Contacts of the helix formed by residues 93 - 112 (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 ILE 93 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E GLY 4.5 0.2 - - - +
92E LYS* 1.3 76.1 - - - +
94E ALA* 1.3 76.5 + - + +
95E HIS* 3.3 29.8 - - + +
96E ASP* 2.9 19.1 + - + +
97E ALA* 3.1 9.2 + - - -
311E GLY 4.4 3.6 - - - +
313E SER* 3.9 19.7 - - - +
315E ASP 4.8 0.7 - - - +
316E SER* 3.7 13.0 - - - -
317E GLY 3.6 20.2 - - - +
318E ASN* 3.2 36.6 - - + +
319E ASP 4.8 0.4 - - - +
320E PHE* 3.8 9.9 - - - -
321E GLY* 3.8 26.2 - - - +
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Residues in contact with ALA 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E CYS* 4.3 9.0 - - + -
92E LYS 3.9 0.4 + - - -
93E ILE* 1.3 75.1 - - + +
95E HIS* 1.3 56.4 + - - +
97E ALA* 3.3 9.3 + - - +
98E MET* 2.8 36.0 + - + +
313E SER* 4.9 6.9 + - - +
316E SER* 4.1 20.2 - - - +
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Residues in contact with HIS 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ILE* 3.0 25.1 + - + +
94E ALA* 1.3 79.7 - - - +
96E ASP* 1.3 73.4 + - - +
98E MET* 4.0 6.8 - - - +
99E GLY* 3.1 21.8 + - - -
317E GLY* 5.3 1.8 + - - -
318E ASN 3.4 24.5 - - - -
319E ASP* 3.6 20.5 + - - -
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Residues in contact with ASP 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E LYS* 4.0 18.0 + - + +
93E ILE* 2.9 10.7 + - - +
95E HIS* 1.3 91.3 + - + +
97E ALA* 1.3 66.5 + - - +
99E GLY* 3.3 1.9 + - - -
100E GLU* 3.0 23.6 + - - +
274E GLY* 4.4 2.1 - - - -
275E SER* 3.0 44.3 + - - +
279E ARG* 3.8 11.3 + - - -
319E ASP 3.9 13.5 - - - +
320E PHE* 4.8 2.9 - - - +
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Residues in contact with ALA 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E CYS* 3.7 36.1 - - + +
86E ILE* 4.1 18.8 - - + +
92E LYS* 3.7 14.3 - - + +
93E ILE 3.1 8.4 + - - +
94E ALA* 3.4 10.3 - - - +
96E ASP* 1.3 79.5 - - - +
98E MET* 1.3 56.5 + - - +
100E GLU* 3.1 5.7 + - - +
101E LEU* 2.9 28.6 + - - +
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Residues in contact with MET 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ALA* 4.0 24.7 - - + +
80E ASP* 5.0 5.8 - - - +
83E CYS* 3.6 22.2 - - + -
94E ALA* 2.8 24.7 + - + +
95E HIS* 4.0 7.0 - - - +
96E ASP 3.3 0.2 - - - -
97E ALA* 1.3 69.5 - - - +
99E GLY* 1.3 60.5 + - - +
101E LEU* 3.2 10.4 + - + +
102E GLN* 2.8 51.2 + - + +
105E ILE* 6.2 0.7 - - + -
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Residues in contact with GLY 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E HIS 3.1 15.2 + - - -
96E ASP* 3.3 4.2 + - - -
97E ALA 3.2 0.2 - - - -
98E MET* 1.3 77.3 - - - +
100E GLU* 1.3 62.0 + - - +
102E GLN* 3.1 5.7 + - - +
103E ARG* 3.1 34.5 + - - +
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Residues in contact with GLU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ILE* 4.2 7.1 - - + +
92E LYS* 2.7 37.8 + - - +
96E ASP 3.0 12.3 + - - +
97E ALA 3.1 8.3 + - - +
99E GLY* 1.3 75.5 - - - +
101E LEU* 1.3 62.5 + - - +
103E ARG* 3.4 4.1 + - - +
104E GLY* 3.0 18.0 + - - -
150E PHE* 3.3 21.2 - - + -
151E PRO* 3.2 12.9 - - - +
152E VAL* 2.7 38.1 + - + +
153E MET* 3.0 32.2 + - + +
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E LEU* 4.0 13.9 - - + +
79E ALA* 3.6 44.0 - - + +
82E ILE* 4.2 24.9 - - + -
83E CYS* 4.4 5.6 - - - -
86E ILE* 5.5 1.3 - - + +
97E ALA 2.9 13.6 + - - +
98E MET* 3.5 14.4 - - + +
100E GLU* 1.3 75.7 - - - +
102E GLN* 1.3 53.2 + - - +
104E GLY* 3.1 3.1 + - - -
105E ILE* 2.7 57.2 + - + +
152E VAL* 3.8 27.8 - - + -
156E LEU* 4.9 1.8 - - + -
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Residues in contact with GLN 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E GLU* 5.3 4.9 + - - +
98E MET* 2.8 35.4 + - + +
99E GLY* 3.5 7.4 - - - +
101E LEU* 1.3 77.1 - - - +
103E ARG* 1.3 59.7 + - + +
105E ILE* 3.0 24.5 + - - +
106E GLU* 3.0 40.1 + - - +
109E GLU* 5.2 0.2 + - - -
66G ARG* 4.3 25.0 - - - +
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Residues in contact with ARG 103 (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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99E GLY* 3.1 21.1 + - - +
100E GLU* 5.2 1.2 - - - +
102E GLN* 1.3 77.6 - - + +
104E GLY* 1.3 57.6 + - - +
106E GLU* 3.4 21.5 + - - +
107E ASN* 2.9 27.2 + - - +
150E PHE* 4.5 12.7 - - - -
153E MET* 3.1 48.0 - - - +
279E ARG* 6.0 1.8 - - - +
442E VAL* 4.0 39.1 - - - +
443E PRO 5.6 2.4 + - - -
444E VAL* 6.6 0.2 - - - +
445E ALA* 5.2 0.2 - - - +
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Residues in contact with GLY 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E GLU 3.0 14.5 + - - -
101E LEU 3.4 4.5 - - - -
103E ARG* 1.3 73.6 - - - +
105E ILE* 1.3 62.8 + - - +
107E ASN* 3.5 14.2 + - - +
108E VAL* 3.5 23.0 + - - +
153E MET* 3.9 7.1 - - - +
156E LEU* 3.6 28.8 - - - +
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Residues in contact with ILE 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LYS* 4.0 14.1 - - + +
75E LEU* 3.7 28.3 - - + -
76E GLU* 3.8 39.5 - - + +
98E MET* 6.2 0.9 - - + -
101E LEU* 2.7 39.7 + - + +
102E GLN* 3.0 24.7 + - - +
104E GLY* 1.3 71.2 - - - +
106E GLU* 1.3 54.5 + - - +
108E VAL* 2.9 10.5 + - - +
109E GLU* 2.7 48.8 + - - +
66G ARG* 5.4 0.2 - - - +
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Residues in contact with GLU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E GLN* 3.0 26.9 + - + +
103E ARG* 3.6 23.0 - - - +
105E ILE* 1.3 77.4 - - - +
107E ASN* 1.3 60.9 + - - +
109E GLU* 3.2 22.1 + - - +
110E TYR* 3.0 18.9 + - - +
444E VAL* 3.7 23.0 - - - +
445E ALA* 3.0 22.5 + - + +
62G LEU* 4.0 11.4 - - + +
66G ARG* 3.4 25.8 + - - +
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Residues in contact with ASN 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E ARG 2.9 18.9 + - - +
104E GLY* 3.6 12.2 - - - +
105E ILE 3.3 0.6 - - - -
106E GLU* 1.3 76.4 - - - +
108E VAL* 1.3 57.8 + - - +
110E TYR* 3.6 4.7 + - - +
111E ALA* 3.1 26.0 + - - +
156E LEU 3.2 25.3 - - - +
157E TRP* 3.3 22.6 + - - -
160E PRO* 4.5 3.3 - - - +
161E MET* 5.3 1.9 + - - +
445E ALA* 3.6 11.1 + - - +
463E TYR* 3.4 44.0 - - + +
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Residues in contact with VAL 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E MET* 3.2 46.8 - - + +
71E PHE* 3.9 22.7 - - + -
72E LYS* 4.1 13.2 - - + +
75E LEU* 4.2 6.7 - - + -
104E GLY 3.5 15.0 - - - +
105E ILE* 2.9 9.9 + - - +
107E ASN* 1.3 75.2 - - - +
109E GLU* 1.3 65.9 + - - +
111E ALA* 3.1 8.3 + - - +
112E CYS* 3.0 21.0 + - - -
156E LEU* 3.9 15.7 - - + -
160E PRO* 4.1 5.2 - - + -
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Residues in contact with GLU 109 (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* 3.0 38.5 + - + -
76E GLU* 4.6 0.3 - - - +
102E GLN* 5.2 0.2 + - - -
105E ILE* 2.7 22.9 + - - +
106E GLU* 3.2 18.6 + - - +
108E VAL* 1.3 72.3 - - - +
110E TYR* 1.3 62.9 + - - +
112E CYS* 3.1 22.6 - - - +
113E GLY 3.9 1.7 + - - -
62G LEU* 3.3 21.5 - - + +
66G ARG* 2.5 35.1 + - - -
69G PHE* 3.9 27.9 - - + -
112G CYS 5.5 1.4 - - - +
113G GLY* 5.9 2.4 - - - -
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Residues in contact with TYR 110 (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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106E GLU 3.0 14.9 + - - +
107E ASN* 3.8 5.4 - - - +
109E GLU* 1.3 76.0 - - - +
111E ALA* 1.3 57.6 + - - +
113E GLY* 3.0 20.4 + - - -
117E LEU* 3.4 40.2 - - + +
161E MET* 3.5 21.1 - - + -
445E ALA* 3.3 21.1 - - + +
446E TYR* 3.5 28.9 - + + +
464E GLY* 3.5 26.2 - - - -
465E PRO* 3.5 22.2 - - + +
468E VAL* 4.9 0.2 - - - +
116G GLU* 3.0 36.4 + - + -
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Residues in contact with ALA 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E MET* 4.3 9.2 - - + -
107E ASN 3.1 14.4 + - - +
108E VAL 3.1 9.9 + - - +
110E TYR* 1.3 73.9 - - - +
112E CYS* 1.3 63.5 + - - +
113E GLY 3.2 0.9 + - - -
114E ALA* 3.2 20.4 + - - +
117E LEU* 5.1 0.2 - - - -
160E PRO* 4.0 31.2 - - + +
161E MET* 4.1 15.3 - - + +
164E VAL* 3.5 17.7 - - + +
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Residues in contact with CYS 112 (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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65E ALA* 3.3 23.9 - - - +
68E MET* 3.6 8.5 - - - -
69E PHE* 3.5 66.8 - - + -
72E LYS* 5.1 1.6 - - - -
108E VAL* 3.0 24.4 + - - -
109E GLU* 3.1 14.1 - - - +
111E ALA* 1.3 77.7 - - - +
113E GLY* 1.3 55.9 + - - +
114E ALA 3.2 3.9 + - - -
115E PRO* 4.1 2.9 - - - +
69G PHE* 4.0 11.7 - - + -
109G GLU 5.6 0.8 - - - +
112G CYS* 5.9 0.4 - - + -
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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