Contacts of the helix formed by residues 439 - 450 (chain A) in PDB entry 1R9J
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 ALA 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A GLU* 3.6 7.9 - - + +
410A HIS* 3.6 24.2 - - + -
413A CYS* 3.6 29.4 - - + -
436A ILE* 2.7 13.9 + - + +
438A TYR* 1.3 80.5 - - - +
440A LEU* 1.3 64.4 + - - +
441A GLY 3.0 4.4 + - - -
442A ALA* 3.1 4.0 + - - -
443A VAL* 3.0 20.4 + - + +
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ILE* 3.3 15.7 + - + +
437A GLY* 3.9 6.5 + - - +
438A TYR 3.7 2.8 - - - -
439A ALA* 1.3 76.2 - - - +
441A GLY* 1.3 62.1 + - - +
443A VAL* 3.7 13.2 - - + +
444A ARG* 2.9 26.7 + - - +
476A LEU* 4.4 15.3 - - + -
479A ALA* 5.2 7.0 - - + -
480A LEU* 3.8 28.9 - - + -
483A MET* 4.7 9.1 - - + +
437B GLY* 3.8 17.8 + - - +
440B LEU* 3.0 35.0 - - + -
476B LEU* 5.6 3.1 - - + -
479B ALA* 6.0 0.2 - - + -
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Residues in contact with GLY 441 (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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115A PRO* 5.6 0.9 - - - +
118A GLN* 3.7 6.9 - - - +
410A HIS* 3.7 13.0 + - - -
439A ALA 3.0 2.2 + - - -
440A LEU* 1.3 80.7 - - - +
442A ALA* 1.3 59.1 + - - +
444A ARG* 3.7 5.6 + - - +
445A LEU* 3.6 24.1 + - - +
437B GLY* 4.3 7.3 + - - -
438B TYR* 3.8 24.4 - - - -
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Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 3.6 20.4 - - - +
410A HIS* 3.5 12.9 + - + -
413A CYS* 3.6 14.4 - - + -
414A ALA* 3.5 30.5 - - - +
417A ASN* 3.1 12.6 + - - +
439A ALA 3.1 5.1 + - - +
441A GLY* 1.3 73.3 - - - +
443A VAL* 1.3 66.2 + - - +
444A ARG 3.2 0.9 - - - -
445A LEU* 3.2 2.6 + - - +
446A ALA* 3.0 18.0 + - - +
455A TYR* 4.7 1.6 - - - -
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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
----------------------------------------------------------
413A CYS* 4.4 5.4 - - - -
436A ILE* 4.1 19.5 - - + -
439A ALA 3.0 20.5 + - - +
440A LEU* 3.3 13.4 + - + +
442A ALA* 1.3 75.7 - - - +
444A ARG* 1.3 62.4 + - - +
446A ALA* 3.1 12.6 + - - +
447A ALA* 3.2 12.5 + - - +
455A TYR* 3.6 40.8 - - + +
480A LEU* 4.6 4.0 - - + -
483A MET* 4.2 6.9 - - + +
486A LEU* 4.2 26.9 - - + -
511A PRO* 5.0 0.5 - - - +
513A VAL* 5.3 1.6 - - + -
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Residues in contact with ARG 444 (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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440A LEU 2.9 18.0 + - - +
441A GLY* 3.8 6.1 - - - +
442A ALA 3.2 0.2 - - - -
443A VAL* 1.3 78.2 - - - +
445A LEU* 1.3 58.8 + - + +
447A ALA* 3.3 4.0 + - - +
448A ILE* 2.9 46.0 + - + +
483A MET* 3.7 23.7 - - + +
434B ASN* 3.2 36.0 + - - +
469B PRO 3.1 20.4 + - - -
470B THR* 4.0 3.6 + - - +
472B GLN 2.8 25.5 + - - -
473B PRO* 3.9 0.8 - - - +
474B VAL* 4.0 1.2 - - - +
475B GLU* 2.9 38.0 + - - -
625B PHE* 3.8 17.9 - - + -
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Residues in contact with LEU 445 (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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112A THR* 4.1 24.9 - - + +
115A PRO* 4.0 17.5 - - + -
118A GLN* 3.4 45.1 - - + +
122A ASN* 5.7 1.3 - - - +
417A ASN* 4.4 8.1 - - - +
441A GLY 3.6 8.4 + - - +
442A ALA 3.2 8.3 + - - +
444A ARG* 1.3 77.1 - - + +
446A ALA* 1.3 61.2 + - - +
448A ILE* 4.1 20.4 - - + -
449A SER* 2.8 38.0 + - - +
451A HIS* 4.0 1.3 - - + -
470B THR* 4.1 19.3 - - + -
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ASN* 3.2 25.7 - - - +
442A ALA 3.0 7.1 + - - +
443A VAL 3.1 5.8 + - - +
445A LEU* 1.3 76.9 - - - +
447A ALA* 1.3 57.4 + - - +
450A HIS* 3.0 9.0 + - - -
451A HIS* 2.9 33.1 + - + -
453A VAL* 3.9 11.4 - - + -
455A TYR* 3.4 22.4 - - - +
511A PRO* 3.9 11.9 - - + +
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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
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443A VAL 3.2 8.7 + - - +
444A ARG 3.5 8.3 - - - +
445A LEU 3.2 0.2 - - - -
446A ALA* 1.3 80.4 - - - +
448A ILE* 1.3 62.4 + - - +
450A HIS* 3.5 4.2 + - - -
483A MET* 4.2 10.5 - - + -
484A PRO 3.3 25.4 - - - +
485A ASN* 2.8 40.4 + - - +
486A LEU* 4.7 1.6 - - + -
511A PRO* 3.9 6.0 - - + +
625B PHE* 3.9 9.5 - - + -
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Residues in contact with ILE 448 (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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102A GLU* 5.5 4.0 - - - +
112A THR* 4.7 16.2 - - + +
444A ARG* 2.9 53.0 + - + +
445A LEU* 3.9 19.5 - - + +
447A ALA* 1.3 78.3 - - - +
449A SER* 1.3 64.1 + - - +
450A HIS* 3.5 15.2 + - - -
469B PRO* 4.1 22.2 - - + +
470B THR* 4.3 7.2 - - + -
625B PHE* 3.6 33.5 - - + -
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Residues in contact with SER 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 2.9 28.4 + - - +
104A PHE* 3.5 9.8 - - - -
112A THR* 3.0 35.5 + - - -
445A LEU* 2.8 24.4 + - - +
448A ILE* 1.3 72.2 - - - +
450A HIS* 1.3 68.6 + - - +
451A HIS* 3.5 24.3 + - - -
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Residues in contact with HIS 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 3.5 6.2 + - - -
104A PHE* 4.2 20.0 - + + -
420A ASP* 4.5 0.2 - - - +
446A ALA 3.0 7.8 + - - -
447A ALA 3.5 2.4 + - - -
448A ILE 3.3 16.1 + - - -
449A SER* 1.3 82.1 - - - +
451A HIS* 1.3 62.7 + - - +
452A ARG 3.9 0.2 + - - -
485A ASN* 3.1 32.8 + - + +
508A ILE 3.9 3.6 - - - +
509A HIS* 3.3 45.5 + + + +
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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