Contacts of the helix formed by residues 659 - 675 (chain I) in PDB entry 1SOJ
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 LEU 659 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660I ASP* 1.3 69.5 + - - +
661I LEU* 3.4 3.9 - - - +
662I ILE* 3.2 17.2 + - - +
663I LEU* 3.0 25.8 + - - +
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Residues in contact with ASP 660 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659I LEU* 1.3 79.9 - - - +
661I LEU* 1.3 61.1 + - - +
663I LEU* 3.4 5.9 + - - +
664I VAL* 3.1 28.2 + - - +
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Residues in contact with LEU 661 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659I LEU 4.4 1.7 - - - +
660I ASP* 1.3 77.6 - - - +
662I ILE* 1.3 60.8 + - - +
664I VAL* 3.1 9.6 + - - +
665I GLU* 2.9 46.8 + - - +
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Residues in contact with ILE 662 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659I LEU* 3.2 22.6 + - - +
661I LEU* 1.3 79.2 - - - +
663I LEU* 1.3 57.2 + - - +
665I GLU* 3.6 13.1 + - - +
666I GLU* 3.1 31.9 + - - +
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Residues in contact with LEU 663 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659I LEU 3.0 16.6 + - - +
660I ASP* 3.8 6.5 - - - +
661I LEU 3.2 0.4 - - - -
662I ILE* 1.3 74.9 - - - +
664I VAL* 1.3 70.7 + - + +
666I GLU* 3.4 17.0 + - - +
667I TYR* 3.2 23.0 + - + +
701I TYR* 5.9 7.6 - - + -
705I GLN* 6.3 0.4 - - - +
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Residues in contact with VAL 664 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660I ASP 3.1 18.6 + - - +
661I LEU* 3.1 10.0 + - - +
663I LEU* 1.3 78.6 - - + +
665I GLU* 1.3 66.8 + - + +
667I TYR* 3.2 9.3 + - + +
668I ASP* 3.0 43.0 + - - +
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Residues in contact with GLU 665 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661I LEU* 2.9 38.8 + - - +
662I ILE* 3.7 11.6 + - - +
663I LEU 3.3 0.2 - - - -
664I VAL* 1.3 77.5 - - + +
666I GLU* 1.3 57.8 + - + +
668I ASP* 3.3 7.7 + - - +
669I SER* 2.8 30.8 + - - -
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Residues in contact with GLU 666 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662I ILE* 3.1 19.3 + - - +
663I LEU* 3.6 18.9 - - + +
664I VAL 3.2 0.6 - - - -
665I GLU* 1.3 78.3 - - + +
667I TYR* 1.3 56.2 + - - +
669I SER* 3.4 7.7 + - - -
670I LEU* 3.0 28.9 + - - +
687I LYS* 5.7 10.2 + - - +
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Residues in contact with TYR 667 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663I LEU* 3.2 15.1 + - + +
664I VAL* 3.5 12.3 - - + +
665I GLU 3.2 0.2 - - - -
666I GLU* 1.3 76.4 - - - +
668I ASP* 1.3 80.9 + - - +
670I LEU* 3.3 4.9 + - - +
671I ILE* 3.0 39.0 + - + +
702I THR* 3.5 38.6 - - + -
705I GLN* 3.9 28.3 - - + -
706I ASP* 3.3 33.3 + - - +
790I LYS* 5.2 5.5 - - - +
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Residues in contact with ASP 668 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664I VAL* 3.0 33.7 + - - +
665I GLU* 3.8 6.3 - - - +
667I TYR* 1.3 92.2 - - - +
669I SER* 1.3 61.2 + - - +
671I ILE* 3.9 4.9 - - - +
672I GLU* 3.0 24.3 + - - +
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Residues in contact with SER 669 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665I GLU 2.8 17.7 + - - -
666I GLU* 3.4 10.1 - - - -
667I TYR 3.2 0.2 - - - -
668I ASP* 1.3 76.4 - - - +
670I LEU* 1.3 64.1 + - - +
672I GLU* 3.1 11.3 + - - +
673I LYS* 3.0 36.8 + - - +
687I LYS* 3.4 23.8 + - - -
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Residues in contact with LEU 670 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666I GLU 3.0 13.6 + - - +
667I TYR* 3.3 4.9 + - - +
669I SER* 1.3 78.8 - - - +
671I ILE* 1.3 54.4 + - - +
673I LYS* 2.9 10.0 + - + +
674I MET* 2.7 60.0 + - + +
679I PHE* 4.2 5.8 - - + -
684I LEU* 4.0 27.4 - - + -
698I GLN* 4.6 6.7 - - + +
699I VAL* 4.6 11.4 - - + -
702I THR* 3.3 34.8 - - + +
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Residues in contact with ILE 671 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667I TYR* 3.0 42.9 + - + +
668I ASP* 3.9 5.6 - - - +
670I LEU* 1.3 75.9 - - - +
672I GLU* 1.3 62.0 + - - +
674I MET* 3.8 6.0 - - - +
675I SER* 2.9 30.4 + - - +
702I THR* 3.6 22.4 - - + +
703I LEU* 5.0 3.4 - - + -
706I ASP* 3.7 31.0 - - + +
750I TRP* 5.0 8.0 - - + -
791I SER* 3.3 30.3 - - - +
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Residues in contact with GLU 672 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668I ASP 3.0 14.7 + - - +
669I SER* 3.3 13.1 - - - +
670I LEU 3.1 0.2 - - - -
671I ILE* 1.3 78.2 - - - +
673I LYS* 1.3 78.9 + - - +
675I SER* 3.2 17.9 + - - -
676I ASN* 3.6 9.0 + - - +
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Residues in contact with LYS 673 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669I SER* 3.0 31.6 + - - +
670I LEU* 2.9 11.1 + - + +
672I GLU* 1.3 88.2 - - - +
674I MET* 1.3 58.8 + - - +
675I SER 3.1 4.7 + - - -
676I ASN* 3.1 26.3 + - - +
679I PHE* 3.7 28.6 - - + +
680I PRO* 4.3 17.8 - - + +
683I GLU* 5.3 6.3 - - - +
687I LYS* 4.3 15.8 - - - +
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Residues in contact with MET 674 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670I LEU* 2.7 53.2 + - + +
671I ILE* 3.8 6.1 - - - +
673I LYS* 1.3 72.1 - - - +
675I SER* 1.3 59.6 + - - +
676I ASN 3.1 2.0 - - - -
679I PHE* 3.8 26.0 - - + -
699I VAL* 3.5 27.8 - - + -
702I THR* 4.9 5.2 - - - -
703I LEU* 3.4 36.3 - - + -
747I HIS* 2.9 41.0 + - + -
750I TRP* 3.2 17.2 - - + -
751I TYR* 4.4 1.0 - - - -
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Residues in contact with SER 675 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671I ILE* 2.9 21.5 + - - +
672I GLU* 3.4 11.7 - - - -
673I LYS 3.1 1.4 - - - -
674I MET* 1.3 77.6 - - - +
676I ASN* 1.3 60.7 + - - +
750I TRP* 4.6 1.1 - - - -
751I TYR* 3.4 18.7 + - - -
755I ARG* 3.4 27.2 + - - +
791I SER* 4.0 17.3 + - - -
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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