Contacts of the helix formed by residues 439 - 458 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A TRP* 4.7 0.4 - - - -
438A MET* 1.3 74.9 - - - +
440A ASN* 1.3 64.3 + - - +
441A GLN* 3.2 12.3 - - - +
442A GLU* 2.9 56.6 + - - +
443A VAL* 3.2 20.9 + - - +
355B LYS* 3.9 9.1 - - + +
356B GLU* 3.2 23.1 - - - +
441B GLN* 3.7 25.2 + - - +
445B GLU* 3.9 8.1 - - - +
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Residues in contact with ASN 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG* 2.7 35.6 + - - +
350A VAL* 3.8 13.9 - - + +
357A ALA* 3.8 15.7 - - + -
359A PRO* 4.0 28.1 - - - +
435A TRP* 3.6 14.8 - - - -
439A ASN* 1.3 72.7 - - - +
441A GLN* 1.3 62.9 + - - +
443A VAL* 3.4 2.6 + - - +
444A CYS* 3.1 28.9 + - - -
356B GLU* 2.9 32.6 + - - +
357B ALA 4.4 4.3 + - - +
358B MET* 5.7 0.6 - - - +
441B GLN* 5.8 0.9 - - - +
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Residues in contact with GLN 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 3.9 3.5 - - - -
355A LYS 2.9 24.6 + - - -
356A GLU* 3.8 5.5 - - - +
357A ALA* 3.0 33.4 + - + +
439A ASN* 3.2 8.3 - - - +
440A ASN* 1.3 79.6 - - - +
442A GLU* 1.3 63.5 + - - +
444A CYS* 3.6 0.9 + - - +
445A GLU* 2.8 60.0 + - - +
439B ASN* 3.7 20.3 + - - +
440B ASN* 5.9 0.2 - - - +
441B GLN* 3.8 27.8 + - + +
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Residues in contact with GLU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A VAL 4.4 1.6 - - - +
438A MET* 3.2 30.3 - - + +
439A ASN* 2.9 50.5 + - - +
441A GLN* 1.3 74.7 - - - +
443A VAL* 1.3 63.6 + - - +
445A GLU* 3.8 9.3 - - - +
446A ILE* 2.9 43.5 + - + +
488A LYS* 4.6 11.5 + - - -
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE* 3.7 20.9 - - + -
434A LEU* 3.8 22.9 - - + -
435A TRP* 3.7 29.6 - - + -
438A MET* 3.8 29.6 - - + -
439A ASN 3.2 18.5 + - - +
440A ASN 3.7 4.5 - - - +
442A GLU* 1.3 76.9 - - - +
444A CYS* 1.3 59.3 + - - +
446A ILE* 3.3 2.8 + - - +
447A ALA* 2.8 28.2 + - - +
481A LEU* 4.0 13.2 - - + +
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Residues in contact with CYS 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A VAL* 3.4 33.2 - - - -
351A LEU 4.3 0.2 - - - -
352A PHE* 3.4 45.0 - - + -
357A ALA* 4.1 7.2 - - + -
426A CYS* 4.3 0.5 - - - -
428A ILE* 4.0 20.0 - - - -
440A ASN 3.1 16.5 + - - +
441A GLN 4.0 3.1 - - - +
443A VAL* 1.3 77.1 - - - +
445A GLU* 1.3 62.7 + - - +
447A ALA* 3.2 1.7 + - - +
448A ARG* 2.9 26.7 + - - +
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Residues in contact with GLU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 4.1 17.5 - - + -
441A GLN* 2.8 54.7 + - - +
442A GLU* 3.8 9.2 - - - +
444A CYS* 1.3 75.7 - - - +
446A ILE* 1.3 64.9 + - + +
448A ARG* 4.0 1.9 + - - +
449A ARG* 3.1 25.3 + - - +
439B ASN* 3.8 8.3 - - - +
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Residues in contact with ILE 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A MET* 3.5 25.1 - - + -
442A GLU* 2.9 28.5 + - + +
443A VAL 3.7 2.7 - - - +
445A GLU* 1.3 76.3 - - + +
447A ALA* 1.3 65.9 + - - +
449A ARG* 3.2 5.5 + - - +
450A ARG* 3.0 31.0 + - + +
480A TYR* 3.6 31.2 - - + -
481A LEU* 3.6 20.2 - - + -
484A LEU* 3.7 14.1 - - + -
488A LYS* 6.1 0.7 - - - -
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Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A CYS* 4.2 7.0 - - - -
428A ILE* 3.8 23.1 - - + -
443A VAL 2.8 20.7 + - - +
444A CYS 3.2 3.3 + - - +
446A ILE* 1.3 76.0 - - - +
448A ARG* 1.3 63.4 + - - +
450A ARG* 3.2 1.7 + - - -
451A ILE* 3.0 27.7 + - - +
477A ALA* 3.8 16.5 - - + +
481A LEU* 4.3 13.4 - - + +
498A VAL* 4.6 5.8 - - + -
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Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 3.7 26.2 - - + -
354A GLY 5.4 0.7 - - - -
425A GLU* 3.3 43.0 + - + +
426A CYS* 4.3 8.8 - - - -
444A CYS 2.9 16.4 + - - +
445A GLU 4.0 2.7 - - - +
447A ALA* 1.3 76.0 - - - +
449A ARG* 1.3 64.7 + - - +
451A ILE* 3.2 7.7 + - - +
452A LEU* 3.0 52.3 + - + +
505A ARG* 4.6 4.9 - - - +
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Residues in contact with ARG 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLU 3.1 19.5 + - - +
446A ILE* 3.7 5.4 - - - +
447A ALA 3.2 0.2 - - - -
448A ARG* 1.3 81.1 - - - +
450A ARG* 1.3 59.5 - - - +
452A LEU* 3.4 7.8 + - + +
453A MET* 2.9 68.6 + - + +
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Residues in contact with ARG 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ILE* 3.0 21.1 + - + +
447A ALA 3.9 0.4 - - - +
449A ARG* 1.3 73.6 - - - +
451A ILE* 1.3 65.5 + - - +
453A MET* 3.6 37.4 - - - +
454A TRP* 3.1 22.7 + - - +
457A LYS* 6.1 1.2 - - - +
473A ALA 4.6 2.1 - - - +
476A ALA* 4.7 9.0 + - + +
477A ALA* 3.8 24.5 - - - +
480A TYR* 3.6 65.3 + - + +
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Residues in contact with ILE 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A CYS* 4.4 15.3 - - + -
447A ALA 3.0 21.9 + - - +
448A ARG* 3.2 6.5 + - - +
450A ARG* 1.3 76.4 - - - +
452A LEU* 1.3 62.7 + - - +
454A TRP* 3.2 10.9 + - - +
455A HIS* 3.2 22.2 + - + -
473A ALA* 3.9 27.8 - - + +
474A CYS* 4.3 10.5 - - - +
477A ALA* 3.9 5.4 - - + -
498A VAL* 3.9 24.5 - - + -
500A ASP* 3.8 16.8 - - + +
505A ARG* 3.5 35.4 - - - +
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Residues in contact with LEU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A ARG* 3.0 62.0 + - + +
449A ARG* 3.7 7.4 - - + +
451A ILE* 1.3 75.5 - - - +
453A MET* 1.3 64.5 + - - +
455A HIS* 3.1 6.0 + - - +
456A LYS* 3.0 38.2 + - - +
505A ARG* 4.0 31.0 - - + +
507A PHE* 3.8 28.7 - - + -
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Residues in contact with MET 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A ARG* 2.9 61.7 + - + +
450A ARG* 3.6 49.8 - - - +
452A LEU* 1.3 72.2 - - - +
454A TRP* 1.3 63.6 + - - +
456A LYS* 3.4 17.3 + - - +
457A LYS* 2.9 47.2 + - - +
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Residues in contact with TRP 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A ARG 3.1 14.8 + - - +
451A ILE 3.5 8.3 - - - +
452A LEU 3.2 0.4 - - - -
453A MET* 1.3 77.4 - - - +
455A HIS* 1.3 86.8 + + - +
457A LYS* 3.2 9.5 + - - +
458A ASN* 2.8 72.6 + - + +
459A GLY 3.9 16.4 - - - -
461A PRO* 3.9 21.5 - - + -
471A ASP* 5.7 1.1 - - - -
472A PRO* 3.6 35.5 - - + +
473A ALA* 3.7 31.0 - - + +
476A ALA* 4.5 11.7 - - + -
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Residues in contact with HIS 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 6.1 0.4 - - - +
451A ILE* 3.2 32.7 + - + +
452A LEU* 3.1 8.7 + - - +
454A TRP* 1.3 99.5 - + - +
456A LYS* 1.3 59.8 + - - +
458A ASN 3.2 18.3 + - - +
460A ALA* 5.4 5.5 - - + +
461A PRO* 5.0 3.7 - - + +
466A ARG* 4.3 27.6 + - - -
471A ASP* 4.8 1.0 + - - -
473A ALA* 3.6 18.5 - - + +
500A ASP* 4.4 5.7 + - - -
505A ARG* 4.0 34.7 + - + +
507A PHE* 3.8 19.6 - - + -
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Residues in contact with LYS 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A LEU* 3.0 33.3 + - - +
453A MET* 3.8 16.8 - - - +
454A TRP 3.3 0.4 - - - -
455A HIS* 1.3 76.2 - - - +
457A LYS* 1.3 64.8 + - + +
458A ASN 3.6 0.4 - - - -
507A PHE* 3.4 40.3 - - + -
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Residues in contact with LYS 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ARG* 6.1 1.2 - - - +
453A MET* 2.9 45.8 + - - +
454A TRP* 3.2 9.1 + - - +
455A HIS 3.1 0.4 - - - -
456A LYS* 1.3 85.0 - - + +
458A ASN* 1.3 74.5 + - - +
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Residues in contact with ASN 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A TRP* 2.8 75.6 + - + +
455A HIS* 3.2 18.8 + - - +
456A LYS 3.6 0.6 - - - -
457A LYS* 1.3 93.5 + - - +
459A GLY* 1.3 63.6 + - - +
460A ALA* 3.7 1.4 + - - -
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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
------------------------------------------------------------
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