Contacts of the helix formed by residues 653 - 662 (chain A) in PDB entry 3RJO
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 SER 653 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614A ASP* 5.4 0.8 + - - -
647A VAL* 3.6 4.4 - - - +
652A LEU* 1.3 80.0 - - - +
654A ILE* 1.3 65.1 + - - +
655A GLU* 3.3 21.2 + - - +
656A LYS* 3.1 39.1 + - - +
657A ALA* 3.2 8.8 + - - +
928A LYS* 6.0 1.8 - - - -
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Residues in contact with ILE 654 (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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644A PHE* 4.2 7.4 - - + -
647A VAL* 3.8 22.4 - - + +
652A LEU 3.7 1.8 + - - -
653A SER* 1.3 71.8 - - - +
655A GLU* 1.3 60.9 + - + +
657A ALA 3.7 0.2 - - - -
658A LEU* 2.8 50.6 + - + +
683A MET* 3.8 29.4 - - + -
921A TRP* 4.3 7.4 - - + -
925A ASN* 3.2 31.0 - - + +
928A LYS* 3.6 29.8 - - + +
929A ILE* 3.7 26.5 - - + +
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Residues in contact with GLU 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A SER* 3.1 21.7 - - - +
654A ILE* 1.3 80.3 + - + +
656A LYS* 1.3 58.8 + - + +
658A LEU* 3.2 1.4 + - - -
659A ASP* 2.8 38.9 + - - +
928A LYS* 3.5 39.5 + - - +
931A VAL* 5.6 4.2 - - + +
932A TRP* 3.7 35.6 + - + -
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Residues in contact with LYS 656 (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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614A ASP* 3.6 46.0 - - - +
617A TRP* 5.5 4.7 - - + -
618A ASP* 2.8 31.1 + - - +
621A THR* 4.7 3.5 + - - -
652A LEU* 3.9 21.1 - - + -
653A SER* 3.1 23.4 + - - +
655A GLU* 1.3 74.9 - - + +
657A ALA* 1.3 61.3 - - - +
659A ASP* 3.3 12.0 + - + +
660A LEU* 2.9 27.7 + - - +
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Residues in contact with ALA 657 (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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643A ALA* 4.2 11.7 - - + -
644A PHE* 3.2 37.2 - - + -
647A VAL* 3.6 28.3 - - + -
652A LEU* 4.4 5.5 - - + +
653A SER 3.2 4.0 + - - -
654A ILE* 3.8 3.8 - - - +
656A LYS* 1.3 76.4 - - - +
658A LEU* 1.3 64.8 + - - +
660A LEU* 3.2 8.5 + - - +
661A SER 3.0 17.3 + - - -
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Residues in contact with LEU 658 (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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644A PHE* 4.0 17.7 - - + -
654A ILE* 2.8 43.7 + - + +
655A GLU 3.8 0.2 - - - +
657A ALA* 1.3 77.9 - - - +
659A ASP* 1.3 59.9 + - - +
661A SER* 2.4 27.4 + - - +
662A LEU* 3.2 5.2 + - - +
680A LEU* 4.2 16.4 - - + -
683A MET* 4.8 1.1 - - - -
699A PHE* 4.7 9.4 - - + -
702A PHE* 4.6 9.6 - - + -
929A ILE* 3.9 18.4 - - + -
932A TRP* 3.5 55.9 - - + -
933A LEU* 6.3 0.2 - - + -
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Residues in contact with ASP 659 (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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2A EDO 3.4 20.7 + - - -
621A THR* 4.2 7.2 - - + -
625A LYS* 3.0 33.0 + - - +
655A GLU* 2.8 28.2 + - - +
656A LYS* 3.5 12.5 - - + +
658A LEU* 1.3 72.7 - - - +
660A LEU* 1.3 66.0 + - - +
662A LEU* 3.4 11.3 + - - +
932A TRP* 2.9 23.0 + - - -
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Residues in contact with LEU 660 (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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617A TRP* 3.8 32.1 - - + -
620A LEU* 5.4 1.1 - - + -
621A THR* 3.9 28.1 - - - +
624A LEU* 3.9 26.2 - - + -
625A LYS* 4.7 0.2 - - - -
639A LEU* 4.6 3.6 - - + +
640A ILE* 4.1 33.7 - - + +
643A ALA* 4.4 8.5 - - + -
644A PHE* 4.9 3.1 - - + -
656A LYS 2.9 13.3 + - - +
657A ALA* 3.5 12.3 - - - +
658A LEU 3.2 0.2 - - - -
659A ASP* 1.3 78.4 - - - +
661A SER* 1.3 67.2 + - - +
662A LEU 3.1 1.4 + - - -
663A TYR* 3.2 22.2 + - + +
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Residues in contact with SER 661 (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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640A ILE* 6.3 0.2 - - - -
644A PHE* 4.0 17.5 - - - -
657A ALA 3.0 12.7 + - - -
658A LEU* 2.4 23.9 + - - +
660A LEU* 1.3 82.0 - - - +
662A LEU* 1.3 61.9 + - - +
663A TYR* 3.0 1.4 + - - -
664A LEU* 3.1 38.5 + - - +
680A LEU* 4.6 7.0 - - - -
702A PHE* 3.3 21.5 - - - -
706A LEU* 3.6 7.5 - - - +
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Residues in contact with LEU 662 (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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2A EDO 3.9 15.0 - - - +
625A LYS* 4.0 20.2 - - - +
658A LEU 3.2 7.3 + - - +
659A ASP* 3.7 12.1 - - - +
660A LEU 3.1 1.4 + - - -
661A SER* 1.3 80.9 + - - +
663A TYR* 1.3 60.7 + - - +
664A LEU 3.0 2.4 + - - -
665A LYS* 3.2 36.7 + - + +
702A PHE* 3.7 22.7 - - + -
706A LEU* 3.7 11.8 - - + +
932A TRP* 3.9 22.2 - - + -
936A GLU* 4.0 17.7 - - - +
940A ARG* 6.3 0.7 - - - -
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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