Contacts of the helix formed by residues 79 - 96 (chain E) in PDB entry 3EGC
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 ASN 79 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76E ASP* 3.1 30.8 + - - +
77E ILE 3.4 4.8 - - - +
78E GLU* 1.3 77.3 - - - +
80E VAL* 1.3 64.0 + - - +
81E PHE* 3.0 16.8 + - - +
82E PHE* 3.1 29.1 + - + -
83E ALA 3.2 8.8 + - - -
253E SER* 5.9 2.2 + - - -
254E HIS* 2.8 30.6 + - - -
255E ARG* 3.9 25.2 - - - +
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Residues in contact with VAL 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E GLU 3.9 1.6 + - - -
79E ASN* 1.3 71.4 + - - +
81E PHE* 1.3 67.2 + - - +
83E ALA* 3.9 8.6 - - + +
84E GLU* 3.1 41.9 + - - +
254E HIS* 4.3 11.8 + - + +
255E ARG* 4.7 0.6 - - - +
283E LEU* 4.2 31.9 - - + -
78F GLU 4.0 19.3 - - - +
80F VAL* 3.3 31.4 - - + +
255F ARG* 5.7 2.9 - - - +
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Residues in contact with PHE 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ASN* 3.0 17.0 + - - +
80E VAL* 1.3 84.4 - - - +
82E PHE* 1.3 92.6 + + - +
84E GLU* 3.4 3.7 + - - +
85E VAL* 3.1 45.1 + - + +
152E VAL* 6.0 0.2 - - + -
153E ASN* 3.8 31.9 - - + -
254E HIS* 4.5 5.1 + - + +
281E ASP* 4.1 9.9 - - - +
298E GLN* 3.3 38.4 - - + -
300E THR* 3.6 27.9 - - + -
303E ILE* 4.4 12.1 - - + -
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Residues in contact with PHE 82 (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 VAL* 3.7 22.1 - - + +
75E SER* 3.3 25.1 - - - -
76E ASP* 3.3 35.9 - - + +
77E ILE* 4.4 2.4 - - - +
79E ASN* 3.1 21.8 + - + -
81E PHE* 1.3 101.1 - + - +
83E ALA* 1.3 59.0 + - - +
85E VAL* 3.1 9.7 + - + +
86E ALA* 2.8 31.3 + - - +
107E GLU* 4.8 4.5 - - - -
130E ALA* 3.8 24.0 - - + -
152E VAL* 5.5 1.3 - - + -
153E ASN* 3.6 21.8 - - + -
154E ARG* 4.9 4.0 - - - -
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Residues in contact with ALA 83 (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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77E ILE* 3.8 23.6 + - + +
79E ASN 3.2 7.8 + - - +
80E VAL* 3.9 13.2 - - + +
82E PHE* 1.3 76.4 - - - +
84E GLU* 1.3 58.3 + - - +
86E ALA* 3.4 8.2 + - - +
87E SER* 3.0 26.3 + - - -
77F ILE* 3.4 32.6 - - + +
78F GLU* 4.5 6.7 - - - -
83F ALA* 4.2 6.3 - - + -
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Residues in contact with GLU 84 (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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80E VAL* 3.1 38.5 + - + +
81E PHE* 5.1 0.3 - - - -
83E ALA* 1.3 74.0 - - - +
85E VAL* 1.3 63.5 + - - +
87E SER* 3.2 9.2 + - - -
88E GLY 3.1 17.3 + - - -
298E GLN 5.5 0.2 - - - +
300E THR* 2.7 43.9 + - - +
301E ARG* 3.5 42.9 + - + +
78F GLU* 4.3 16.5 - - + +
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Residues in contact with VAL 85 (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 LEU* 5.6 5.2 - - + -
81E PHE* 3.1 37.6 + - + +
82E PHE* 3.1 13.4 + - + +
84E GLU* 1.3 75.2 - - - +
86E ALA* 1.3 57.3 + - - +
88E GLY 3.4 0.3 + - - -
89E VAL* 3.1 29.6 + - + +
152E VAL* 4.2 26.0 - - + -
300E THR* 3.5 26.5 - - - +
303E ILE* 4.4 7.9 - - + -
304E GLY* 3.2 19.7 - - - +
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Residues in contact with ALA 86 (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 LEU* 3.9 28.5 - - + +
74E VAL* 5.2 1.3 - - + -
77E ILE* 4.0 17.5 - - + -
82E PHE 2.8 15.9 + - - +
83E ALA 3.4 7.2 - - - +
85E VAL* 1.3 74.4 - - - +
87E SER* 1.3 57.5 + - - +
89E VAL* 3.6 3.6 - - - +
90E GLU* 2.8 37.6 + - - +
77F ILE* 5.1 4.7 - - + -
102F LEU* 5.0 10.3 - - + +
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Residues in contact with SER 87 (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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83E ALA 3.0 14.5 + - - -
84E GLU 3.3 9.9 - - - -
86E ALA* 1.3 75.5 - - - +
88E GLY* 1.3 63.9 + - - +
90E GLU* 4.1 6.0 - - - +
91E SER* 3.0 26.9 + - - -
301E ARG* 4.6 2.6 - - - +
77F ILE* 3.9 11.0 - - - -
78F GLU* 2.6 37.8 + - - +
104F ASN* 3.7 13.7 + - - +
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Residues in contact with GLY 88 (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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84E GLU 3.1 9.0 + - - -
85E VAL 3.4 1.7 + - - -
86E ALA 3.3 0.2 - - - -
87E SER* 1.3 80.0 - - - +
89E VAL* 1.3 59.8 + - - +
91E SER* 3.3 5.8 + - - -
92E GLU* 3.0 24.9 + - - +
301E ARG* 3.4 29.8 - - - +
305E GLN* 3.7 13.1 - - - +
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Residues in contact with VAL 89 (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 LEU* 4.4 20.9 - - + -
85E VAL* 3.1 21.0 + - + +
86E ALA* 3.6 9.6 - - - +
88E GLY* 1.3 76.0 - - - +
90E GLU* 1.3 60.0 + - - +
92E GLU 3.4 0.2 + - - -
93E ALA* 2.9 27.5 + - - +
100E VAL* 4.5 5.4 - - + -
128E ILE* 3.7 24.7 - - + -
304E GLY* 3.2 26.8 - - - +
308E MET* 2.9 35.9 - - + +
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Residues in contact with GLU 90 (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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86E ALA 2.8 21.6 + - - +
87E SER* 4.1 5.0 - - - +
89E VAL* 1.3 73.7 - - - +
91E SER* 1.3 68.4 + - - +
93E ALA* 4.1 0.3 - - - +
94E ARG* 3.1 52.0 + - + +
100E VAL* 4.4 17.0 - - + -
77F ILE* 6.4 0.2 - - + -
102F LEU* 3.9 30.2 - - + +
103F ALA* 3.6 7.0 - - - +
104F ASN* 3.0 45.0 + - + +
111F ARG* 4.9 2.3 + - - -
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Residues in contact with SER 91 (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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87E SER* 3.0 20.7 + - - -
88E GLY* 3.6 6.5 - - - -
89E VAL 3.2 0.2 - - - -
90E GLU* 1.3 85.6 + - - +
92E GLU* 1.3 60.2 + - - +
94E ARG* 3.8 4.6 - - - +
95E HIS* 3.3 21.8 + - - +
305E GLN* 5.9 3.1 + - - -
111F ARG* 6.2 2.2 - - - +
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Residues in contact with GLU 92 (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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88E GLY 3.0 16.1 + - - +
91E SER* 1.3 74.9 - - - +
93E ALA* 1.3 67.2 + - - +
95E HIS* 3.1 10.7 + - - +
96E LYS* 2.7 60.5 + - - +
305E GLN* 3.4 36.9 + - + +
308E MET* 3.8 21.8 - - + -
309E ARG* 3.3 26.1 + - + +
312E ILE* 4.4 1.1 - - + -
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Residues in contact with ALA 93 (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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89E VAL 2.9 18.6 + - - +
90E GLU 4.1 1.6 - - - +
92E GLU* 1.3 76.3 - - - +
94E ARG* 1.3 59.0 + - - +
96E LYS* 3.2 6.0 + - - +
97E GLY 3.0 5.0 + - - -
98E TYR* 2.6 54.1 + - + +
100E VAL* 3.6 22.4 - - + -
308E MET* 3.6 17.6 - - + +
312E ILE* 4.9 1.3 - - - -
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Residues in contact with ARG 94 (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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90E GLU* 3.1 36.4 + - - +
91E SER* 3.8 4.7 - - - +
93E ALA* 1.3 78.3 - - - +
95E HIS* 1.3 61.6 + - - +
97E GLY* 3.1 13.7 + - - +
98E TYR 3.7 6.7 + - - -
103F ALA* 5.3 1.7 - - - +
104F ASN 2.9 31.7 + - - +
105F THR* 4.1 2.0 - - - +
111F ARG* 2.8 60.5 + - - +
114F GLU* 4.1 10.9 + - - +
115F ALA* 3.7 20.4 - - - +
118F GLN* 4.9 20.3 + - - +
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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
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91E SER 3.3 11.1 + - - +
92E GLU* 3.1 15.7 + - - +
94E ARG* 1.3 78.4 - - - +
96E LYS* 1.3 68.2 + - + +
97E GLY 3.4 1.2 + - - -
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Residues in contact with LYS 96 (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 ASN* 4.5 2.8 + - - -
92E GLU* 2.7 45.6 + - - +
93E ALA 3.9 2.2 - - - +
95E HIS* 1.3 88.6 - - + +
97E GLY* 1.3 63.5 + - - +
98E TYR* 3.4 14.7 + - + -
309E ARG* 3.9 13.7 - - - +
312E ILE* 3.6 46.1 - - + +
313E HIS* 5.8 5.6 + - - -
316E GLU* 5.5 1.5 - - - +
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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