Contacts of the helix formed by residues 49 - 66 (chain 6) 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 VAL 49 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 TYR* 3.8 10.1 - - + -
135 ARG* 3.7 27.6 - - + +
456 PHE* 3.0 62.5 + - + +
486 ASN* 1.3 71.7 - - - +
506 PRO* 1.4 60.8 - - + +
516 LYS 3.0 4.0 - - - -
526 PHE* 2.8 30.7 + - - +
536 THR 3.2 6.6 + - - -
3438 A 3.9 27.8 - - + +
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Residues in contact with PRO 50 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 TYR* 3.5 36.3 - - + +
466 GLN 3.1 24.7 - - - +
476 THR 3.7 6.3 - - - +
486 ASN 3.4 2.5 - - - -
496 VAL* 1.4 96.4 - - + +
516 LYS* 1.3 65.9 + - + +
536 THR* 3.7 4.7 - - - +
546 SER* 3.1 24.3 + - - -
50a PRO* 5.8 2.0 - - + -
9b SER* 6.4 2.2 - - - -
10b TYR* 4.1 20.4 - - + -
11b SER* 5.7 0.7 - - - -
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Residues in contact with LYS 51 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476 THR* 3.4 27.3 + - - +
486 ASN* 3.0 33.7 + - - +
496 VAL 2.9 0.4 + - - -
506 PRO* 1.3 81.1 - - + +
526 PHE* 1.3 63.0 + - + +
546 SER* 2.9 19.3 + - - -
556 VAL* 3.4 12.1 - - - +
846 ALA* 5.7 0.4 - - - +
886 ASN* 3.8 30.6 + - - +
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Residues in contact with PHE 52 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135 ARG* 4.6 5.2 - - - +
486 ASN* 3.1 28.5 - - + -
496 VAL* 2.8 8.0 + - - +
516 LYS* 1.3 76.5 - - + +
536 THR* 1.3 66.4 + - - +
546 SER 3.2 1.6 - - - -
556 VAL* 3.1 7.4 + - + +
566 ASN* 3.0 27.9 + - - +
816 LEU* 3.5 43.7 - - + +
846 ALA* 3.6 13.5 - - + -
856 ARG* 3.5 14.4 - - - -
886 ASN* 3.4 28.3 - - - -
3428 T 3.6 24.7 - - + +
3438 A 3.5 29.6 - - - +
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Residues in contact with THR 53 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85 ARG 4.8 2.2 - - - +
95 SER* 4.3 5.4 - - - -
105 TYR* 3.5 42.6 - - + +
135 ARG* 2.8 36.2 + - - +
496 VAL 3.2 8.3 + - - -
506 PRO* 3.3 7.8 + - - -
526 PHE* 1.3 77.5 - - - +
546 SER* 1.3 62.3 + - - +
566 ASN* 3.1 17.5 + - + +
576 GLU* 3.1 13.5 + - + +
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Residues in contact with SER 54 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506 PRO 3.1 12.2 + - - -
516 LYS* 2.9 22.0 + - - -
536 THR* 1.3 77.1 - - - +
556 VAL* 1.3 63.5 + - - +
576 GLU* 3.4 9.6 + - - +
586 ASN* 3.2 28.5 + - - +
50a PRO 5.3 1.6 - - - -
54a SER* 3.3 35.6 - - - -
58a ASN* 5.3 6.0 + - - -
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Residues in contact with VAL 55 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516 LYS 3.4 17.5 - - - +
526 PHE* 3.1 13.8 + - - +
546 SER* 1.3 81.2 + - - +
566 ASN* 1.3 61.2 + - - +
586 ASN* 3.3 4.2 + - - +
596 VAL* 2.8 52.9 + - + +
776 GLN* 5.4 0.7 - - - +
806 GLY 4.5 8.1 - - - +
816 LEU* 4.5 13.0 - - + +
846 ALA* 4.2 17.7 - - + -
1246 ILE* 6.1 1.3 - - - -
1256 ILE* 4.0 25.4 - - + -
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Residues in contact with ASN 56 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135 ARG* 4.3 13.9 - - - +
526 PHE 3.0 16.1 + - - -
536 THR* 3.1 15.7 + - + +
556 VAL* 1.3 77.7 - - - +
576 GLU* 1.3 57.2 + - - +
606 SER* 2.9 33.1 + - - -
776 GLN* 3.4 21.6 + - - +
816 LEU* 3.4 30.4 - - - +
87 T 5.2 4.6 + - - +
97 A 4.4 31.4 + - - +
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Residues in contact with GLU 57 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536 THR* 3.1 12.0 + - + +
546 SER* 3.7 10.8 - - - +
556 VAL 3.2 0.2 - - - -
566 ASN* 1.3 76.4 - - - +
586 ASN* 1.3 69.4 + - - +
606 SER* 3.6 4.1 - - - -
616 ALA* 3.0 23.2 + - + +
51a LYS* 4.2 30.3 - - - +
54a SER* 5.7 0.3 + - - -
87a LEU* 5.8 3.6 - - - +
88a ASN* 5.2 4.5 - - - +
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Residues in contact with ASN 58 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546 SER* 3.2 15.5 + - - +
556 VAL* 4.0 2.4 - - - +
576 GLU* 1.3 86.3 - - - +
596 VAL* 1.3 66.0 + - - +
616 ALA* 3.2 8.5 + - - +
626 VAL* 3.1 26.1 + - - +
1246 ILE* 3.6 28.4 - - + +
54a SER* 5.5 4.6 + - - -
58a ASN* 4.2 18.0 - - - +
124a ILE* 4.3 10.2 + - - +
125a ILE* 4.2 17.6 + - - +
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Residues in contact with VAL 59 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556 VAL* 2.8 41.7 + - + +
586 ASN* 1.3 72.5 - - - +
606 SER* 1.3 62.5 + - - +
626 VAL* 3.1 9.3 + - - +
636 LEU* 3.0 30.7 + - + +
766 TYR 4.4 6.7 - - - +
776 GLN* 3.3 27.6 - - - +
806 GLY* 5.0 1.6 - - - -
1216 VAL* 4.1 37.5 - - + +
1246 ILE* 4.9 9.0 - - + -
1256 ILE* 4.6 6.7 - - + -
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Residues in contact with SER 60 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894 ARG 4.5 4.2 + - - -
904 ILE 4.9 1.8 + - - -
566 ASN 2.9 21.8 + - - -
576 GLU* 3.6 5.4 - - - -
596 VAL* 1.3 78.2 - - - +
616 ALA* 1.3 62.2 + - - +
636 LEU* 3.1 3.4 + - - -
646 THR* 3.0 10.3 + - - -
736 ARG* 2.7 43.0 + - - +
776 GLN* 3.5 8.7 - - - +
97 A 4.8 0.9 - - - -
107 T 2.9 19.9 + - - -
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Residues in contact with ALA 61 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904 ILE 5.8 0.4 - - - -
576 GLU* 3.0 15.3 + - + +
586 ASN* 3.2 13.2 + - - +
606 SER* 1.3 76.3 - - - +
626 VAL* 1.3 63.5 + - + +
646 THR* 3.2 10.0 + - - -
656 GLN* 3.1 26.8 + - + +
126a THR 5.9 2.9 - - - +
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Residues in contact with VAL 62 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586 ASN 3.1 14.1 + - - +
596 VAL* 3.1 9.4 + - + +
616 ALA* 1.3 77.2 - - + +
636 LEU* 1.3 63.4 + - + +
656 GLN* 2.9 12.6 + - + +
666 TYR* 2.9 50.1 + - + -
1176 VAL* 5.5 0.4 - - + -
1206 ALA* 3.8 18.2 - - + +
1216 VAL* 5.0 4.5 - - + +
1246 ILE* 3.7 32.8 - - + -
126a THR 5.0 9.2 - - - +
127a GLY* 5.1 2.0 - - - -
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Residues in contact with LEU 63 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596 VAL* 3.0 33.2 + - + +
606 SER* 3.1 7.6 + - - +
626 VAL* 1.3 76.7 - - + +
646 THR* 1.3 60.1 + - - +
666 TYR* 3.2 2.7 + - - +
676 GLY 3.0 4.3 + - - -
686 ILE* 2.9 39.4 + - + +
736 ARG* 3.5 47.6 - - + +
766 TYR* 3.6 32.5 - - + -
776 GLN* 4.0 10.8 - - - +
1176 VAL* 3.6 19.1 - - + -
1216 VAL* 5.0 2.7 - - + -
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Residues in contact with THR 64 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904 ILE* 2.6 28.7 + - + +
914 GLY 3.6 13.7 - - - +
924 SER 3.4 26.9 - - - +
934 GLY* 4.5 1.3 - - - -
944 PRO* 3.3 4.6 - - + +
954 ALA* 3.2 20.4 + - + +
606 SER 3.0 5.8 + - - -
616 ALA* 3.4 11.2 - - - -
626 VAL 3.1 0.2 - - - -
636 LEU* 1.3 77.4 - - - +
656 GLN* 1.3 63.6 + - - +
676 GLY 3.1 10.0 + - - -
736 ARG* 2.9 23.2 + - - +
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Residues in contact with GLN 65 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924 SER 4.9 8.3 + - - -
934 GLY* 5.3 1.0 - - - -
944 PRO* 3.4 30.4 - - - +
616 ALA* 3.1 17.3 + - + +
626 VAL* 2.9 12.4 + - - +
646 THR* 1.3 77.6 - - - +
666 TYR* 1.3 63.7 + - + +
676 GLY 3.3 0.4 - - - -
92a SER* 4.4 18.0 + - - -
126a THR 6.0 0.9 - - - +
133a VAL* 3.9 20.8 - - - +
134a SER* 3.0 41.9 + - - +
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Residues in contact with TYR 66 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944 PRO* 4.7 0.7 - - - -
626 VAL* 2.9 33.2 + - + +
636 LEU* 3.2 5.8 + - - +
656 GLN* 1.3 80.5 - - + +
676 GLY* 1.3 61.6 + - - +
686 ILE* 3.2 21.4 + - + +
1166 GLN* 3.2 42.9 + - + -
1176 VAL* 3.9 19.7 - - + -
1206 ALA* 3.5 31.3 - - + +
134a SER* 5.9 4.9 - - - -
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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