 3.3 25.1 + - - +
445B ALA* 3.3 11.8 + - - +
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Residues in contact with GLN 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B HIS* 3.3 24.9 + - + +
292B PHE* 4.8 0.2 - - - -
294B PHE* 3.7 34.6 - - + -
301B LYS* 3.2 23.7 - - + +
302B VAL* 2.9 53.0 + - + +
304B PRO* 4.7 9.5 - - - +
438B ASP* 4.4 2.0 + - - -
440B VAL 3.5 0.2 - - - -
441B THR* 1.3 77.5 - - + +
443B VAL* 1.3 58.2 + - + +
445B ALA* 3.4 8.1 + - - +
446B PHE* 3.0 26.0 + - - +
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Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.8 9.2 - - + +
194B HIS* 3.5 40.2 - - + +
197B SER* 3.4 28.5 - - - +
439B ASN 3.5 22.9 - - - +
440B VAL 3.0 8.2 + - - +
442B GLN* 1.3 74.3 - - + +
444B ARG* 1.3 60.2 + - - +
446B PHE* 3.1 3.1 + - + +
447B TYR* 2.9 27.7 + - - +
485B VAL* 3.8 22.2 - - + -
489B TYR* 4.6 2.2 - - + -
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Residues in contact with ARG 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B VAL* 2.9 25.8 + - - +
441B THR* 3.5 27.6 + - - +
443B VAL* 1.3 77.6 - - - +
445B ALA* 1.3 57.2 + - - +
447B TYR* 3.2 3.5 + - - +
448B VAL* 2.8 40.0 + - + +
484B GLU 3.1 25.1 + - - -
485B VAL* 2.7 30.7 + - - +
486B HIS* 4.2 18.2 + - - +
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Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B THR 3.3 9.7 + - - +
442B GLN* 3.6 11.7 - - - +
443B VAL 3.2 0.2 - - - -
444B ARG* 1.3 78.0 - - - +
446B PHE* 1.3 57.1 + - - +
448B VAL* 4.7 1.8 - - - -
449B ASN* 2.7 47.3 + - + +
450B VAL* 3.4 6.3 + - - +
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Residues in contact with PHE 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B HIS* 4.2 15.0 - + - +
197B SER* 3.6 45.5 - - - -
198B PHE* 4.0 27.1 - + + -
201B SER* 4.3 7.0 - - - -
442B GLN 3.0 13.8 + - - +
443B VAL* 3.1 11.4 + - - +
445B ALA* 1.3 76.3 - - - +
447B TYR* 1.3 68.1 + - + +
450B VAL* 3.1 58.8 + - + +
451B LEU* 3.2 40.9 + - + +
459B LEU* 4.9 0.9 - - + -
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Residues in contact with TYR 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B VAL 2.9 15.9 + - - +
444B ARG* 3.6 6.3 - - - +
446B PHE* 1.3 85.5 - - + +
448B VAL* 1.3 64.3 + - + +
451B LEU* 3.8 7.2 - - + +
456B ARG* 2.8 65.2 + - + +
459B LEU* 3.9 19.5 - - + -
460B CYS* 4.3 9.1 - - - -
485B VAL* 4.8 0.2 - - + -
486B HIS* 4.1 26.0 - + + -
488B ASP* 2.9 27.8 + - - -
489B TYR* 3.6 59.3 - + + -
492B HIS* 4.9 2.4 + - - -
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Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ARG* 2.8 30.3 + - + +
445B ALA* 4.2 1.1 - - - +
447B TYR* 1.3 80.8 - - + +
449B ASN* 1.3 75.5 + - - +
451B LEU 3.2 3.5 - - - +
456B ARG* 2.8 29.5 + - - +
486B HIS* 3.7 32.8 - - + +
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Residues in contact with ASN 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B ALA* 2.7 32.9 + - + +
448B VAL* 1.3 87.2 + - - +
450B VAL* 1.3 66.8 - - + +
451B LEU 3.2 6.4 + - - +
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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