Contacts of the helix formed by residues 70 - 91 (chain 2) in PDB entry 3J9X
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 GLY 70 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692 THR* 1.3 74.3 - - - +
712 PRO* 1.3 66.9 - - - +
732 ARG* 2.9 35.8 + - - +
347 T 3.5 25.3 + - - +
357 A 4.4 2.4 + - - -
111y PHE* 3.5 19.0 - - - -
90z ILE* 5.6 0.6 - - - +
99z MET* 5.3 0.2 - - - +
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Residues in contact with PRO 71 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692 THR 4.4 0.2 - - - +
702 GLY* 1.3 82.2 - - - +
722 ASN* 1.3 64.7 + - - +
732 ARG 3.1 0.2 - - - -
742 ALA* 3.1 4.8 + - - +
752 ILE* 3.0 24.9 + - - +
347 T 3.6 23.1 - - + +
357 A 3.9 32.8 - - - +
71y PRO* 3.6 19.6 - - + +
74y ALA* 4.8 2.5 - - + -
75y ILE* 3.5 36.1 - - + +
107y TYR* 6.5 0.9 - - + -
111y PHE* 4.6 7.4 - - + -
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Residues in contact with ASN 72 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682 ILE* 3.5 15.3 - - + -
692 THR* 3.3 15.0 + - - +
702 GLY 3.0 0.4 - - - -
712 PRO* 1.3 76.2 - - - +
732 ARG* 1.3 64.8 + - - +
752 ILE* 3.3 18.6 + - + +
762 TYR* 3.0 26.3 - - + -
72y ASN* 3.1 24.8 - - - +
75y ILE* 3.5 12.4 - - - +
111y PHE* 3.3 24.9 + - - +
112y ASN* 4.8 8.5 + - - +
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Residues in contact with ARG 73 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602 SER* 2.7 46.3 + - - -
632 LEU* 3.5 16.2 - - + +
642 THR* 2.9 31.9 + - - +
682 ILE* 2.8 56.9 + - + +
692 THR* 3.8 7.9 - - - +
702 GLY 2.9 15.0 + - - +
722 ASN* 1.3 77.6 - - - +
742 ALA* 1.3 59.3 + - - +
762 TYR* 3.0 5.0 + - - -
772 GLN* 2.8 30.1 + - - +
347 T 3.0 36.7 + - - +
89z ARG 4.6 0.6 + - - -
90z ILE* 3.7 28.5 + - - +
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Residues in contact with ALA 74 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702 GLY 3.6 0.6 + - - -
712 PRO 3.1 9.4 + - - +
732 ARG* 1.3 76.3 - - - +
752 ILE* 1.3 65.1 + - - +
772 GLN* 3.6 10.2 - - - +
782 GLY* 2.9 21.5 + - - -
337 A 4.1 17.5 - - + +
347 T 3.0 41.0 + - + +
3158 A 4.7 4.7 - - + -
3168 T 4.4 5.8 - - - +
71y PRO* 4.8 4.0 - - + -
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Residues in contact with ILE 75 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712 PRO 3.0 15.0 + - - +
722 ASN* 3.4 23.8 - - + +
732 ARG 3.2 0.4 - - - -
742 ALA* 1.3 76.6 - - - +
762 TYR* 1.3 66.0 + - + +
782 GLY* 3.4 0.5 + - - -
792 PHE* 3.1 21.3 + - - +
1072 TYR* 3.5 31.6 - - + -
1112 PHE* 4.6 10.5 - - + +
1122 ASN 5.9 0.4 - - - +
1132 ALA* 4.1 19.5 - - + -
71y PRO* 3.6 26.2 - - + -
72y ASN* 3.5 35.9 - - - +
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Residues in contact with TYR 76 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592 VAL* 4.4 2.9 - - - +
632 LEU* 3.6 28.7 - - + -
682 ILE* 4.0 18.7 - - + +
722 ASN* 3.0 28.0 - - + -
732 ARG 3.0 5.6 + - - +
752 ILE* 1.3 80.1 - - + +
772 GLN* 1.3 61.5 + - - +
792 PHE* 3.3 5.6 + - - +
802 GLY* 2.8 26.3 + - - -
1122 ASN 5.0 0.2 + - - -
1132 ALA* 3.9 10.2 - - + -
1142 ASN* 2.9 38.0 + - - +
1172 VAL* 3.7 31.8 - - + +
1182 LEU* 3.7 29.8 - - + -
1212 VAL* 4.2 12.0 - - + +
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Residues in contact with GLN 77 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552 VAL* 5.4 0.7 - - - +
562 ASN* 3.4 24.1 + - - +
592 VAL* 3.3 20.5 - - - +
602 SER* 3.5 26.7 - - - +
632 LEU* 4.0 2.1 - - + +
732 ARG 2.8 22.4 + - - +
742 ALA* 3.2 9.4 + - - +
762 TYR* 1.3 77.2 - - - +
782 GLY* 1.3 57.6 + - - +
802 GLY* 3.3 0.9 + - - -
812 LEU* 2.9 41.3 + - + +
337 A 3.4 33.5 + - + +
347 T 3.1 21.1 + - - +
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Residues in contact with GLY 78 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742 ALA 2.9 15.4 + - - -
752 ILE 3.8 2.0 - - - -
772 GLN* 1.3 77.6 - - - +
792 PHE* 1.3 62.5 + - - +
812 LEU* 3.8 4.7 - - - +
822 LYS* 3.0 25.3 + - - +
1072 TYR* 3.5 13.8 + - - -
337 A 5.4 1.0 + - - -
3168 T 5.1 3.6 - - - -
3178 A 4.1 24.3 - - - +
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Residues in contact with PHE 79 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752 ILE 3.1 13.5 + - - +
762 TYR 3.5 7.2 - - - +
772 GLN 3.3 0.2 - - - -
782 GLY* 1.3 75.9 - - - +
802 GLY* 1.3 63.8 + - - +
822 LYS* 3.1 5.1 + - - +
832 VAL* 2.9 32.9 + - + +
1002 ILE* 5.1 2.5 - - + -
1032 LEU* 3.7 24.2 - - + -
1042 LYS* 3.8 23.6 - - + -
1072 TYR* 3.5 33.9 + + + -
1182 LEU* 3.3 52.7 - - + -
1212 VAL* 3.8 16.4 - - + -
1222 VAL* 3.7 23.6 - - + -
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Residues in contact with GLY 80 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552 VAL* 4.5 6.3 - - - -
592 VAL* 5.0 2.0 - - - -
762 TYR 2.8 16.6 + - - -
772 GLN* 3.8 1.1 - - - -
792 PHE* 1.3 75.1 - - - +
812 LEU* 1.3 62.1 + - - +
832 VAL* 3.1 2.6 + - - -
842 ALA* 3.0 19.6 + - - +
1212 VAL* 3.5 26.7 - - - -
1252 ILE* 3.1 17.8 - - - +
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Residues in contact with LEU 81 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522 PHE* 3.5 42.8 - - + +
552 VAL* 4.5 6.9 - - + +
562 ASN* 3.4 31.2 - - - +
772 GLN* 2.9 29.0 + - + +
782 GLY* 3.8 4.3 - - - +
802 GLY* 1.3 75.4 - - - +
822 LYS* 1.3 57.7 + - - +
842 ALA* 3.2 3.8 + - - -
852 ARG 2.9 23.6 + - - -
327 T 5.5 1.6 - - - +
337 A 5.6 3.1 - - - +
3178 A 4.1 20.0 - - + +
3188 T 3.4 37.4 - - - +
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Residues in contact with LYS 82 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061 TYR* 2.8 32.8 + - - -
782 GLY 3.0 18.2 + - - +
792 PHE* 3.5 4.9 - - - +
812 LEU* 1.3 75.3 - - - +
832 VAL* 1.3 64.0 + - - +
852 ARG* 3.3 10.2 + - - +
862 ALA* 3.1 22.5 + - - +
992 MET* 5.9 3.1 - - - -
1032 LEU* 3.5 35.3 - - + +
1062 TYR* 5.0 5.4 - - - -
1072 TYR* 4.6 3.6 - - + -
237 A 6.3 0.2 - - - -
247 T 3.2 15.0 + - - -
3178 A 3.7 26.9 + - - +
3188 T 3.3 27.4 + - - +
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Residues in contact with VAL 83 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792 PHE* 2.9 42.5 + - + +
802 GLY* 3.1 8.3 + - - +
822 LYS* 1.3 77.2 - - - +
842 ALA* 1.3 62.0 + - - +
862 ALA* 3.3 8.0 + - - +
872 LEU* 3.0 20.4 + - + +
962 LEU* 4.5 2.3 - - + +
1002 ILE* 4.3 28.7 - - + -
1032 LEU* 3.7 19.3 - - + -
1222 VAL* 4.6 8.5 - - + -
1252 ILE* 3.9 26.7 - - + -
1262 THR* 4.5 5.8 - - + -
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Residues in contact with ALA 84 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512 LYS 5.7 0.4 - - - +
522 PHE* 3.6 20.4 - - + -
552 VAL* 4.2 20.9 - - + -
802 GLY 3.0 11.2 + - - +
812 LEU* 3.5 9.0 - - - +
832 VAL* 1.3 74.1 - - - +
852 ARG* 1.3 65.5 + - - +
872 LEU* 3.1 12.2 + - + +
882 ASN* 3.0 25.5 + - - +
1252 ILE* 4.4 10.5 - - + +
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Residues in contact with ARG 85 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522 PHE* 3.5 11.1 - - - -
812 LEU 2.9 14.1 + - - +
822 LYS* 3.3 20.4 - - - +
842 ALA* 1.3 76.1 - - - +
862 ALA* 1.3 63.4 + - - +
882 ASN* 3.0 6.1 + - - +
892 ARG* 3.0 45.3 + - - +
237 A 3.8 35.9 + - - -
247 T 2.9 33.5 + - - +
3188 T 3.0 37.0 + - - +
3198 A 3.4 30.3 + - - +
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Residues in contact with ALA 86 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822 LYS 3.1 9.7 + - - +
832 VAL* 3.6 9.9 - - - +
852 ARG* 1.3 77.5 - - - +
872 LEU* 1.3 58.8 + - - +
892 ARG* 4.5 2.9 - - - +
902 ILE* 2.7 47.1 + - + +
962 LEU* 3.8 16.4 - - + -
992 MET* 3.8 28.7 - - + -
237 A 5.6 2.2 - - - -
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Residues in contact with LEU 87 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832 VAL* 3.0 13.3 + - + +
842 ALA* 3.2 12.6 - - + +
862 ALA* 1.3 76.9 - - - +
882 ASN* 1.3 64.0 + - - +
912 GLY* 2.7 30.7 + - - +
922 SER* 3.6 29.4 - - - +
962 LEU* 3.6 24.0 - - + +
1252 ILE* 4.5 25.6 - - + +
1262 THR* 6.0 2.2 - - + -
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Residues in contact with ASN 88 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482 ASN* 4.9 5.8 + - - -
512 LYS* 3.8 31.3 + - - +
522 PHE* 3.4 34.1 - - + -
842 ALA* 3.0 12.7 + - - +
852 ARG* 3.0 8.0 + - - +
872 LEU* 1.3 85.5 - - - +
892 ARG* 1.3 64.4 + - + +
902 ILE 4.8 0.5 - - - -
912 GLY* 4.5 1.4 + - - -
73 SER* 4.6 13.1 - - - +
3198 A 5.4 1.7 + - - +
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Residues in contact with ARG 89 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852 ARG* 3.0 46.9 + - - +
862 ALA* 4.3 2.5 - - - +
882 ASN* 1.3 79.7 - - + +
902 ILE* 1.3 62.3 + - + +
73 SER* 4.1 33.7 - - - +
604 SER* 4.5 5.7 + - - -
734 ARG* 4.6 2.1 + - - -
217 A 4.6 9.9 + - - -
227 T 3.6 28.7 + - - +
237 A 3.3 32.0 + - - +
3198 A 4.1 17.1 + - - +
3208 T 4.3 15.6 + - - -
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Residues in contact with ILE 90 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862 ALA* 2.7 28.9 + - + +
882 ASN 4.8 0.7 - - - -
892 ARG* 1.3 79.1 - - + +
912 GLY* 1.3 68.0 + - - +
952 ALA* 3.6 26.7 - - + +
962 LEU* 4.0 4.7 - - + +
992 MET* 3.8 38.1 - - + -
604 SER* 4.9 1.7 + - - -
614 ALA* 5.8 0.7 - - - -
644 THR* 2.6 36.9 + - - +
694 THR* 4.4 10.8 - - + -
704 GLY 5.6 0.4 - - - +
734 ARG* 3.7 18.7 + - - +
227 T 5.6 0.7 - - - +
237 A 4.5 10.3 - - - +
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Residues in contact with GLY 91 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862 ALA 3.6 0.6 + - - -
872 LEU* 2.7 30.8 + - - -
882 ASN 4.5 1.1 - - - -
902 ILE* 1.3 88.8 - - - +
922 SER* 1.3 67.8 + - - +
962 LEU* 3.4 9.2 - - - +
644 THR* 3.6 1.8 - - - +
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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