Contacts of the helix formed by residues 475 - 483 (chain B) 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 GLU 475 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A ARG* 2.9 37.5 + - - -
479A ALA 4.9 3.3 - - - +
482A ALA* 3.5 28.3 - - - +
483A MET* 3.8 37.0 - - + +
484A PRO* 4.1 5.4 - - + -
434B ASN* 4.9 0.2 - - - +
473B PRO* 5.5 0.2 - - - -
474B VAL* 1.3 93.1 + - + +
476B LEU* 1.3 74.4 + - - +
477B VAL 3.5 2.5 - - - -
478B ALA* 3.6 7.9 + - - +
479B ALA* 3.4 18.4 + - - +
608B VAL* 4.1 5.8 - - + -
625B PHE* 4.2 0.7 - - - -
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Residues in contact with LEU 476 (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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440A LEU* 5.6 2.5 - - + -
433B LEU* 3.0 37.9 - - + +
434B ASN* 4.1 11.0 - - - +
436B ILE* 4.1 5.8 - - + -
437B GLY* 3.8 24.0 - - - +
440B LEU* 4.4 20.6 - - + -
473B PRO* 4.5 14.1 - - + +
474B VAL 3.9 1.4 - - - +
475B GLU* 1.3 88.9 - - - +
477B VAL* 1.3 65.6 + - - +
479B ALA* 3.2 14.7 + - + +
480B LEU* 3.0 34.8 + - + +
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Residues in contact with VAL 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 3.9 18.6 - - + -
473B PRO* 5.7 0.8 - - + +
474B VAL 5.5 0.6 - - - -
475B GLU 3.5 0.4 - - - -
476B LEU* 1.3 73.8 - - - +
478B ALA* 1.3 64.9 + - - +
480B LEU* 3.3 7.9 + - - +
481B ARG* 2.9 60.8 + - - +
488B VAL* 4.0 13.0 - - + -
490B ARG* 5.7 1.3 - - + -
515B CYS* 4.2 12.3 - - - -
607B TYR* 3.3 45.1 - - + +
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Residues in contact with ALA 478 (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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478A ALA 6.0 0.4 - - - -
479A ALA* 5.6 0.2 - - - -
482A ALA* 3.9 18.6 - - + -
610A PHE* 3.4 23.0 - - + -
475B GLU 3.6 11.8 + - - +
476B LEU 3.2 0.6 - - - -
477B VAL* 1.3 78.8 - - - +
479B ALA* 1.3 63.3 + - - +
481B ARG* 3.2 7.6 + - - +
482B ALA* 3.1 18.4 + - - +
607B TYR* 6.1 2.3 - - + +
608B VAL* 4.6 8.5 - - + +
610B PHE* 3.9 21.3 - - - +
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Residues in contact with ALA 479 (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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440A LEU* 6.0 0.7 - - + -
475A GLU* 5.0 3.3 - - - +
479A ALA* 3.3 40.3 - - + +
440B LEU* 5.3 6.5 - - + -
475B GLU 3.4 8.5 + - - +
476B LEU* 3.2 21.9 + - + +
478B ALA* 1.3 80.9 - - - +
480B LEU* 1.3 61.9 + - + +
482B ALA* 3.1 16.0 + - - +
483B MET* 3.4 10.8 + - - +
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Residues in contact with LEU 480 (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 LEU* 4.3 18.2 - - + -
436B ILE* 4.6 8.7 - - + -
440B LEU* 3.8 28.5 - - + -
443B VAL* 4.3 7.6 - - + -
476B LEU* 3.0 36.1 + - + +
477B VAL* 3.3 6.5 + - + +
479B ALA* 1.3 75.7 - - - +
481B ARG* 1.3 60.4 + - - +
483B MET* 3.2 24.6 - - + +
486B LEU* 3.5 27.9 - - + +
488B VAL* 3.7 21.3 - - + +
513B VAL* 4.3 19.5 - - + -
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Residues in contact with ARG 481 (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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610A PHE* 3.8 27.2 - - + -
477B VAL* 2.9 43.0 + - + +
478B ALA* 3.5 8.2 - - - +
480B LEU* 1.3 75.6 - - - +
482B ALA* 1.3 61.4 + - - +
483B MET 3.2 4.4 + - - +
488B VAL* 4.3 15.9 + - + +
490B ARG* 5.1 7.9 - - - +
552B SER* 4.4 5.5 + - - -
577B MET 5.0 3.8 + - - -
578B PRO 5.5 2.2 + - - -
580B GLN* 3.3 45.1 + - - +
581B GLU* 3.6 28.7 - - - +
605B GLU* 2.8 42.2 + - - -
607B TYR* 5.0 0.4 - - - -
612B TRP* 3.9 7.3 - - - +
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Residues in contact with ALA 482 (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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475A GLU* 3.6 16.0 - - + +
478A ALA* 3.8 20.9 - - + -
608A VAL* 3.8 13.3 - - + +
610A PHE* 3.8 28.9 - - + +
478B ALA 3.1 11.3 + - - +
479B ALA* 3.1 12.3 + - - +
481B ARG* 1.3 76.5 - - - +
483B MET* 1.3 62.5 + - - +
484B PRO* 3.4 9.2 - - - +
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Residues in contact with MET 483 (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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475A GLU* 4.0 19.0 - - + +
625A PHE* 4.1 17.3 - - - -
440B LEU* 4.7 13.0 - - + +
443B VAL* 4.1 15.9 - - + -
444B ARG* 3.6 45.5 - - + +
447B ALA* 4.2 3.6 - - + -
479B ALA 3.4 6.9 + - - +
480B LEU* 3.2 22.7 - - + +
481B ARG 3.2 4.0 - - - +
482B ALA* 1.3 77.8 - - - +
484B PRO* 1.3 78.5 - - - +
485B ASN 3.6 1.2 + - - -
486B LEU* 3.7 25.7 + - + +
581B GLU* 5.7 1.6 - - - +
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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