Contacts of the helix formed by residues 435 - 450 (chain B) in PDB entry 4RDO
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 THR 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434B SER* 1.3 84.8 + - - +
436B GLU* 1.3 59.9 + - - +
437B HIS* 3.5 9.4 + - - +
438B GLY* 2.8 22.0 + - - -
439B ASN* 2.8 28.6 + - - +
490B LYS* 6.2 0.7 - - - +
491B TRP* 3.9 28.6 - - + +
528B ASP* 4.6 8.6 + - + +
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Residues in contact with GLU 436 (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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435B THR* 1.3 73.7 - - - +
437B HIS* 1.3 57.1 + - - +
439B ASN* 3.5 6.4 + - - +
440B LYS* 3.0 58.3 + - + +
479B TYR* 5.2 11.8 - - + -
491B TRP* 5.3 2.2 - - - +
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Residues in contact with HIS 437 (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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435B THR* 3.2 8.2 + - - +
436B GLU* 1.3 76.4 + - - +
438B GLY* 1.3 67.2 + - - +
440B LYS* 3.3 8.1 + - - +
441B ARG* 3.1 50.9 + - + +
529B THR* 5.2 3.6 - - - -
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Residues in contact with GLY 438 (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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434B SER* 3.5 21.3 - - - -
435B THR* 2.8 15.6 + - - -
437B HIS* 1.3 74.5 - - - +
439B ASN* 1.3 57.2 + - - +
441B ARG* 3.1 4.3 + - - +
442B LEU* 2.9 33.0 + - - +
528B ASP* 5.0 0.2 - - - -
529B THR* 3.6 22.0 - - - -
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Residues in contact with ASN 439 (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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433B CYS* 3.5 16.2 - - - -
434B SER* 2.9 39.2 + - - -
435B THR 2.8 19.6 + - - +
436B GLU* 3.9 4.5 - - - +
438B GLY* 1.3 72.3 - - - +
440B LYS* 1.3 58.3 + - - +
442B LEU* 4.5 3.1 - - - +
443B ASP* 2.8 32.4 + - - +
477B VAL* 3.8 21.2 - - + +
479B TYR* 3.7 21.1 - - + +
492B LYS 5.3 0.8 + - - -
493B GLY* 4.6 4.9 - - - -
494B ARG 6.0 0.2 - - - -
495B PHE* 3.6 17.1 - - - -
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Residues in contact with LYS 440 (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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436B GLU* 3.0 44.9 + - + +
437B HIS* 3.6 7.2 - - - +
438B GLY 3.3 0.2 - - - -
439B ASN* 1.3 76.8 - - - +
441B ARG* 1.3 62.4 + - - +
443B ASP* 3.7 2.8 - - - +
444B ALA* 3.0 25.6 + - - +
479B TYR* 3.6 19.3 - - + +
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Residues in contact with ARG 441 (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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413B PHE* 4.0 19.5 - - + -
437B HIS* 3.1 39.3 + - + +
438B GLY* 3.1 8.5 + - - +
440B LYS* 1.3 77.5 - - - +
442B LEU* 1.3 62.7 + - + +
444B ALA* 3.5 5.1 + - - +
445B ALA* 3.1 21.7 + - - +
528B ASP 4.6 1.4 + - - -
529B THR* 2.8 54.2 + - - -
530B GLN* 4.2 5.5 - - - +
531B GLU* 4.7 2.9 - - - +
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Residues in contact with LEU 442 (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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413B PHE* 3.6 44.4 - - + -
415B ILE* 4.2 18.4 - - + -
434B SER* 4.6 7.4 - - - -
438B GLY 2.9 19.4 + - - +
439B ASN* 4.1 3.1 - - - +
441B ARG* 1.3 72.8 - - - +
443B ASP* 1.3 60.4 + - - +
445B ALA* 3.8 4.4 - - - +
446B TYR* 2.9 24.8 + - - +
457B LEU* 4.0 11.4 - - + -
473B MET* 3.4 26.4 - - + +
495B PHE* 3.6 31.6 - - + -
529B THR* 4.3 13.9 - - + -
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Residues in contact with ASP 443 (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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439B ASN 2.8 19.7 + - - +
440B LYS* 3.7 4.3 - - - +
442B LEU* 1.3 77.4 - - - +
444B ALA* 1.3 57.8 + - - +
446B TYR* 3.3 1.0 + - - +
447B ARG* 2.9 67.2 + - - +
473B MET* 4.2 3.5 - - - +
476B ALA* 3.5 13.5 - - - +
477B VAL* 2.8 40.9 + - + +
479B TYR* 4.1 18.4 + - - +
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Residues in contact with ALA 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 LYS 3.0 16.8 + - - +
441B ARG* 3.8 5.4 - - - +
443B ASP* 1.3 75.5 - - - +
445B ALA* 1.3 60.3 + - - +
447B ARG* 4.1 5.5 - - - +
448B SER* 3.0 30.6 + - - -
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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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411B ARG* 3.7 28.9 + - - +
413B PHE* 3.6 36.6 - - + -
441B ARG 3.1 13.5 + - - +
442B LEU 3.8 4.0 - - - +
444B ALA* 1.3 76.0 - - - +
446B TYR* 1.3 61.7 + - - +
448B SER* 3.3 1.6 + - - -
449B MET* 3.1 26.3 + - - +
455B VAL* 4.4 6.8 - - + +
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Residues in contact with TYR 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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442B LEU 2.9 17.8 + - - +
443B ASP* 3.8 3.4 - - - +
445B ALA* 1.3 77.5 - - - +
447B ARG* 1.3 65.3 + - + +
449B MET* 3.6 4.7 - - + +
450B ASN* 3.3 15.2 + - - -
451B GLY 4.9 2.6 + - - -
455B VAL* 4.2 15.8 - - + +
473B MET* 3.4 49.8 - - + -
474B LYS* 3.3 17.2 + - - -
475B SER* 3.6 12.5 - - - -
476B ALA* 3.5 30.5 - - + -
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Residues in contact with ARG 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 ASP* 2.9 54.0 + - - +
444B ALA* 4.1 4.9 - - - +
446B TYR* 1.3 76.9 - - + +
448B SER* 1.3 60.8 + - - +
450B ASN* 2.9 32.4 + - - +
476B ALA* 4.2 20.7 - - + +
477B VAL 5.0 5.1 + - - -
479B TYR* 5.8 1.6 - - - -
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Residues in contact with SER 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ARG* 3.8 14.2 + - - -
444B ALA 3.0 18.5 + - - -
445B ALA 3.3 5.0 + - - -
447B ARG* 1.3 78.9 - - - +
449B MET* 1.3 64.8 + - - +
450B ASN* 3.2 6.8 + - - +
452B LYS* 5.3 1.7 - - - +
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Residues in contact with MET 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B HIS* 3.5 23.8 - - - +
411B ARG* 3.4 50.0 - - + +
445B ALA 3.1 16.5 + - - +
446B TYR* 3.6 9.6 - - + +
447B ARG 3.2 0.2 - - - -
448B SER* 1.3 80.5 + - - +
450B ASN* 1.3 68.5 + - - +
451B GLY 4.6 2.2 - - - +
452B LYS* 2.8 33.6 + - - +
453B GLY 3.1 33.7 - - - +
454B PRO 4.4 1.8 - - - +
455B VAL* 4.2 11.0 - - + -
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Residues in contact with ASN 450 (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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446B TYR 3.3 5.6 + - - -
447B ARG* 2.9 19.3 + - - +
448B SER* 3.6 6.5 - - - +
449B MET* 1.3 77.4 - - - +
451B GLY* 1.3 56.9 + - - +
452B LYS* 3.0 25.6 + - + +
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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