Contacts of the helix formed by residues 49 - 69 (chain A) in PDB entry 3ZJU
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 HIS 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A SER* 5.7 1.6 + - - -
47A ARG 3.6 3.1 + - - +
48A LEU* 1.3 76.5 - - - +
50A MET* 1.3 61.0 + - - +
51A GLY* 3.1 34.4 - - - -
52A HIS* 3.0 61.8 + + - +
53A VAL* 3.3 10.6 + - - +
628A ILE 5.6 1.3 - - - +
630A PRO* 3.9 9.2 - - - -
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Residues in contact with MET 50 (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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49A HIS* 1.3 74.9 - - - +
51A GLY* 1.3 62.4 + - - +
53A VAL* 3.8 8.2 - - - +
54A ARG* 3.0 25.3 + - - +
569A VAL* 3.9 30.0 - - + +
620A MET* 4.2 15.9 - - + -
628A ILE* 3.3 30.7 + - + +
630A PRO* 3.9 24.7 - - + +
642A VAL* 5.6 2.7 - - - -
646A MET* 4.3 11.3 - - - +
658A TRP* 2.7 57.9 - - + -
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A HIS* 3.1 16.6 - - - -
50A MET* 1.3 77.0 - - - +
52A HIS* 1.3 58.0 + - - +
54A ARG* 3.8 1.3 - - - +
55A ASN* 2.9 31.4 + - - +
566A GLN* 3.8 10.1 + - - -
569A VAL* 4.4 9.6 - - - +
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Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 4.0 22.2 - - + +
43A TYR* 4.8 6.8 + - + -
45A SER* 5.1 3.2 + - - -
47A ARG 4.7 1.6 + - - -
48A LEU* 3.6 25.8 - - + -
49A HIS* 3.0 63.0 + + - +
51A GLY* 1.3 73.7 - - - +
53A VAL* 1.3 55.3 + - - +
55A ASN* 3.1 4.7 + - - +
56A TYR* 2.7 70.0 + - + -
108A MET* 4.5 7.7 - - - +
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.4 7.4 - - + -
49A HIS 3.3 10.2 + - - +
50A MET* 3.9 7.9 - - - +
51A GLY 3.2 0.8 - - - -
52A HIS* 1.3 74.8 - - - +
54A ARG* 1.3 55.5 + - - +
56A TYR* 5.0 0.2 - - - -
57A THR* 2.6 47.6 + - - +
115A LEU* 4.0 35.7 - - + -
117A PHE* 4.0 6.5 - - + -
630A PRO* 3.6 31.9 - - + -
642A VAL* 4.4 13.7 - - + -
643A ARG* 5.6 0.7 - - + -
646A MET* 4.2 15.3 - - + -
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET 3.0 14.0 + - - +
51A GLY* 3.9 3.1 - - - +
53A VAL* 1.3 74.1 - - - +
55A ASN* 1.3 67.4 + - - +
57A THR* 4.1 3.3 - - - -
58A ILE* 3.1 43.5 + - + +
566A GLN* 4.0 7.6 - - + -
567A GLY 3.2 33.2 + - - +
568A MET 3.9 0.6 + - - -
569A VAL* 4.3 8.7 - - + -
646A MET* 3.3 36.6 + - + +
647A MET* 5.0 0.8 - - - +
650A SER* 3.4 14.5 + - - -
651A PRO 2.9 27.3 + - - -
652A ALA* 3.6 9.8 + - - +
654A MET 2.9 21.4 + - - -
656A LEU* 3.6 33.9 - - - +
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Residues in contact with ASN 55 (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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39A SER* 3.5 10.4 + - - -
40A MET* 4.3 10.1 + - - +
51A GLY 2.9 19.3 + - - +
52A HIS* 3.4 6.5 - - - +
54A ARG* 1.3 79.5 - - - +
56A TYR* 1.3 77.2 + - + +
58A ILE* 3.3 5.2 + - - +
59A GLY 3.2 15.6 + - - -
528A ILE* 2.8 32.9 + - - +
529A GLY* 3.7 12.9 - - - -
530A GLY 4.7 1.2 - - - +
566A GLN* 3.6 24.5 - - - +
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Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 3.5 28.0 - - - -
40A MET 2.7 29.4 + - - -
42A PRO* 3.3 30.8 - - + +
48A LEU* 4.8 0.4 - - + -
52A HIS* 2.7 54.8 + + + +
53A VAL* 5.0 0.2 - - - -
55A ASN* 1.3 80.1 + - + +
57A THR* 1.3 60.4 + - - +
59A GLY* 3.9 0.3 - - - -
60A ASP* 2.9 29.8 + - - +
75A GLN* 4.2 2.8 + - - +
77A ILE* 4.9 4.3 - - + -
112A LEU* 3.8 27.4 - - + -
117A PHE* 3.5 16.9 - + + -
119A TYR* 3.3 21.1 - - + +
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Residues in contact with THR 57 (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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53A VAL* 2.6 34.3 + - - +
54A ARG* 4.1 5.2 - - - -
56A TYR* 1.3 77.9 - - - +
58A ILE* 1.3 56.1 + - - +
60A ASP* 3.2 3.1 + - - +
61A VAL* 2.9 38.4 + - + +
117A PHE* 3.6 17.5 - - - -
643A ARG* 3.8 36.3 - - + +
646A MET* 5.0 3.6 - - + +
647A MET* 3.4 30.7 - - + -
764A PHE 5.2 0.2 - - - +
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Residues in contact with ILE 58 (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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54A ARG* 3.1 43.2 + - + +
55A ASN* 3.6 4.5 - - - +
57A THR* 1.3 76.6 - - - +
59A GLY* 1.3 63.9 + - - +
61A VAL* 3.3 2.1 + - - +
62A ILE* 3.2 28.7 + - + +
528A ILE* 4.2 18.6 - - + -
564A LEU* 4.4 17.0 - - + -
566A GLN* 3.6 24.2 - - + -
647A MET* 3.5 26.2 - - + -
652A ALA* 4.4 13.5 - - + -
722A PHE* 4.5 15.4 - - + -
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Residues in contact with GLY 59 (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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37A CYS* 3.4 11.3 - - - -
39A SER* 3.9 9.0 - - - -
55A ASN 3.2 8.1 + - - -
56A TYR 3.6 0.6 + - - -
58A ILE* 1.3 77.2 - - - +
60A ASP* 1.3 58.8 + - - +
62A ILE 3.2 1.9 + - - -
63A ALA* 2.9 25.6 + - - +
75A GLN* 3.2 12.8 - - - -
528A ILE* 3.4 24.7 - - - +
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Residues in contact with ASP 60 (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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56A TYR 2.9 20.1 + - - +
57A THR 3.2 3.1 + - - +
59A GLY* 1.3 73.0 - - - +
61A VAL* 1.3 66.0 + - - +
64A ARG* 2.8 54.8 + - - +
75A GLN* 2.9 30.2 - - - +
116A GLY 3.6 1.9 - - - +
117A PHE* 3.8 11.7 - - + -
118A GLY* 3.0 20.8 + - - +
643A ARG* 3.0 24.6 + - - +
763A PRO 4.5 0.9 - - - -
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Residues in contact with VAL 61 (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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57A THR* 2.9 24.4 + - + +
58A ILE 3.5 5.2 - - - +
60A ASP* 1.3 75.4 - - - +
62A ILE* 1.3 59.3 + - - +
65A TYR* 3.0 30.8 + - - +
643A ARG* 4.8 0.2 - - - +
647A MET* 3.8 18.2 - - + -
716A ILE* 4.8 5.2 - - + -
722A PHE* 3.8 31.6 - - + -
763A PRO* 3.5 31.6 - - + +
764A PHE* 3.8 31.2 - - + -
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Residues in contact with ILE 62 (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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35A TYR* 3.8 32.5 - - + +
37A CYS* 3.9 7.0 - - - -
58A ILE* 3.3 17.7 - - + +
59A GLY 3.2 6.7 + - - +
61A VAL* 1.3 77.5 - - - +
63A ALA* 1.3 53.7 + - - +
65A TYR* 3.1 8.4 + - + +
66A GLN* 2.7 45.4 + - + +
526A ILE* 3.8 31.2 - - + -
528A ILE* 4.3 7.2 - - + -
564A LEU* 5.2 1.1 - - + -
716A ILE* 5.8 0.9 - - + -
720A GLN* 4.8 7.0 - - + +
722A PHE* 4.1 27.8 - - + -
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Residues in contact with ALA 63 (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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37A CYS* 4.1 7.1 - - + -
59A GLY 2.9 13.8 + - - +
60A ASP* 3.9 2.5 - - - +
62A ILE* 1.3 76.4 - - - +
64A ARG* 1.3 63.4 + - + +
66A GLN* 3.4 1.7 + - - -
67A ARG* 3.1 23.4 + - - +
73A VAL* 3.7 29.8 - - + +
75A GLN* 3.4 35.9 - - + +
118A GLY 5.6 0.2 - - - +
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Residues in contact with ARG 64 (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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18A TRP* 3.3 25.9 - - - -
24A PHE* 3.3 28.6 - - + -
60A ASP* 2.8 44.7 + - - +
61A VAL 4.0 1.8 - - - +
63A ALA* 1.3 73.7 - - + +
65A TYR* 1.3 65.7 + - - +
67A ARG* 3.3 8.5 + - - +
68A MET* 3.1 29.7 + - + +
116A GLY 2.8 25.5 + - - -
118A GLY* 3.7 9.5 - - - +
762A ASN* 4.1 16.1 + - - +
763A PRO* 3.9 24.0 - - + -
766A PRO* 3.6 14.5 - - - +
783A ASP* 3.2 25.9 + - - -
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Residues in contact with TYR 65 (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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61A VAL 3.0 18.4 + - - +
62A ILE* 3.6 5.2 - - + +
64A ARG* 1.3 75.8 - - - +
66A GLN* 1.3 83.1 + - + +
68A MET* 3.0 16.0 + - - +
69A LEU* 3.1 40.9 + - + +
713A THR* 3.7 20.1 + - - +
716A ILE* 3.7 26.7 - - + -
717A GLY* 3.6 33.7 - - - -
763A PRO* 4.1 14.1 - - + +
787A TRP* 3.6 49.8 - + - -
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Residues in contact with GLN 66 (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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35A TYR* 3.8 42.6 + - + -
62A ILE* 2.7 24.7 + - + +
63A ALA 3.9 0.4 - - - +
65A TYR* 1.3 97.9 - - + +
67A ARG* 1.3 61.4 + - - +
69A LEU* 3.1 23.3 + - - +
71A LYS* 3.1 54.7 + - + +
73A VAL* 3.7 18.6 - - + -
717A GLY* 5.6 3.6 + - - -
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Residues in contact with ARG 67 (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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23A THR* 3.2 33.3 + - - +
24A PHE* 3.7 38.4 - - - +
26A VAL* 3.8 22.6 - - - +
63A ALA 3.1 14.0 + - - +
64A ARG* 3.6 10.1 - - - +
65A TYR 3.2 0.2 - - - -
66A GLN* 1.3 75.8 - - - +
68A MET* 1.3 58.4 + - - +
70A GLY* 2.9 21.0 + - - -
71A LYS 3.9 9.7 + - - +
72A ASN* 5.7 0.2 - - - +
73A VAL* 3.5 25.5 + - + +
783A ASP* 3.2 26.7 - - - +
784A ASN* 3.4 24.6 - - - +
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Residues in contact with MET 68 (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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64A ARG* 3.1 14.3 + - + +
65A TYR 3.0 7.4 + - - +
67A ARG* 1.3 76.5 - - - +
69A LEU* 1.3 58.5 + - - +
70A GLY 3.2 1.5 + - - -
759A ARG* 3.8 45.1 - - + +
762A ASN* 3.7 22.7 - - - +
763A PRO* 4.4 4.9 - - - -
782A ILE* 4.0 11.7 - - + +
783A ASP* 4.3 12.1 - - - +
784A ASN 5.8 0.4 - - - -
785A ALA 3.5 23.3 - - - +
786A PRO* 3.5 10.5 - - - +
787A TRP* 2.7 54.0 + - + +
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Residues in contact with LEU 69 (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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65A TYR* 3.1 47.1 + - + +
66A GLN* 3.3 30.1 - - - +
67A ARG 3.1 0.8 - - - -
68A MET* 1.3 78.2 - - - +
70A GLY* 1.3 57.5 + - - +
71A LYS* 3.5 17.0 - - - +
713A THR* 5.8 1.6 - - + -
787A TRP* 3.9 29.4 - - + -
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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
------------------------------------------------------------
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