Contacts of the strand formed by residues 439 - 443 (chain B) in PDB entry 2DH3
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 ASP 439 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A ASP* 4.1 1.2 - - - +
455A HIS* 3.5 19.0 + - - -
456A TRP* 6.1 0.2 - - - -
457A ASP* 5.2 18.5 + - - +
485A SER* 4.0 14.6 + - - -
527A TYR* 6.1 2.6 - - - -
327B ASN* 5.8 0.7 + - - -
438B GLY* 1.3 76.5 - - - -
440B PHE* 1.3 79.9 + - - +
441B HIS* 3.2 23.4 - - - -
454B ARG* 3.3 27.2 - - - -
455B HIS* 2.9 32.1 + - + +
456B TRP* 5.2 1.6 - - - -
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Residues in contact with PHE 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A PRO* 4.5 6.8 - - - +
484A ALA* 3.8 30.4 + - + -
485A SER* 5.0 4.2 + - - -
318B VAL* 4.3 15.0 - - + -
319B THR* 4.5 7.9 - - + -
322B LEU* 4.2 5.2 - - + -
359B LEU* 3.8 14.6 - - + -
360B PRO* 3.9 34.8 - - + -
439B ASP* 1.3 89.9 + - - +
441B HIS* 1.3 73.9 + - - +
442B ALA* 3.7 31.6 - - + -
450B PHE* 4.5 6.1 - + - -
452B TYR* 3.5 36.6 - + + -
453B ILE 3.6 2.7 - - - -
454B ARG* 4.3 2.7 - - - -
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Residues in contact with HIS 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ASP* 3.4 10.0 + - - -
441A HIS* 3.4 14.3 + + - -
455A HIS* 3.9 1.6 + + - -
483A PRO* 4.0 14.2 - - + +
601A ZN 2.1 36.7 - - - -
439B ASP* 3.2 24.5 - - - -
440B PHE* 1.3 81.8 + - - +
442B ALA* 1.3 65.1 + - - +
443B PHE* 3.9 5.7 - - - -
452B TYR* 3.4 2.1 - - - -
453B ILE* 3.0 36.2 + - + +
455B HIS* 3.0 26.3 + + - +
481B ASP 4.3 7.0 - - - -
482B LEU* 3.7 17.0 - - + +
483B PRO* 4.0 11.3 - - + +
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Residues in contact with ALA 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A PRO* 5.7 3.8 - - - +
315B LYS* 4.6 16.6 - - + -
319B THR* 4.9 6.3 - - + -
440B PHE* 3.7 27.9 - - + -
441B HIS* 1.3 77.0 - - - +
443B PHE* 1.3 65.7 + - - +
450B PHE* 4.3 13.0 - - + -
451B SER 3.4 14.8 - - - +
452B TYR* 3.7 2.7 - - - -
480B SER 4.7 2.1 - - - +
481B ASP 5.6 0.7 - - - +
482B LEU* 4.6 2.8 - - - +
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Residues in contact with PHE 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LYS* 3.9 14.2 + - - +
441B HIS 3.9 6.7 - - - -
442B ALA* 1.3 82.1 - - - +
444B SER* 1.3 70.6 + - - +
445B ALA* 3.6 2.3 + - + -
450B PHE* 5.6 0.9 - - - -
451B SER* 3.3 36.9 + - - +
452B TYR* 4.0 9.6 - - - -
453B ILE* 4.2 9.9 - - + -
463B LEU* 4.0 18.6 - - + -
477B LEU* 3.5 35.0 - - + -
478B GLN 3.4 24.5 - - - -
480B SER* 3.9 24.5 - - - +
482B LEU* 4.3 9.4 - - + -
488B LEU* 4.0 15.3 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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