Contacts of the helix formed by residues 565 - 574 (chain B) in PDB entry 3GJN
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 THR 565 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B ALA* 2.9 26.6 + - + +
469B GLY* 4.0 7.9 - - - +
529B THR* 5.0 0.2 - - + -
533B ASP* 3.9 34.9 + - + +
541B PHE* 4.0 20.3 - - + -
564B VAL* 1.3 72.3 - - - +
566B PRO* 1.3 74.6 - - - +
567B LYS* 3.5 4.6 + - - +
568B ARG* 3.2 22.0 + - - +
569B HIS* 2.9 19.7 + - - +
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Residues in contact with PRO 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B THR* 3.7 13.0 - - + -
533B ASP 3.7 10.8 - - - +
535B SER* 3.9 7.9 - - - +
538B ARG* 3.5 44.9 + - + +
539B THR* 4.2 2.9 - - - +
540B SER 3.3 27.8 - - - +
542B GLU* 4.0 14.1 - - + +
564B VAL 3.8 2.0 - - - +
565B THR* 1.3 86.9 - - - +
567B LYS* 1.3 61.5 + - - +
569B HIS* 3.9 1.6 - - - +
570B ILE* 3.1 29.3 + - - +
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Residues in contact with LYS 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B GLN 2.8 25.7 + - - +
533B ASP* 3.8 12.6 + - + +
534B VAL 3.2 26.1 + - - +
535B SER* 3.9 12.3 - - - +
565B THR* 3.1 5.5 + - - +
566B PRO* 1.3 76.2 - - - +
568B ARG* 1.3 58.8 + - - +
570B ILE* 3.2 11.5 - - - +
571B ASP* 3.0 32.0 + - - +
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Residues in contact with ARG 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ALA 3.9 11.0 - - - +
469B GLY* 3.6 30.5 - - - +
470B LYS* 3.7 3.9 - - - +
471B ASP* 3.0 42.1 + - - +
564B VAL* 4.6 4.5 - - + -
565B THR* 3.1 19.6 + - - +
567B LYS* 1.3 76.6 - - - +
569B HIS* 1.3 64.8 + - - +
571B ASP* 3.1 36.7 + - - +
572B ILE* 3.1 33.7 + - + +
576B LYS 3.5 25.0 + - - -
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Residues in contact with HIS 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B ARG* 4.1 6.7 + - - +
542B GLU* 2.8 36.1 + - + +
543B LEU 3.7 20.2 - - - -
544B HIS* 3.2 17.3 + - + +
564B VAL* 3.5 15.6 - - + +
565B THR 2.9 14.2 + - - +
566B PRO 3.9 1.3 - - - +
568B ARG* 1.3 73.4 - - - +
570B ILE* 1.3 64.2 + - - +
572B ILE* 3.6 6.5 + - + +
573B HIS* 2.9 28.5 + + - -
600B ZN 1.9 37.9 - - - -
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Residues in contact with ILE 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B SER* 5.2 10.1 - - - +
538B ARG* 2.7 44.0 - - - +
566B PRO 3.1 18.9 + - - +
567B LYS* 3.2 13.0 - - - +
569B HIS* 1.3 76.8 - - - +
571B ASP* 1.3 57.8 + - - +
573B HIS* 3.3 6.8 + - + +
574B ARG* 3.0 58.5 + - - +
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Residues in contact with ASP 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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567B LYS* 3.0 20.4 + - - +
568B ARG* 3.1 30.0 + - - +
570B ILE* 1.3 75.3 - - - +
572B ILE* 1.4 57.7 + - - +
574B ARG* 3.6 27.9 + - - -
575B GLY 3.1 5.5 + - - -
576B LYS* 2.4 49.4 + - + +
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Residues in contact with ILE 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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471B ASP 3.8 17.9 - - - +
472B LEU* 4.4 14.4 - - + -
544B HIS* 3.4 40.6 - - + +
546B GLU* 4.9 2.2 - - - +
564B VAL* 4.1 14.1 - - + -
568B ARG* 3.1 44.0 + - + +
569B HIS* 3.6 10.5 - - - +
571B ASP* 1.4 76.5 - - - +
573B HIS* 1.3 64.0 + - + +
575B GLY* 3.2 13.2 + - - -
576B LYS 4.5 4.5 - - - -
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Residues in contact with HIS 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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538B ARG* 6.0 1.1 - - - -
544B HIS* 4.0 11.0 - + - -
545B ALA 5.4 2.2 - - - -
569B HIS* 2.9 31.6 + + - +
570B ILE* 3.3 7.8 + - + +
572B ILE* 1.3 82.3 - - + +
574B ARG* 1.3 55.8 + - - +
575B GLY 3.2 2.1 + - - -
600B ZN 2.0 36.7 - - - -
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Residues in contact with ARG 574 (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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570B ILE* 3.0 41.3 + - - +
571B ASP* 3.6 21.4 + - - +
573B HIS* 1.3 76.0 - - - +
575B GLY* 1.3 59.9 + - - +
576B LYS* 3.3 41.1 + - - +
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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
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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