Contacts of the helix formed by residues 439 - 459 (chain B) in PDB entry 3RT0
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 ASN 439 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LYS* 4.4 12.0 - - - +
356A GLU* 3.1 23.8 - - - +
441A GLN* 3.7 21.6 + - - +
445A GLU* 3.8 8.0 - - - +
435B TRP* 4.6 0.2 - - - -
438B MET* 1.3 73.1 - - - +
440B ASN* 1.3 65.1 + - - +
441B GLN* 3.1 12.1 - - - +
442B GLU* 2.9 43.2 + - - +
443B VAL* 3.1 23.0 + - - +
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Residues in contact with ASN 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLU* 3.0 31.3 + - - +
357A ALA 4.5 2.6 + - - -
441A GLN* 5.9 0.2 - - - +
348B ARG* 2.8 33.0 + - - +
350B VAL* 3.8 14.8 - - + -
357B ALA* 3.8 17.3 - - + -
359B PRO* 4.0 28.1 - - - +
435B TRP* 3.4 15.7 - - - -
439B ASN* 1.3 71.3 - - - +
441B GLN* 1.3 64.3 + - - +
443B VAL* 3.4 1.7 + - - +
444B CYS* 3.1 27.7 + - - -
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Residues in contact with GLN 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLU* 4.8 0.2 + - - -
439A ASN* 3.7 21.5 + - - +
440A ASN* 5.8 0.7 - - - +
441A GLN* 3.8 27.6 + - + +
352B PHE* 4.0 2.9 - - - -
355B LYS 2.8 26.3 + - - -
356B GLU* 3.8 4.9 - - - +
357B ALA* 3.0 32.7 + - + +
439B ASN* 3.1 9.0 - - - +
440B ASN* 1.3 79.7 - - - +
442B GLU* 1.3 64.2 + - - +
444B CYS* 3.4 2.1 + - - +
445B GLU* 3.0 56.8 + - - +
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Residues in contact with GLU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B VAL 4.2 2.4 - - - +
438B MET* 3.4 26.2 - - + +
439B ASN* 2.9 50.2 + - - +
441B GLN* 1.3 75.9 - - - +
443B VAL* 1.3 60.2 + - - +
445B GLU* 3.8 11.6 - - - +
446B ILE* 2.9 43.0 + - + +
488B LYS* 4.0 16.3 + - - -
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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
----------------------------------------------------------
428B ILE* 4.2 13.5 - - + -
434B LEU* 3.9 22.9 - - + -
435B TRP* 3.5 28.0 - - + -
438B MET* 3.8 29.6 - - + -
439B ASN 3.1 17.0 + - - +
440B ASN 3.8 4.0 - - - +
442B GLU* 1.3 77.0 - - - +
444B CYS* 1.3 57.6 + - - +
446B ILE* 3.8 1.2 - - - +
447B ALA* 2.9 28.2 + - - +
481B LEU* 3.7 25.3 - - + +
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Residues in contact with CYS 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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350B VAL* 3.4 33.9 - - - -
352B PHE* 3.4 44.1 - - + -
357B ALA* 3.9 7.9 - - + -
426B CYS* 4.4 0.3 - - - -
428B ILE* 4.2 18.8 - - - -
440B ASN 3.1 15.2 + - - +
441B GLN 3.8 3.4 - - - +
443B VAL* 1.3 76.9 - - - +
445B GLU* 1.3 65.7 + - - +
447B ALA* 3.3 1.7 + - - +
448B ARG* 3.0 26.9 + - - +
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ASN* 3.9 8.1 - - - +
352B PHE* 4.1 15.9 - - + -
441B GLN* 3.0 52.6 + - - +
442B GLU* 3.8 11.0 - - - +
444B CYS* 1.3 76.1 - - - +
446B ILE* 1.3 63.5 + - - +
448B ARG* 3.5 3.2 + - - +
449B ARG* 3.0 47.6 + - - +
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Residues in contact with ILE 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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438B MET* 3.3 29.4 - - + -
442B GLU* 2.9 29.2 + - + +
443B VAL 3.8 2.9 - - - +
445B GLU* 1.3 76.7 - - - +
447B ALA* 1.3 63.1 + - - +
449B ARG* 3.2 25.3 + - - +
450B ARG* 2.9 26.0 + - + +
480B TYR* 3.6 36.1 - - + -
481B LEU* 3.6 13.5 - - + -
484B LEU* 3.5 13.9 - - + -
488B LYS* 5.9 0.2 - - - -
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Residues in contact with ALA 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B CYS* 4.3 5.2 - - - -
428B ILE* 4.0 23.1 - - + -
443B VAL 2.9 18.5 + - - +
444B CYS 3.3 3.3 + - - +
446B ILE* 1.3 77.7 - - - +
448B ARG* 1.3 58.9 + - - +
450B ARG 3.4 0.3 + - - -
451B ILE* 3.0 36.1 + - + +
477B ALA* 3.8 17.1 - - + +
481B LEU* 4.2 14.8 - - + +
498B VAL* 4.5 5.8 - - + -
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Residues in contact with ARG 448 (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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352B PHE* 3.5 25.1 - - + -
354B GLY 5.2 1.7 + - - -
425B GLU* 3.1 43.1 + - + +
426B CYS* 4.5 6.0 - - - -
444B CYS 3.0 17.2 + - - +
445B GLU* 3.9 4.2 + - - +
447B ALA* 1.3 78.3 - - - +
449B ARG* 1.3 66.0 + - - +
451B ILE* 3.3 10.6 + - - +
452B LEU* 2.9 60.6 + - + +
505B ARG* 4.7 3.6 - - - +
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Residues in contact with ARG 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU* 3.0 37.3 + - - +
446B ILE* 3.5 32.9 - - + +
448B ARG* 1.3 84.9 - - - +
450B ARG* 1.3 59.5 + - + +
452B LEU* 3.2 9.4 + - + +
453B MET* 2.8 53.9 + - + +
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Residues in contact with ARG 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ILE* 2.9 21.7 + - + +
447B ALA 3.8 3.4 - - - +
449B ARG* 1.3 73.9 - - + +
451B ILE* 1.3 66.7 + - - +
453B MET* 3.5 31.8 + - + +
454B TRP* 3.0 29.6 + - - +
457B LYS* 5.9 3.6 - - - +
473B ALA 4.7 1.5 - - - +
476B ALA* 3.9 24.3 + - - +
477B ALA* 3.9 17.9 - - + -
480B TYR* 3.5 57.7 - - + +
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Residues in contact with ILE 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B CYS* 4.4 16.4 - - + -
447B ALA 3.0 25.4 + - - +
448B ARG* 3.6 6.5 - - - +
450B ARG* 1.3 75.7 - - - +
452B LEU* 1.3 64.4 + - - +
454B TRP* 3.3 1.9 + - - +
455B HIS* 3.1 30.9 + - + -
473B ALA* 4.0 29.2 - - + +
474B CYS* 4.4 1.1 - - - -
477B ALA* 4.1 4.9 - - + -
498B VAL* 4.1 21.8 - - + -
500B ASP* 3.8 22.7 - - + +
505B ARG* 3.4 35.9 - - - +
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Residues in contact with LEU 452 (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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448B ARG* 2.9 62.5 + - - +
449B ARG* 3.2 7.6 + - + +
451B ILE* 1.3 72.1 - - - +
453B MET* 1.3 66.7 + - + +
455B HIS* 3.3 4.8 + - + +
456B LYS* 2.9 25.2 + - - +
505B ARG* 3.7 38.4 - - + +
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Residues in contact with MET 453 (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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449B ARG* 2.8 50.1 + - + +
450B ARG* 3.6 36.1 - - + +
452B LEU* 1.3 72.9 - - - +
454B TRP* 1.3 63.0 + - - +
456B LYS* 3.2 7.9 + - - +
457B LYS* 3.0 28.0 + - + +
480B TYR* 6.4 1.1 - - + -
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Residues in contact with TRP 454 (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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450B ARG* 3.0 26.8 + - - +
451B ILE 3.7 4.9 - - - +
452B LEU 3.3 0.2 - - - -
453B MET* 1.3 76.5 - - - +
455B HIS* 1.3 70.1 + + - +
457B LYS* 4.2 3.4 - - + -
458B ASN* 2.9 62.9 + - + +
459B GLY 2.9 27.1 - - - -
461B PRO* 3.8 30.5 - - + -
472B PRO* 3.4 42.3 - - + +
473B ALA* 3.6 26.0 - - + -
476B ALA* 4.0 11.4 - - + -
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Residues in contact with HIS 455 (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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451B ILE* 3.1 31.9 + - + +
452B LEU* 3.7 9.4 - - + +
454B TRP* 1.3 94.6 - + - +
456B LYS* 1.3 59.3 + - - +
459B GLY* 2.7 35.0 + - - +
460B ALA* 4.4 8.2 - - + +
461B PRO* 4.3 6.7 - - + -
466B ARG* 3.9 28.7 + - - -
471B ASP* 5.0 0.2 + - - -
473B ALA* 3.6 22.9 - - + +
500B ASP* 4.4 4.4 + - - -
505B ARG* 4.1 42.9 + - + +
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Residues in contact with LYS 456 (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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452B LEU 2.9 17.3 + - - +
453B MET* 3.2 7.4 + - - +
455B HIS* 1.3 79.7 - - - +
457B LYS* 1.3 66.3 + - + +
459B GLY* 4.4 1.4 + - - -
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Residues in contact with LYS 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ARG* 5.9 3.6 - - - +
453B MET* 3.0 20.2 + - + +
454B TRP* 4.2 4.0 - - + -
456B LYS* 1.3 82.9 - - + +
458B ASN* 1.3 88.5 + - - +
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Residues in contact with ASN 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B TRP* 2.9 69.8 + - + +
457B LYS* 1.3 106.0 - - - +
459B GLY* 1.3 59.5 + - - +
460B ALA 5.1 0.9 - - - +
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Residues in contact with GLY 459 (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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454B TRP* 2.9 26.9 - - - -
455B HIS* 2.7 26.9 + - - -
456B LYS 4.4 1.4 + - - -
457B LYS 3.8 0.6 - - - -
458B ASN* 1.3 75.2 - - - +
460B ALA* 1.3 64.1 + - - -
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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
------------------------------------------------------------
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