Contacts of the helix formed by residues 49 - 68 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E THR 2.7 13.1 + - - -
45E CYS* 3.3 4.7 + - - -
48E VAL* 1.3 82.5 - - - +
50E CYS* 1.3 59.0 + - - -
51E ILE 3.4 0.4 - - - -
52E PRO* 3.2 5.4 - - - +
53E SER* 2.8 34.1 + - - -
480E FAD 3.3 25.0 - - - +
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Residues in contact with CYS 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E CYS* 2.0 51.4 + - - -
49E GLY* 1.3 69.8 - - - -
51E ILE* 1.3 63.0 + - + +
53E SER* 3.0 2.1 + - - -
54E LYS* 3.0 34.9 + - - +
328E ALA* 3.7 2.2 - - - -
480E FAD 3.3 56.9 - - + +
452F HIS* 4.1 1.6 - - + -
453F PRO* 4.4 10.1 - - + -
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Residues in contact with ILE 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E CYS* 3.0 18.9 + - - +
46E LEU* 3.6 27.8 - - + +
50E CYS* 1.3 81.9 - - + +
52E PRO* 1.3 73.8 - - + +
54E LYS* 4.8 0.7 - - - -
55E ALA* 3.1 19.1 + - - +
92E LYS 5.2 0.2 - - - +
95E ALA* 4.2 2.9 - - + -
96E VAL* 3.8 25.8 - - + +
99E LEU* 3.5 29.8 - - + -
392F SER* 4.9 6.5 - - - +
396F THR* 3.5 28.5 - - + +
452F HIS* 4.5 9.2 - - - +
453F PRO* 5.7 3.6 - - + -
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Residues in contact with PRO 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E LEU 3.4 20.4 - - - +
47E ASN 3.9 4.0 - - - +
48E VAL* 3.7 6.5 - - - -
49E GLY 3.2 30.7 - - - +
51E ILE* 1.3 87.6 - - + +
53E SER* 1.3 63.9 + - - +
55E ALA* 3.2 3.7 + - + +
56E LEU* 3.1 23.7 + - - +
92E LYS* 3.8 28.5 - - + +
96E VAL* 3.9 10.8 - - + -
172E LEU* 3.6 21.3 - - + -
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Residues in contact with SER 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLY 2.8 22.8 + - - -
50E CYS 3.0 1.2 + - - -
52E PRO* 1.3 80.0 - - - +
54E LYS* 1.3 91.9 + - - +
56E LEU* 3.1 2.6 + - - +
57E LEU* 2.9 28.3 + - - +
172E LEU* 3.5 20.1 - - - +
192E GLU* 4.4 4.9 - - - -
193E LEU* 4.2 15.3 - - - -
196E VAL* 4.8 0.3 - - - +
480E FAD 3.6 11.7 - - - -
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Residues in contact with LYS 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E CYS 3.0 22.9 + - - +
51E ILE* 4.0 2.9 - - - +
53E SER* 1.3 100.7 + - - +
55E ALA* 1.3 57.7 + - - +
57E LEU* 3.3 8.5 + - - +
58E ASN* 2.9 31.5 + - - +
192E GLU* 3.0 24.7 + - - -
359E TYR* 3.4 39.5 - - + -
480E FAD 2.8 37.1 + - - +
393F ARG* 5.6 7.0 - - + +
396F THR* 4.3 11.4 - - + -
397F ASN* 4.2 3.6 - - - +
453F PRO* 3.9 24.0 - - + -
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Residues in contact with ALA 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ILE 3.1 18.8 + - - +
52E PRO* 3.6 4.3 - - + +
54E LYS* 1.3 75.4 - - - +
56E LEU* 1.3 58.4 + - - +
58E ASN* 3.3 6.0 + - - +
59E ASN* 2.9 35.7 + - - -
91E GLN* 4.0 8.5 - - - +
92E LYS* 3.9 30.5 - - + +
95E ALA* 5.1 1.1 - - + -
396F THR* 3.6 21.0 - - + +
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Residues in contact with LEU 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E PRO 3.1 12.3 + - - +
53E SER* 3.7 6.3 - - - +
55E ALA* 1.3 74.5 - - - +
57E LEU* 1.3 60.1 + - - +
59E ASN* 4.2 2.0 - - - +
60E SER* 2.8 35.3 + - - -
85E LEU* 6.0 0.2 - - + -
88E MET* 4.4 25.0 - - + +
89E MET* 3.9 22.7 - - + -
92E LYS* 3.9 22.2 - - + -
171E ALA 4.9 1.8 - - - +
172E LEU* 3.5 47.1 - - + +
193E LEU* 5.7 0.9 - - + -
196E VAL* 4.0 24.7 - - + -
197E TRP* 5.0 1.1 - - + +
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Residues in contact with LEU 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E SER* 2.9 21.4 + - - +
54E LYS* 3.7 14.1 - - - +
56E LEU* 1.3 75.9 - - - +
58E ASN* 1.3 59.0 + - - +
60E SER* 3.6 3.4 - - - -
61E HIS* 2.9 16.6 + - - +
192E GLU* 3.5 49.1 - - + +
193E LEU* 5.8 0.2 - - + -
195E SER* 4.8 0.9 - - - -
196E VAL* 3.5 11.2 - - + -
199E ARG* 2.9 37.4 + - - +
359E TYR* 3.6 45.8 - - + +
360E THR* 4.4 1.8 - - - -
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Residues in contact with ASN 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LYS 2.9 16.2 + - - +
55E ALA* 3.4 6.3 - - - +
57E LEU* 1.3 78.0 - - - +
59E ASN* 1.3 64.5 + - - +
61E HIS* 3.4 6.0 + - - +
62E TYR* 3.0 59.3 + - - -
74F ARG* 3.6 10.1 + - - +
393F ARG* 5.6 4.8 - - - +
396F THR 5.7 0.2 - - - +
397F ASN* 2.7 42.8 + - - +
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Residues in contact with ASN 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E ALA* 2.9 21.5 + - - +
56E LEU* 4.2 2.3 - - - +
58E ASN* 1.3 73.2 - - - +
60E SER* 1.3 62.0 + - - +
62E TYR* 3.3 7.0 + - - +
63E TYR* 2.9 28.2 + - - +
88E MET* 3.5 46.7 + - + +
91E GLN* 2.6 29.7 + - - +
92E LYS 4.6 0.4 - - - +
74F ARG* 2.6 47.1 + - + +
76F ILE* 3.9 1.9 - - - +
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Residues in contact with SER 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E LEU 2.8 26.0 + - - -
57E LEU* 3.6 2.3 - - - -
59E ASN* 1.3 73.1 - - - +
61E HIS* 1.3 60.9 + - - +
63E TYR* 3.4 2.8 + - - +
64E HIS* 3.0 22.5 + - - +
88E MET* 4.2 1.5 - - - -
196E VAL* 3.7 22.0 - - - -
199E ARG* 3.0 33.5 + - - +
200E LEU* 3.8 30.3 - - - -
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Residues in contact with HIS 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E LEU 2.9 20.1 + - - +
58E ASN* 3.7 5.8 - - - +
59E ASN 3.2 0.2 - - - -
60E SER* 1.3 78.1 + - - +
62E TYR* 1.3 85.2 + + - +
64E HIS* 3.2 8.6 + - - +
65E MET* 3.0 56.1 + - + +
199E ARG* 3.7 16.4 - - - +
361E HIS* 3.4 54.1 + + + +
62F TYR* 5.5 3.8 + - - -
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Residues in contact with TYR 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ASN* 3.0 47.8 + - - +
59E ASN 3.3 1.3 + - - +
61E HIS* 1.3 92.4 - + - +
63E TYR* 1.3 66.2 + - - +
65E MET* 3.3 9.0 + - + +
66E ALA* 3.0 25.1 + - - +
71E PHE* 5.6 0.2 - + - -
62F TYR* 3.9 32.0 + + - -
65F MET* 6.3 0.7 - - + -
70F ASP* 5.4 0.4 - - - -
71F PHE* 3.6 25.2 - + + -
74F ARG* 3.9 28.2 + - - -
76F ILE* 3.5 18.6 - - + -
397F ASN* 6.1 0.2 - - - +
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Residues in contact with TYR 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ASN 2.9 17.3 + - - +
60E SER* 3.5 6.7 - - - +
62E TYR* 1.3 75.7 - - - +
64E HIS* 1.3 57.5 + - - +
66E ALA* 3.2 1.9 + - - +
67E HIS* 2.7 72.9 + + + +
81E VAL* 4.0 17.4 + - + -
82E ARG 4.0 6.3 - - - -
83E LEU* 3.8 43.3 + - + +
88E MET* 4.3 4.3 - - + -
199E ARG 3.5 25.1 - - - -
200E LEU* 4.0 24.0 + - + -
76F ILE* 3.5 23.0 - - + +
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Residues in contact with HIS 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E SER 3.0 13.9 + - - +
61E HIS* 3.4 14.6 + - - +
63E TYR* 1.3 83.3 - - - +
65E MET* 1.3 73.4 + - + +
67E HIS* 4.7 1.8 - - - -
68E GLY* 2.8 31.7 + - - +
69E THR 4.8 0.2 + - - -
70E ASP 5.2 0.3 + - - -
199E ARG* 4.5 27.2 + - + +
233E GLN* 5.6 12.3 - - + -
2015E SO4 2.8 38.4 + - - -
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Residues in contact with MET 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E HIS* 3.0 50.6 + - + +
62E TYR* 3.7 12.1 - - + +
63E TYR 3.3 0.2 - - - -
64E HIS* 1.3 111.6 - - + +
66E ALA* 1.3 60.9 + - - +
68E GLY 4.0 1.4 + - - +
70E ASP* 3.5 36.5 + - + +
71E PHE* 3.0 47.4 + - + -
361E HIS* 5.6 4.0 - - + +
2015E SO4 5.2 3.4 - - - +
62F TYR* 6.4 1.8 - - + -
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Residues in contact with ALA 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E TYR 3.0 16.7 + - - +
63E TYR 3.8 2.2 - - - +
65E MET* 1.3 78.7 - - - +
67E HIS* 1.3 62.2 + - - +
68E GLY 3.7 4.2 + - - +
71E PHE* 4.0 8.1 - - + +
78E MET* 3.1 36.8 - - + +
81E VAL* 3.5 6.1 - - + +
71F PHE* 3.6 24.9 - - + -
76F ILE* 4.2 11.4 - - + -
78F MET* 4.4 0.9 - - - -
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Residues in contact with HIS 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E TYR* 2.7 54.3 + + + +
64E HIS* 4.4 2.0 - - - +
66E ALA* 1.3 70.7 - - - +
68E GLY* 1.3 65.3 + - - +
81E VAL* 3.3 42.0 + - + -
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Residues in contact with GLY 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E HIS* 2.8 24.2 + - - -
65E MET 4.1 0.9 - - - +
66E ALA 3.4 7.5 - - - +
67E HIS* 1.3 81.2 + - - +
69E THR* 1.3 65.6 + - - -
70E ASP 3.5 2.8 + - - -
71E PHE 4.8 0.9 + - - -
72E ALA* 5.0 6.1 + - - +
2015E SO4 3.2 16.2 - - - -
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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