Contacts of the helix formed by residues 69 - 86 (chain 9) in PDB entry 2J28
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 69 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689 LEU* 1.3 35.4 - - - +
709 PRO* 1.3 78.8 - - + +
719 GLY* 3.9 13.2 - - - +
729 GLN* 3.3 13.7 - - + +
93T LEU 3.1 2.4 + - - -
94T ASP* 1.1 56.2 + - - +
95T PHE* 2.6 10.9 + - - +
96T VAL* 0.8 99.6 - - + +
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Residues in contact with PRO 70 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639 GLU* 6.3 2.5 - - + -
649 VAL* 3.6 17.7 - - + +
689 LEU 3.2 4.0 - - - +
699 THR* 1.3 86.7 - - + +
719 GLY* 1.3 71.8 + - - +
729 GLN 2.5 3.3 + - - -
739 GLU* 2.6 21.7 + - - +
749 PHE* 3.1 4.3 + - - -
52T GLU* 5.9 4.0 - - - +
93T LEU 4.3 5.6 - - - +
94T ASP* 5.1 2.2 - - + -
96T VAL* 4.8 0.4 - - + -
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Residues in contact with GLY 71 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129 THR* 5.9 6.6 - - - +
699 THR* 3.5 8.3 - - - +
709 PRO* 1.3 81.6 - - - +
729 GLN* 1.3 66.8 + - - +
749 PHE* 2.7 28.9 - - - +
759 VAL* 3.7 3.2 + - - +
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Residues in contact with GLN 72 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139 LEU* 6.4 1.8 - - + -
689 LEU* 3.1 25.8 - - + +
699 THR* 3.3 15.7 + - + +
709 PRO 2.5 3.0 + - - -
719 GLY* 1.3 69.5 - - - +
739 GLU* 1.3 52.7 + - - +
759 VAL* 2.5 46.8 + - - +
769 LYS 4.8 0.4 - - - -
95T PHE 3.3 9.8 - - - +
96T VAL* 3.2 23.0 + - - +
97T GLY 2.9 26.4 + - - +
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Residues in contact with GLU 73 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629 HIS* 5.2 7.8 - - + -
639 GLU 4.8 3.5 - - - +
649 VAL* 2.1 61.1 - - + +
659 ASN 5.0 1.2 + - - -
689 LEU* 4.2 4.5 - - - +
699 THR 3.7 1.6 + - - -
709 PRO 2.6 4.9 + - - +
729 GLN* 1.3 72.9 - - - +
749 PHE* 1.3 69.9 + - - +
759 VAL 2.6 2.3 + - - -
769 LYS* 2.7 37.4 + - - +
779 ILE* 3.0 32.9 + - + +
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Residues in contact with PHE 74 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129 THR* 5.4 13.5 - - + -
279 VAL* 3.5 51.4 - - + -
309 THR* 4.9 15.7 - - + -
319 LEU* 5.5 6.7 - - + -
559 VAL* 5.1 14.4 - - + -
629 HIS* 6.3 0.2 - - - -
709 PRO 3.1 3.6 + - - +
719 GLY* 2.7 26.9 - - - +
729 GLN 2.7 1.4 + - - -
739 GLU* 1.3 75.9 - - - +
759 VAL* 1.3 51.7 + - + -
779 ILE* 2.6 38.2 - - + +
789 VAL* 2.7 32.3 + - + +
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Residues in contact with VAL 75 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99 LEU* 5.0 19.7 - - + -
129 THR* 6.4 2.5 - - + -
139 LEU* 6.5 1.3 - - + -
719 GLY 4.3 5.2 - - - +
729 GLN* 2.5 23.8 + - - +
749 PHE* 1.3 73.8 - - + +
769 LYS* 1.3 66.0 + - - +
779 ILE 2.6 1.6 - - - -
789 VAL* 2.2 48.8 + - + -
799 ARG* 2.5 23.6 + - + +
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Residues in contact with LYS 76 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729 GLN 3.9 0.6 + - - -
739 GLU* 2.7 36.4 + - - +
759 VAL* 1.3 82.5 - - - +
779 ILE* 1.3 55.2 + - + +
799 ARG* 3.5 26.8 + - - +
809 ASN* 2.4 44.4 + - + +
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Residues in contact with ILE 77 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559 VAL* 5.2 11.9 - - + +
589 LYS* 4.2 32.3 - - + -
629 HIS* 4.9 13.9 - - + +
739 GLU* 3.0 39.5 - - + +
749 PHE* 2.6 23.1 - - + +
759 VAL 2.4 6.7 + - - -
769 LYS* 1.3 76.4 - - + +
789 VAL* 1.3 69.2 + - + +
809 ASN* 2.8 25.7 - - + +
819 GLU* 2.8 11.4 + - + +
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Residues in contact with VAL 78 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99 LEU* 6.6 0.2 - - + -
519 PHE* 5.0 6.1 - - + -
559 VAL* 6.0 6.1 - - + -
749 PHE* 2.7 55.0 + - + +
759 VAL* 2.2 43.3 + - + +
779 ILE* 1.3 71.7 - - - +
799 ARG* 1.3 93.0 + - + +
819 GLU* 2.8 8.0 + - - +
829 LEU* 2.9 29.3 + - + +
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Residues in contact with ARG 79 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759 VAL* 2.5 24.7 + - + +
769 LYS* 3.5 31.7 + - - +
789 VAL* 1.3 81.3 - - + +
809 ASN* 1.3 74.6 + - - +
829 LEU* 2.5 38.0 + - + +
839 VAL* 3.0 10.2 + - + +
2889 ASP* 3.4 24.5 + - - +
2919 ALA 4.7 13.0 - - - +
2929 SER 6.2 1.8 - - - +
2949 ILE 5.6 2.7 - - - +
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Residues in contact with ASN 80 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589 LYS* 5.1 8.5 - - - +
769 LYS* 2.4 34.4 + - + +
779 ILE* 2.8 22.0 + - - +
799 ARG* 1.3 83.5 + - - +
819 GLU* 1.3 84.4 + - - +
839 VAL* 2.9 28.5 - - - +
849 ALA* 3.6 1.9 + - - +
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Residues in contact with GLU 81 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519 PHE* 2.9 32.0 - - + -
549 ARG* 3.4 42.6 + - + +
559 VAL* 5.0 7.9 - - + +
589 LYS* 4.5 12.5 - - - +
779 ILE* 2.8 16.2 + - + +
789 VAL 3.7 2.2 - - - +
809 ASN* 1.3 92.4 + - - +
829 LEU* 1.3 55.2 + - - +
839 VAL 3.0 1.8 - - - -
849 ALA* 3.3 20.0 - - + +
859 ALA* 2.5 37.5 + - - +
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Residues in contact with LEU 82 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349 VAL* 6.2 4.3 - - + -
519 PHE* 3.3 21.8 - - + -
789 VAL* 2.9 32.4 + - + +
799 ARG* 2.5 33.6 + - + +
819 GLU* 1.3 70.5 - - - +
839 VAL* 1.3 69.2 + - - +
859 ALA* 2.9 9.0 - - - +
869 MET* 2.7 26.0 + - - +
2919 ALA* 4.6 13.0 - - + +
2949 ILE 4.5 9.0 - - - +
2959 LEU* 4.5 22.7 - - + -
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Residues in contact with VAL 83 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799 ARG* 3.8 13.9 - - + +
809 ASN* 2.9 17.9 - - - +
829 LEU* 1.3 75.8 - - + +
849 ALA* 1.3 55.2 + - - +
869 MET* 2.4 40.4 + - - +
879 GLY 3.7 0.2 + - - -
889 GLU* 2.6 35.9 - - + +
899 GLU* 4.7 6.5 - - + +
2879 PRO* 4.1 13.7 - - + -
2889 ASP* 3.0 38.1 - - - +
2919 ALA 5.6 2.4 - - - +
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Residues in contact with ALA 84 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549 ARG* 4.5 14.1 - - - +
809 ASN 3.6 1.2 + - - +
819 GLU* 3.3 28.7 + - + +
839 VAL* 1.3 79.6 - - - +
859 ALA* 1.3 56.3 + - - +
869 MET 2.5 17.2 - - - +
889 GLU* 3.4 26.7 - - + +
2649 HIS* 2.6 17.3 + - - -
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Residues in contact with ALA 85 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519 PHE* 3.8 21.5 - - + -
819 GLU* 2.5 24.3 + - - +
829 LEU* 2.9 14.4 - - - +
839 VAL 2.8 0.6 + - - -
849 ALA* 1.3 73.8 - - - +
869 MET* 1.3 59.7 + - + +
2619 SER* 5.1 4.0 - - - +
2649 HIS* 3.2 14.7 - - - +
2659 ILE* 4.6 7.7 - - - +
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Residues in contact with MET 86 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829 LEU* 2.7 13.5 + - - +
839 VAL* 2.4 14.6 + - - +
849 ALA 2.5 7.8 - - - +
859 ALA* 1.3 74.7 - - + +
879 GLY* 1.3 54.4 + - - +
889 GLU 2.3 22.4 + - - -
2609 LEU* 3.7 49.1 - - + +
2619 SER* 5.6 2.5 - - - +
2649 HIS* 2.3 26.5 - - - -
2859 PHE* 5.0 9.4 - - + -
2879 PRO* 5.0 9.2 - - + -
2909 ILE* 4.9 30.1 - - + -
2919 ALA* 5.5 5.8 - - - -
2959 LEU 5.5 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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