Contacts of the helix formed by residues 60 - 78 (chain E) in PDB entry 4ZZ7
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 PRO 60 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58E ASN 3.4 8.9 - - - +
59E THR* 1.4 87.0 - - + +
61E PRO* 1.3 63.2 - - + +
62E LEU* 4.2 9.2 - - + +
63E LYS* 2.8 38.8 + - + +
64E ARG 3.1 8.7 + - - -
125H ASN* 3.4 19.5 - - + +
126H VAL 4.8 1.6 - - - +
127H GLY* 4.1 5.8 - - - -
128H PRO* 4.0 35.9 - - + -
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Residues in contact with PRO 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E THR 3.3 6.6 - - - +
60E PRO* 1.3 83.1 - - + +
62E LEU* 1.3 55.2 + - - +
64E ARG* 3.3 20.4 + - + +
65E ALA* 2.8 31.7 + - - +
114E ALA* 4.7 3.3 - - + +
115E PRO* 4.1 24.0 - - + +
118E LEU* 3.9 31.9 - - + -
164E VAL 5.0 0.7 - - - +
446G TYR* 5.4 3.6 - - - +
124H ARG* 3.6 18.4 - - - +
125H ASN* 3.4 18.4 - - + +
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Residues in contact with LEU 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E PRO* 2.9 8.6 + - + +
61E PRO* 1.3 77.9 - - - +
63E LYS* 1.3 58.7 + - - +
65E ALA* 3.4 6.5 + - + +
66E ARG* 3.2 44.2 + - - +
69E PHE* 6.5 0.4 - - + -
115E PRO* 4.0 12.6 - - + +
106G GLU* 3.8 22.4 - - + +
109G GLU* 3.3 27.6 - - + +
444G VAL* 3.8 26.5 - - + -
445G ALA* 6.5 0.7 - - + -
446G TYR* 3.9 20.5 + - + +
126H VAL 4.2 14.1 - - - +
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Residues in contact with LYS 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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56E TRP* 5.0 1.2 - - + -
59E THR* 3.9 21.6 - - + +
60E PRO* 2.8 24.4 + - + +
62E LEU* 1.3 75.1 - - - +
64E ARG* 1.3 65.1 + - - +
66E ARG* 3.6 24.8 + - + +
67E VAL* 3.8 9.7 + - - +
70E ARG* 5.5 1.4 + - - +
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Residues in contact with ARG 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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56E TRP* 3.1 60.6 + - + +
57E ARG 3.1 23.6 + - - -
59E THR* 2.7 42.2 + - + +
60E PRO 3.1 6.2 + - - +
61E PRO* 3.6 18.2 - - - +
63E LYS* 1.3 76.0 - - - +
65E ALA* 1.3 63.0 + - - +
67E VAL* 3.2 21.8 + - - +
68E MET* 3.9 2.6 + - - +
118E LEU* 3.6 18.8 - - - +
138E PRO* 5.0 2.6 - - - +
163E ILE* 3.9 3.0 - - - +
164E VAL* 2.9 41.1 + - + +
165E CYS 3.6 12.5 + - - -
166E GLY* 3.4 10.9 - - - -
124H ARG* 4.9 5.3 - - - +
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Residues in contact with ALA 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 PRO 2.8 17.6 + - - +
62E LEU* 3.6 8.1 - - + +
63E LYS 3.2 0.4 - - - -
64E ARG* 1.3 74.7 - - - +
66E ARG* 1.3 59.8 + - - +
68E MET* 2.9 22.7 + - - +
69E PHE* 3.0 19.1 + - + -
111E ALA 4.4 1.1 - - - +
112E CYS* 3.3 29.2 - - - +
115E PRO* 4.4 8.3 - - + -
164E VAL* 3.7 15.2 - - + +
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Residues in contact with ARG 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 LEU* 3.2 33.7 + - - +
63E LYS* 3.7 17.6 - - + +
64E ARG 3.3 0.6 - - - -
65E ALA* 1.3 77.5 - - + +
67E VAL* 1.3 60.4 + - - +
69E PHE* 3.5 14.5 + - + +
70E ARG* 3.2 51.2 + - - +
72G LYS* 5.3 6.1 - - - +
76G GLU* 5.6 2.7 - - - -
102G GLN* 4.1 22.2 - - - +
106G GLU* 3.1 26.9 + - - +
109G GLU* 2.4 51.3 + - - +
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Residues in contact with VAL 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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56E TRP* 4.2 17.9 - - + -
63E LYS 3.9 9.2 - - - +
64E ARG 3.2 14.8 + - - +
65E ALA 3.1 0.6 - - - -
66E ARG* 1.3 76.4 - - - +
68E MET* 1.3 63.9 + - + +
70E ARG* 3.3 15.7 + - - +
71E PHE* 2.8 25.5 + - - +
163E ILE* 6.2 0.4 - - + -
188E LEU* 4.5 10.3 - - + -
191E ALA* 3.5 19.6 - - + +
192E GLY 4.2 16.4 - - - +
193E LEU* 3.9 28.9 - - + +
194E PRO* 5.3 0.2 - - + -
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Residues in contact with MET 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 ARG 4.3 2.0 - - - +
65E ALA 2.9 7.2 + - - +
67E VAL* 1.3 82.6 - - - +
69E PHE* 1.3 59.2 + - - +
71E PHE* 3.3 34.5 - - + -
72E LYS* 2.9 24.3 + - - +
108E VAL* 3.2 23.4 - - + +
111E ALA* 4.3 7.4 - - + -
112E CYS* 3.6 16.9 - - - +
159E PHE* 5.6 0.4 - - + -
160E PRO* 3.5 42.4 - - + +
163E ILE* 5.0 13.2 - - - -
164E VAL* 4.0 26.2 - - + -
188E LEU* 4.7 9.4 - - + -
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Residues in contact with PHE 69 (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 LEU* 6.5 0.4 - - + -
65E ALA* 3.0 26.4 + - + -
66E ARG* 3.5 17.5 - - + +
68E MET* 1.3 74.5 - - - +
70E ARG* 1.3 65.3 + - + +
72E LYS* 3.3 17.7 - - - +
73E GLU* 3.6 12.4 + - - +
112E CYS* 3.5 32.7 - - + -
69G PHE* 3.2 40.2 - + - -
72G LYS* 3.7 35.7 - - + +
109G GLU* 3.8 44.6 - - + -
112G CYS* 4.1 4.7 - - + -
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Residues in contact with ARG 70 (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 LYS* 5.5 1.0 + - - +
66E ARG* 3.2 45.4 + - - +
67E VAL* 3.6 15.1 - - - +
69E PHE* 1.3 78.0 - - + +
71E PHE* 1.3 62.5 + - - +
73E GLU* 3.2 23.9 + - - +
74E LEU* 3.2 18.2 + - + +
190E GLU 5.3 1.6 - - - -
191E ALA* 2.9 40.8 + - + +
192E GLY* 4.5 4.6 - - - -
72G LYS* 6.2 1.3 - - - +
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Residues in contact with PHE 71 (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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67E VAL 2.8 17.7 + - - +
68E MET* 3.3 29.6 - - + +
69E PHE 3.3 0.2 - - - -
70E ARG* 1.3 73.1 - - - +
72E LYS* 1.3 65.3 + - - +
74E LEU* 3.5 3.5 + - + -
75E LEU* 3.2 54.3 + - + +
108E VAL* 3.9 10.8 - - + -
156E LEU* 3.6 29.6 - - + -
159E PHE* 4.0 14.1 - + - -
184E ILE* 3.6 26.2 - - + -
187E LEU* 4.2 11.2 - - + -
188E LEU* 3.3 35.2 - - + -
191E ALA* 3.8 5.6 - - + +
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Residues in contact with LYS 72 (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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68E MET 2.9 13.6 + - - +
69E PHE* 3.3 14.6 - - - +
71E PHE* 1.3 78.0 - - - +
73E GLU* 1.3 64.0 + - + +
75E LEU* 3.6 7.6 + - - +
76E GLU* 3.2 50.8 + - - +
105E ILE* 4.0 13.2 - - + +
108E VAL* 4.1 11.8 - - + +
109E GLU* 3.0 41.4 + - + -
112E CYS* 5.1 0.7 - - - -
66G ARG* 4.6 12.1 + - - +
69G PHE* 3.7 44.2 - - + +
70G ARG* 6.0 1.6 - - - +
73G GLU* 6.1 0.4 - - - +
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Residues in contact with GLU 73 (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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69E PHE 3.6 13.3 + - - +
70E ARG* 3.2 16.6 + - - +
72E LYS* 1.3 83.9 - - + +
74E LEU* 1.3 55.2 + - + +
76E GLU* 3.0 17.2 + - - +
77E GLN* 2.7 56.5 + - - +
73G GLU* 2.6 51.4 - - - +
77G GLN* 5.5 1.0 + - - -
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Residues in contact with LEU 74 (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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70E ARG* 3.2 10.3 + - + +
71E PHE* 3.8 7.9 - - - +
73E GLU* 1.3 76.4 - - + +
75E LEU* 1.3 59.1 + - - +
77E GLN* 3.8 23.3 - - - +
78E HIS* 2.9 47.7 + - + +
187E LEU* 3.3 39.3 - - + +
190E GLU* 4.1 27.4 - - + +
191E ALA* 3.7 26.0 - - + +
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Residues in contact with LEU 75 (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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71E PHE* 3.2 56.6 + - + +
72E LYS* 3.8 5.6 - - - +
74E LEU* 1.3 76.8 - - - +
76E GLU* 1.3 62.4 + - - +
78E HIS 3.5 1.2 + - - -
79E ALA* 3.1 25.3 + - - +
82E ILE* 4.0 11.7 - - + +
101E LEU* 4.0 12.9 - - + +
105E ILE* 3.7 30.3 - - + -
108E VAL* 4.2 14.1 - - + -
156E LEU* 4.6 9.6 - - + -
184E ILE* 4.0 25.4 - - + -
187E LEU* 4.3 4.3 - - + -
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Residues in contact with GLU 76 (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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72E LYS* 3.2 49.7 + - - +
73E GLU* 3.0 18.1 + - - +
75E LEU* 1.3 74.7 - - - +
77E GLN* 1.3 66.7 + - - +
79E ALA* 3.4 18.1 - - - +
102E GLN* 5.3 5.2 + - - +
105E ILE* 3.8 23.8 - - + +
109E GLU* 4.6 0.3 - - - +
66G ARG* 5.9 0.7 - - - -
73G GLU* 5.4 0.9 - - - +
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Residues in contact with GLN 77 (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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73E GLU* 2.7 44.8 + - + +
74E LEU* 3.6 24.6 - - - +
76E GLU* 1.3 75.7 - - + +
78E HIS* 1.3 67.1 + - + +
79E ALA* 3.2 3.6 + - - +
80E ASP* 4.8 1.6 + - - +
81E GLU* 4.4 4.2 - - - +
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Residues in contact with HIS 78 (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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74E LEU* 2.9 42.0 + - + +
75E LEU 3.5 2.7 - - - -
77E GLN* 1.3 81.1 + - + +
79E ALA* 1.3 61.9 + - - +
80E ASP 3.3 2.8 + - - -
81E GLU* 3.5 21.5 + - - +
82E ILE* 3.1 24.4 + - + +
183E TYR* 2.9 35.2 + - + +
187E LEU* 3.4 29.4 - - + +
190E GLU* 4.6 6.6 + - - -
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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