Contacts of the helix formed by residues 49 - 68 (chain H) in PDB entry 1ZMD
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 49 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H THR 2.7 12.8 + - - -
45H CYS* 3.3 5.9 + - - -
48H VAL* 1.3 81.5 - - - +
50H CYS* 1.3 59.9 + - - -
51H ILE 3.4 0.4 - - - -
52H PRO* 3.3 4.3 - - - +
53H SER* 2.8 33.8 + - - -
480H FAD 3.3 25.0 - - - +
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Residues in contact with CYS 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452G HIS* 4.1 7.6 - - + -
453G PRO* 4.5 5.2 - - + -
45H CYS* 2.0 51.2 + - - -
49H GLY* 1.3 70.5 - - - -
51H ILE* 1.3 61.5 + - + +
53H SER* 3.1 0.6 + - - -
54H LYS* 2.9 36.3 + - - +
328H ALA* 3.8 0.2 - - - -
480H FAD 3.2 59.4 - - + +
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Residues in contact with ILE 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392G SER* 4.2 18.8 - - - +
396G THR* 3.4 34.6 - - - +
452G HIS* 4.6 6.5 - - - +
453G PRO* 4.8 5.6 - - + -
45H CYS 3.1 3.6 + - - +
46H LEU* 3.7 31.0 - - + +
50H CYS* 1.3 80.6 - - + +
52H PRO* 1.3 73.6 - - + +
54H LYS* 6.0 0.2 - - + -
55H ALA* 3.1 19.4 + - - +
95H ALA* 4.2 5.2 - - + -
96H VAL* 3.9 26.0 - - + +
99H LEU* 3.7 26.5 - - + -
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Residues in contact with PRO 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H LEU 3.5 14.8 - - - +
47H ASN 3.9 4.3 - - - +
48H VAL* 3.8 6.5 - - - -
49H GLY 3.3 27.8 - - - +
51H ILE* 1.3 93.9 - - + +
53H SER* 1.3 61.6 + - - +
55H ALA* 3.3 2.3 + - + +
56H LEU* 3.1 26.7 + - - +
92H LYS* 3.8 29.2 - - + +
96H VAL* 3.9 10.8 - - + -
172H LEU* 3.7 20.0 - - + -
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Residues in contact with SER 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H GLY 2.8 24.1 + - - -
50H CYS 3.1 1.2 + - - -
52H PRO* 1.3 77.7 - - - +
54H LYS* 1.3 87.2 + - - +
56H LEU* 3.2 4.0 + - - +
57H LEU* 2.8 32.7 + - - +
172H LEU* 3.5 20.3 - - - +
192H GLU* 4.4 4.7 - - - -
193H LEU* 4.2 15.5 - - - -
196H VAL* 4.7 0.3 - - - +
480H FAD 3.6 10.6 - - - -
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Residues in contact with LYS 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393G ARG* 5.6 6.1 - - + +
396G THR* 4.2 11.7 - - + -
397G ASN* 4.8 4.6 - - - +
453G PRO* 3.9 22.2 - - + -
50H CYS 2.9 22.3 + - - +
51H ILE* 4.0 2.9 - - + +
53H SER* 1.3 102.7 + - - +
55H ALA* 1.3 58.5 + - - +
57H LEU* 3.2 18.2 + - - +
58H ASN* 2.8 31.9 + - - +
192H GLU* 3.0 20.4 + - - -
359H TYR* 3.5 34.3 - - + -
480H FAD 2.9 35.8 + - - +
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Residues in contact with ALA 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396G THR* 3.4 25.2 - - + +
51H ILE 3.1 13.5 + - - +
52H PRO* 3.6 4.3 - - + +
54H LYS* 1.3 75.4 - - - +
56H LEU* 1.3 58.8 + - - +
58H ASN* 3.3 5.5 + - - +
59H ASN* 2.8 36.5 + - - -
91H GLN* 3.8 16.8 - - - +
92H LYS* 3.9 22.9 - - + +
95H ALA* 5.0 1.1 - - + -
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Residues in contact with LEU 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H PRO 3.1 11.7 + - - +
53H SER* 3.8 3.8 - - - +
55H ALA* 1.3 77.5 - - - +
57H LEU* 1.3 60.8 + - - +
59H ASN* 4.1 1.1 - - - +
60H SER* 2.7 35.1 + - - -
85H LEU* 5.8 0.4 - - + -
88H MET* 4.2 29.5 - - + +
89H MET* 3.7 20.9 - - + +
92H LYS* 3.9 25.1 - - + -
171H ALA 5.0 1.6 - - - +
172H LEU* 3.4 41.7 - - + +
193H LEU* 6.0 0.7 - - + -
196H VAL* 3.9 24.0 - - + -
197H TRP* 5.0 0.9 - - + -
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Residues in contact with LEU 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H SER* 2.8 22.6 + - - +
54H LYS* 3.7 17.7 - - - +
56H LEU* 1.3 76.5 - - - +
58H ASN* 1.3 58.2 + - - +
60H SER* 3.6 2.7 - - - -
61H HIS* 3.0 17.2 + - - +
192H GLU* 3.4 35.2 - - + +
193H LEU* 5.7 0.4 - - + -
195H SER* 4.9 0.4 - - - -
196H VAL* 3.4 21.8 - - + -
199H ARG* 3.0 36.7 + - - +
359H TYR* 3.5 44.9 - - + +
360H THR* 4.5 1.8 - - - -
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Residues in contact with ASN 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G ARG* 2.6 32.3 + - - +
397G ASN* 3.6 32.0 + - - +
54H LYS 2.8 17.8 + - - +
55H ALA* 3.4 6.7 - - - +
57H LEU* 1.3 76.0 - - - +
59H ASN* 1.3 62.4 + - - +
61H HIS* 3.4 7.8 + - - +
62H TYR* 3.1 53.6 + - - -
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Residues in contact with ASN 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G ARG* 2.8 48.7 + - + +
76G ILE* 3.9 4.5 - - - +
55H ALA 2.8 24.1 + - - +
56H LEU* 4.1 3.2 - - - +
58H ASN* 1.3 69.9 - - - +
60H SER* 1.3 59.1 + - - +
62H TYR* 3.3 5.1 + - - +
63H TYR* 3.0 27.2 + - - +
88H MET* 3.4 46.3 + - + +
91H GLN* 2.8 29.6 + - - +
92H LYS 4.5 0.6 - - - +
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Residues in contact with SER 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H LEU 2.7 28.0 + - - -
57H LEU* 3.6 2.1 - - - -
59H ASN* 1.3 70.0 - - - +
61H HIS* 1.3 63.6 + - - +
63H TYR* 3.3 2.8 + - - +
64H HIS* 3.0 23.6 + - - +
88H MET* 4.2 1.3 - - - -
196H VAL* 3.7 28.6 - - - -
199H ARG* 3.1 31.5 + - - +
200H LEU* 3.9 23.3 - - - -
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Residues in contact with HIS 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G TYR* 5.6 3.0 + - - -
57H LEU 3.0 20.1 + - - +
58H ASN* 3.7 7.2 - - - +
59H ASN 3.2 0.2 - - - -
60H SER* 1.3 79.1 + - - +
62H TYR* 1.3 77.5 + + - +
64H HIS* 3.2 9.0 + - - +
65H MET* 3.0 67.1 + - + +
199H ARG* 3.6 15.8 - - - +
361H HIS* 3.4 55.2 - + + +
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Residues in contact with TYR 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G HIS* 5.9 0.7 + - - -
62G TYR* 4.2 27.4 + + - -
65G MET* 6.3 1.3 - - + -
70G ASP* 5.3 0.4 - - - -
71G PHE* 3.6 26.9 - + + -
74G ARG* 3.9 25.8 - - - -
76G ILE* 3.6 18.6 - - + -
397G ASN* 6.0 0.5 - - - +
58H ASN* 3.1 54.0 + - - +
59H ASN 3.8 0.9 - - - +
61H HIS* 1.3 88.5 - + - +
63H TYR* 1.3 66.9 + - - +
65H MET* 3.2 9.7 + - + +
66H ALA* 3.1 24.4 + - - +
71H PHE* 5.6 0.4 - + - -
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Residues in contact with TYR 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G ILE* 3.5 29.3 - - + +
59H ASN 3.0 13.7 + - - +
60H SER* 3.5 10.8 - - - +
62H TYR* 1.3 75.8 - - - +
64H HIS* 1.3 56.5 + - - +
66H ALA* 3.2 1.0 + - - +
67H HIS* 2.7 73.4 + + + +
81H VAL* 3.9 12.5 + - + -
82H ARG* 3.9 5.9 - - - -
83H LEU* 3.7 42.9 + - + +
88H MET* 4.3 4.3 - - + -
199H ARG 3.6 25.4 - - - -
200H LEU* 3.9 24.6 + - + -
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Residues in contact with HIS 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H SER 3.0 13.5 + - - +
61H HIS* 3.3 15.2 + - - +
63H TYR* 1.3 83.0 - - - +
65H MET* 1.3 76.5 + - + +
67H HIS* 4.7 2.5 - - + -
68H GLY* 2.8 29.7 + - - -
70H ASP 5.3 0.3 + - - -
199H ARG* 4.4 28.7 + - + +
233H GLN* 5.7 13.0 - - + -
361H HIS* 6.3 0.6 - + - -
2027H SO4 2.9 37.0 + - - -
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Residues in contact with MET 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G TYR* 6.4 1.3 - - + -
61H HIS* 3.0 52.0 + - + +
62H TYR* 3.2 12.8 + - + +
64H HIS* 1.3 112.1 - - + +
66H ALA* 1.3 60.9 + - - +
68H GLY 4.1 0.9 + - - +
70H ASP* 3.6 35.4 + - + +
71H PHE* 3.0 48.0 + - + -
361H HIS* 5.5 3.4 - - + -
2027H SO4 5.1 3.4 - - - +
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Residues in contact with ALA 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G PHE* 3.7 20.9 - - + -
76G ILE* 4.1 12.1 - - + -
78G MET* 4.2 2.0 - - - -
62H TYR 3.1 15.5 + - - +
63H TYR 3.8 2.2 - - - +
65H MET* 1.3 77.9 - - - +
67H HIS* 1.3 64.7 + - - +
68H GLY 3.5 6.2 + - - +
71H PHE* 4.1 6.6 - - - +
72H ALA 5.7 0.2 + - - -
78H MET* 3.5 34.5 - - + +
81H VAL* 3.8 9.3 - - + +
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Residues in contact with HIS 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H TYR* 2.7 59.4 + + + +
64H HIS* 4.3 2.0 - - - +
66H ALA* 1.3 74.3 - - - +
68H GLY* 1.3 60.8 + - - +
81H VAL* 3.3 37.5 + - + -
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Residues in contact with GLY 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H HIS* 2.8 23.4 + - - -
65H MET 4.2 0.7 - - - +
66H ALA 3.4 7.6 - - - +
67H HIS* 1.3 81.3 + - - +
69H THR* 1.3 66.0 + - - -
70H ASP 3.5 3.4 + - - -
71H PHE 4.8 0.9 + - - -
72H ALA* 4.8 6.2 + - - +
2027H SO4 3.2 16.4 - - - -
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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
------------------------------------------------------------
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