Contacts of the helix formed by residues 49 - 68 (chain F) in PDB entry 1ZMC
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44F THR 2.6 17.4 + - - -
45F CYS* 3.3 4.8 + - - -
48F VAL* 1.3 76.0 - - - +
50F CYS* 1.3 59.5 + - - -
51F ILE 3.2 0.5 + - - -
52F PRO* 3.4 4.4 - - - +
53F SER* 2.5 34.6 + - - -
480F FAD 3.3 25.4 - - - +
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Residues in contact with CYS 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E HIS* 4.2 1.3 - - - -
453E PRO* 4.1 12.6 - - + -
45F CYS* 2.1 48.7 + - - -
49F GLY* 1.3 69.7 - - - -
51F ILE* 1.3 60.4 + - + +
53F SER* 2.9 5.6 + - - -
54F LYS* 2.8 36.3 + - - +
328F ALA* 3.9 5.2 - - - -
480F FAD 3.3 53.2 - - + +
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Residues in contact with ILE 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392E SER* 4.1 24.0 - - - +
396E THR* 3.1 50.5 - - + +
452E HIS* 4.1 13.9 - - - +
453E PRO* 4.3 9.2 - - + -
45F CYS* 3.2 5.1 + - - +
46F LEU* 3.5 33.0 - - + +
50F CYS* 1.3 77.7 - - + +
52F PRO* 1.4 70.7 - - + +
54F LYS* 4.9 0.2 - - - -
55F ALA* 3.1 4.2 + - + +
95F ALA* 4.8 2.0 - - + -
96F VAL* 3.9 20.4 - - + +
99F LEU* 3.8 18.8 - - + -
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Residues in contact with PRO 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F CYS 3.7 3.4 - - - +
46F LEU 3.3 15.0 - - - +
47F ASN 3.8 13.0 - - - +
49F GLY 3.4 23.1 - - - +
51F ILE* 1.4 93.0 - - + +
53F SER* 1.3 59.8 + - - +
55F ALA* 3.4 4.1 + - + +
56F LEU* 3.1 26.3 + - - +
92F LYS* 3.6 32.9 - - + +
96F VAL* 3.9 9.6 - - + -
172F LEU* 3.8 18.6 - - + -
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Residues in contact with SER 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F GLY 2.5 27.0 + - - -
50F CYS 2.9 10.6 + - - -
52F PRO* 1.3 78.3 - - - +
54F LYS* 1.3 74.2 + - - +
56F LEU* 3.2 4.9 + - - +
57F LEU* 2.9 33.2 + - - +
172F LEU* 3.7 18.3 - - - +
192F GLU* 4.4 6.7 - - - -
193F LEU* 5.0 7.0 - - - -
196F VAL* 4.7 1.8 - - - +
480F FAD 3.5 12.6 - - - -
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Residues in contact with LYS 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393E ARG* 5.3 5.8 - - + +
396E THR* 3.9 14.1 - - + -
397E ASN* 4.8 3.2 - - - +
453E PRO* 4.0 19.5 - - + +
50F CYS 2.8 23.3 + - - +
53F SER* 1.3 86.0 + - - +
55F ALA* 1.3 58.0 + - - +
57F LEU* 3.2 24.7 + - + +
58F ASN* 2.8 31.4 + - - +
192F GLU* 2.6 25.8 + - - -
359F TYR* 3.6 38.6 - - + -
480F FAD 2.9 30.1 + - - +
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Residues in contact with ALA 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E THR* 3.1 39.3 - - + +
51F ILE 3.1 3.8 + - - +
52F PRO* 3.5 9.9 - - + +
54F LYS* 1.3 75.8 - - - +
56F LEU* 1.3 56.0 + - - +
58F ASN* 3.3 3.9 + - - +
59F ASN* 2.9 35.9 + - - +
91F GLN* 3.9 11.2 - - - +
92F LYS* 4.1 20.6 - - + +
95F ALA* 5.2 1.6 - - + -
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Residues in contact with LEU 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F PRO 3.1 8.7 + - - +
53F SER* 3.2 8.7 + - - +
55F ALA* 1.3 73.7 - - - +
57F LEU* 1.3 55.0 + - - +
59F ASN* 4.5 2.0 - - - +
60F SER* 2.6 40.9 + - - -
88F MET* 4.2 32.1 - - + +
89F MET* 4.0 23.3 - - + -
92F LYS* 4.0 12.6 - - + -
171F ALA 5.1 1.6 - - - +
172F LEU* 3.6 47.1 - - + +
193F LEU* 5.9 1.8 - - + -
196F VAL* 3.9 23.3 - - + +
197F TRP* 5.3 2.0 - - + +
200F LEU* 5.9 2.0 - - + -
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Residues in contact with LEU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F SER* 2.9 14.1 + - - +
54F LYS* 3.4 28.5 - - + +
56F LEU* 1.3 76.5 - - - +
58F ASN* 1.3 62.3 + - - +
60F SER* 3.7 3.4 - - - -
61F HIS* 3.1 9.9 + - - +
192F GLU* 3.7 29.6 - - + +
195F SER* 5.0 0.4 - - - -
196F VAL* 3.6 20.4 - - + +
199F ARG* 2.9 32.4 + - - +
359F TYR* 3.4 48.9 - - + +
360F THR* 4.3 7.4 - - + -
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Residues in contact with ASN 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ARG* 3.7 23.6 + - - +
396E THR 5.3 0.2 - - - +
397E ASN* 3.4 36.1 + - - +
54F LYS 2.8 17.0 + - - +
55F ALA* 3.6 5.6 - - - +
57F LEU* 1.3 76.6 - - - +
59F ASN* 1.3 66.0 + - - +
61F HIS* 3.2 6.2 + - - +
62F TYR* 3.1 52.8 + - - -
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Residues in contact with ASN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ARG* 2.7 51.0 + - + +
76E ILE* 3.8 4.0 - - - +
396E THR 5.5 0.2 - - - +
55F ALA 2.9 20.7 + - - +
56F LEU* 4.3 3.3 - - - +
58F ASN* 1.3 77.6 - - - +
60F SER* 1.3 56.6 + - - +
62F TYR* 3.3 3.7 + - - +
63F TYR* 2.8 27.9 + - - +
88F MET* 3.6 44.6 + - + +
91F GLN* 2.7 26.7 + - - +
92F LYS 4.8 0.4 - - - +
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Residues in contact with SER 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F LEU 2.6 25.4 + - - -
57F LEU* 3.7 0.9 - - - -
59F ASN* 1.3 73.2 - - - +
61F HIS* 1.3 65.7 + - - +
63F TYR* 3.7 1.9 - - - +
64F HIS* 3.0 21.7 + - - +
88F MET* 4.3 1.9 - - - -
196F VAL* 3.8 16.9 - - - -
199F ARG* 3.1 35.5 + - - +
200F LEU* 3.6 30.7 - - - -
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Residues in contact with HIS 61 (chain F).
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* 6.1 0.4 - - - -
57F LEU 3.1 21.3 + - - +
58F ASN* 3.6 6.0 + - - +
60F SER* 1.3 78.3 + - - +
62F TYR* 1.3 81.8 + + - +
64F HIS* 3.1 10.9 + - - +
65F MET* 2.9 67.4 + - + +
199F ARG* 3.6 15.5 - - - +
361F HIS* 3.3 59.0 + + + -
399F ASP* 5.4 0.2 - - - -
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Residues in contact with TYR 62 (chain F).
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* 5.9 0.2 + - - -
62E TYR* 3.7 39.5 + + - -
70E ASP* 5.9 0.2 - - - -
71E PHE* 3.6 41.8 - + + -
74E ARG* 5.1 9.6 - - - -
76E ILE* 3.6 9.0 - - + -
58F ASN* 3.1 48.7 + - - +
59F ASN* 3.8 4.3 - - - +
61F HIS* 1.3 99.4 + + - +
63F TYR* 1.3 64.2 + - - +
65F MET* 3.2 12.6 + - + +
66F ALA* 3.1 17.7 + - - +
71F PHE* 5.1 1.1 - + - -
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Residues in contact with TYR 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ILE* 3.4 22.4 - - + +
59F ASN 2.8 17.3 + - - +
60F SER* 3.7 6.7 - - - +
61F HIS 3.3 0.2 - - - -
62F TYR* 1.3 76.1 - - - +
64F HIS* 1.3 60.5 + - - +
66F ALA* 3.3 1.2 + - - +
67F HIS* 2.9 81.0 + + + +
81F VAL* 4.1 15.8 + - + -
82F ARG 4.2 0.7 - - - -
83F LEU* 3.9 39.4 + - + +
88F MET* 4.2 6.1 - - + -
199F ARG 3.3 27.4 - - - -
200F LEU* 3.6 26.8 + - + -
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Residues in contact with HIS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F SER 3.0 13.8 + - - +
61F HIS* 3.1 15.7 - - - +
63F TYR* 1.3 84.2 - - - +
65F MET* 1.3 76.2 + - + +
67F HIS* 4.7 2.7 - - + -
68F GLY* 2.7 31.9 + - - +
69F THR 4.8 0.2 + - - -
199F ARG* 4.4 24.1 + - + +
233F GLN* 5.3 15.7 - - + -
2022F SO4 2.7 38.2 + - - -
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Residues in contact with MET 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F HIS* 2.9 52.6 + - + +
62F TYR* 3.2 15.0 + - + +
64F HIS* 1.3 116.2 - - + +
66F ALA* 1.3 58.4 + - - +
68F GLY 4.2 0.5 - - - +
70F ASP* 3.6 35.0 + - + +
71F PHE* 3.0 49.4 + - + +
361F HIS* 5.6 2.7 - - + -
2022F SO4 5.4 2.2 - - - +
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Residues in contact with ALA 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E PHE* 3.8 20.2 - - + -
76E ILE* 4.1 14.1 - - + -
62F TYR 3.1 14.5 + - - +
63F TYR 4.0 2.0 - - - +
65F MET* 1.3 76.8 - - - +
67F HIS* 1.3 66.5 + - - +
68F GLY 3.3 6.6 - - - +
71F PHE* 4.0 3.6 - - + +
78F MET* 3.4 36.8 - - + +
81F VAL* 3.6 10.2 - - + +
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Residues in contact with HIS 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F TYR* 2.9 57.4 + + + +
64F HIS* 4.3 2.3 - - - +
66F ALA* 1.3 75.5 - - - +
68F GLY* 1.3 64.8 + - - +
81F VAL* 3.4 34.4 + - + +
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Residues in contact with GLY 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F HIS* 2.7 16.1 + - - -
65F MET 4.2 1.7 - - - +
66F ALA 3.3 9.2 - - - +
67F HIS* 1.3 86.0 + - - +
69F THR* 1.3 62.5 + - - -
70F ASP 3.6 2.4 + - - -
71F PHE 4.7 0.9 + - - -
72F ALA* 4.9 5.4 + - - +
2022F SO4 3.2 20.9 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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