Contacts of the helix formed by residues 563 - 573 (chain B) in PDB entry 1J38
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 PRO 563 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B ARG* 3.4 23.1 - - - +
209B GLU* 3.4 26.9 - - + +
562B LYS* 1.3 99.9 - - + +
564B TRP* 1.3 66.1 + - - +
565B PRO* 3.1 14.3 - - + -
566B ASP* 3.1 21.1 + - - +
567B ALA 3.7 4.2 + - - -
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Residues in contact with TRP 564 (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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208B TYR 2.8 30.8 + - - -
209B GLU* 4.2 6.3 + - + -
210B ASP* 4.6 12.3 - - + +
213B PHE* 3.7 26.9 - + - -
216B GLN* 4.7 4.0 - - - -
389B ALA* 3.7 24.4 - - - +
390B ASN* 3.1 41.8 - - + +
393B PHE* 3.9 14.6 - + + -
513B ILE* 4.9 4.0 - - + -
562B LYS 3.5 1.0 + - - -
563B PRO* 1.3 70.5 - - - +
565B PRO* 1.3 87.4 - - + +
566B ASP 3.1 0.2 - - - -
567B ALA* 3.1 1.9 + - - +
568B LEU* 3.0 34.3 + - + +
575B ARG 4.5 1.8 - - - -
576B ILE* 4.5 3.1 - - - -
577B MET* 3.6 43.5 - - + -
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Residues in contact with PRO 565 (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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209B GLU 5.8 2.7 - - - +
563B PRO* 3.3 15.9 - - + -
564B TRP* 1.3 122.0 - - + +
566B ASP* 1.3 57.2 + - - +
568B LEU* 3.7 3.8 + - + +
569B GLU* 3.1 26.0 + - - +
575B ARG* 3.6 45.0 + - - +
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Residues in contact with ASP 566 (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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558B MET* 4.1 7.3 - - + +
562B LYS* 3.9 29.3 - - + +
563B PRO* 3.1 17.4 + - - +
564B TRP 3.1 0.6 - - - -
565B PRO* 1.3 74.1 - - - +
567B ALA* 1.3 67.2 + - - +
568B LEU 3.2 1.3 - - - -
569B GLU* 3.6 8.7 - - - +
570B ALA* 2.9 24.6 + - - +
575B ARG* 2.8 30.7 + - - +
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Residues in contact with ALA 567 (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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374B TYR* 5.5 0.4 - - - +
389B ALA* 3.5 31.9 - - + -
393B PHE* 3.8 11.2 - - + -
555B MET* 3.6 21.6 - - + +
558B MET* 4.0 21.2 - - + +
562B LYS 5.1 0.9 - - - +
563B PRO 3.7 3.1 + - - +
564B TRP* 3.1 7.9 + - - +
566B ASP* 1.3 80.3 - - - +
568B LEU* 1.3 64.9 + - - +
570B ALA* 3.3 9.4 + - - +
571B PHE 3.4 6.9 + - - -
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Residues in contact with LEU 568 (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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393B PHE* 4.0 10.9 - - + -
513B ILE* 4.1 12.6 - - + -
516B GLN* 4.5 7.2 - - + +
517B PHE* 3.4 28.7 - - + -
555B MET* 4.8 0.2 - - - -
564B TRP* 3.0 26.3 + - + +
565B PRO 3.7 2.9 - - - +
567B ALA* 1.3 77.9 - - - +
569B GLU* 1.3 54.2 + - - +
571B PHE* 2.7 27.4 + - + +
572B ASN* 2.9 29.2 + - - +
573B GLY 4.1 0.2 + - - -
574B GLU* 3.6 14.4 - - + +
575B ARG 4.0 2.9 - - - -
576B ILE 3.7 40.2 - - - +
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Residues in contact with GLU 569 (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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565B PRO 3.1 14.9 + - - +
566B ASP* 3.6 12.2 - - - +
568B LEU* 1.3 78.8 - - - +
570B ALA* 1.3 62.7 + - - +
573B GLY* 2.5 41.2 + - - +
574B GLU 3.0 15.0 + - - +
575B ARG* 2.7 40.8 + - + +
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Residues in contact with ALA 570 (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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554B ASN* 3.5 49.1 + - + +
555B MET 4.8 0.2 - - - -
558B MET* 3.8 10.3 - - - -
566B ASP 2.9 13.4 + - - +
567B ALA 3.4 11.2 - - - +
569B GLU* 1.3 76.4 - - - +
571B PHE* 1.3 61.2 + - - +
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Residues in contact with PHE 571 (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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517B PHE* 3.2 40.6 - + + -
520B SER* 3.3 25.1 - - - -
521B ALA* 3.8 15.7 - - + -
524B LYS* 3.0 26.4 + - - -
548B ALA 4.7 0.9 - - - -
551B ALA* 3.4 42.9 - - + +
552B PHE* 4.0 25.6 - + - -
555B MET* 3.9 29.6 - - + +
567B ALA 3.4 1.2 + - - -
568B LEU* 2.7 16.2 + - - +
570B ALA* 1.3 76.1 - - - +
572B ASN* 1.3 78.6 + - + +
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Residues in contact with ASN 572 (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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516B GLN* 4.2 7.3 + - - +
520B SER* 3.1 30.6 + - - +
524B LYS* 4.1 10.1 - - - +
568B LEU* 2.9 22.2 + - - +
571B PHE* 1.3 98.5 - - + +
573B GLY* 1.3 59.1 + - - +
574B GLU* 2.9 44.2 + - - +
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Residues in contact with GLY 573 (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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569B GLU* 2.5 40.3 + - - +
572B ASN* 1.3 70.6 - - - +
574B GLU* 1.3 63.4 + - - +
575B ARG* 4.0 5.0 + - - +
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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