Contacts of the helix formed by residues 440 - 449 (chain D) in PDB entry 1DGB
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LEU* 4.5 5.6 - - + -
438D ASP* 2.8 10.6 + - - +
439D ASN* 1.3 90.2 - - + +
441D THR* 1.3 79.0 + - - +
442D GLN 3.4 1.6 - - - -
443D VAL* 2.8 11.4 + - - +
444D ARG* 2.8 39.3 + - - +
484D GLU* 4.1 39.5 - - + +
485D VAL* 4.1 17.0 - - + +
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Residues in contact with THR 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D PHE* 3.9 19.3 - - + -
438D ASP* 2.6 36.5 + - - -
440D VAL* 1.3 79.3 - - - +
442D GLN* 1.3 64.7 + - + +
444D ARG* 3.0 26.3 + - - +
445D ALA* 3.1 13.0 + - + +
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Residues in contact with GLN 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D HIS* 3.4 20.4 + - + +
292D PHE* 4.9 1.4 - - - -
294D PHE* 3.4 33.2 - - + -
301D LYS* 3.3 27.9 - - + +
302D VAL* 3.0 53.2 + - + +
304D PRO* 5.0 7.7 - - - +
438D ASP* 4.5 1.0 + - - -
440D VAL 3.4 0.4 - - - -
441D THR* 1.3 77.2 - - + +
443D VAL* 1.3 59.4 + - + +
445D ALA* 3.0 10.1 + - - +
446D PHE* 2.8 27.4 + - - +
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Residues in contact with VAL 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D LEU* 4.0 9.0 - - + +
194D HIS* 3.5 33.7 - - + +
197D SER* 3.5 27.1 - - - +
439D ASN 3.4 26.0 - - - +
440D VAL* 2.8 8.5 + - - +
442D GLN* 1.3 77.9 - - + +
444D ARG* 1.3 63.4 + - - +
446D PHE* 3.0 9.3 + - - +
447D TYR* 2.9 22.3 + - - +
485D VAL* 3.8 23.3 - - + -
489D TYR* 4.7 1.3 - - + -
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Residues in contact with ARG 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440D VAL* 2.8 28.3 + - - +
441D THR* 3.4 18.7 + - - +
443D VAL* 1.3 75.2 - - - +
445D ALA* 1.3 58.7 + - - +
447D TYR* 3.3 2.4 + - - +
448D VAL* 2.9 47.9 + - + +
484D GLU 2.9 19.0 + - - -
485D VAL* 2.6 50.6 + - + +
486D HIS* 4.3 12.5 - - + +
487D PRO* 6.0 1.0 - - - +
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Residues in contact with ALA 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441D THR* 3.1 10.7 + - + +
442D GLN* 3.0 13.5 + - - +
444D ARG* 1.3 74.9 - - - +
446D PHE* 1.3 61.7 + - - +
448D VAL* 3.9 1.3 - - - -
449D ASN* 2.9 40.4 + - + +
450D VAL* 3.4 8.4 + - - +
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Residues in contact with PHE 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D HIS* 4.4 16.2 - + + +
197D SER* 3.8 38.4 - - - -
198D PHE* 4.0 34.3 - + + -
201D SER* 4.4 5.8 - - - -
442D GLN 2.8 11.9 + - - +
443D VAL* 3.0 12.8 + - - +
445D ALA* 1.3 77.3 - - - +
447D TYR* 1.3 66.9 + - + +
450D VAL* 3.2 54.6 + - + +
451D LEU* 3.2 41.3 + - + +
459D LEU* 4.8 1.3 - - + -
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Residues in contact with TYR 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D SER* 6.5 0.2 - - - -
443D VAL* 2.9 15.2 + - + +
444D ARG* 3.7 6.5 - - - +
446D PHE* 1.3 83.9 - - + +
448D VAL* 1.3 59.3 + - + +
451D LEU* 3.8 6.0 - - + +
453D GLU* 5.7 0.2 + - - -
456D ARG* 2.7 74.1 + - + +
459D LEU* 4.2 10.3 - - + -
460D CYS* 4.2 8.5 - - - -
485D VAL* 4.9 0.7 - - + -
486D HIS* 4.1 27.4 - + + -
488D ASP* 3.8 11.0 + - + +
489D TYR* 3.5 70.2 + + + -
492D HIS* 4.9 3.6 + - - +
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Residues in contact with VAL 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D ARG* 2.9 34.2 + - + +
445D ALA* 4.7 0.4 - - - -
447D TYR* 1.3 84.9 - - + +
449D ASN* 1.3 76.7 + - - +
456D ARG* 2.8 25.7 + - - +
486D HIS* 4.1 20.2 - - + +
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Residues in contact with ASN 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445D ALA* 2.9 26.0 + - - +
448D VAL* 1.3 95.6 + - - +
450D VAL* 1.3 66.0 - - + +
451D LEU 3.2 7.3 + - - +
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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