Contacts of the helix formed by residues 79 - 96 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ASP* 3.1 23.9 + - - +
77F ILE 3.4 4.1 - - - +
78F GLU* 1.3 78.5 - - - +
80F VAL* 1.3 62.4 + - - +
81F PHE* 2.8 33.6 + - - +
82F PHE* 3.1 31.0 + - + -
83F ALA 3.1 9.2 + - - -
253F SER* 5.6 2.2 + - - -
254F HIS* 2.8 27.1 + - - -
255F ARG* 3.8 31.8 - - - +
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Residues in contact with VAL 80 (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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78E GLU 4.0 19.7 - - - +
80E VAL* 3.3 31.4 - - + +
255E ARG* 5.7 2.9 - - - +
78F GLU 3.5 4.2 + - - -
79F ASN* 1.3 73.7 + - - +
81F PHE* 1.3 67.3 + - - +
83F ALA* 3.9 7.6 - - + -
84F GLU* 3.3 38.7 + - - +
254F HIS* 4.4 14.3 + - + +
255F ARG* 4.7 0.4 - - - +
283F LEU* 4.3 29.8 - - + -
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Residues in contact with PHE 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ASN* 2.8 24.9 + - - +
80F VAL* 1.3 78.4 - - - +
82F PHE* 1.3 92.6 + + + +
84F GLU* 3.5 3.9 + - - +
85F VAL* 3.2 40.7 + - + +
152F VAL* 6.1 0.4 - - + -
153F ASN* 3.8 30.5 - - + -
254F HIS* 4.8 5.2 - - + +
281F ASP* 4.1 9.4 - - - +
298F GLN* 3.5 37.7 - - + -
300F THR* 3.7 26.9 - - + -
303F ILE* 4.5 11.9 - - + -
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Residues in contact with PHE 82 (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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74F VAL* 3.8 22.4 - - + +
75F SER* 3.2 26.2 - - - -
76F ASP* 3.2 35.2 - - + +
77F ILE* 4.3 4.0 - - - +
79F ASN* 3.1 22.2 + - + -
81F PHE* 1.3 94.1 - + - +
83F ALA* 1.3 66.3 + - - +
84F GLU 3.2 1.3 - - - -
85F VAL* 3.2 7.7 + - + +
86F ALA* 3.0 25.1 + - - +
107F GLU* 4.8 3.4 - - - -
130F ALA* 3.7 24.9 - - + -
152F VAL* 5.5 1.8 - - + -
153F ASN* 3.4 26.9 - - + -
154F ARG* 4.8 4.9 - - - -
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Residues in contact with ALA 83 (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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77E ILE* 3.5 38.5 - - + +
78E GLU* 4.6 5.6 - - - -
79E ASN 6.2 0.2 - - - -
83E ALA* 4.2 7.0 - - + -
77F ILE* 3.6 28.3 + - + +
79F ASN 3.1 10.6 + - - +
80F VAL* 4.0 11.2 - - + +
81F PHE 3.4 0.2 - - - -
82F PHE* 1.3 77.3 - - - +
84F GLU* 1.4 57.9 + - - +
86F ALA* 3.6 1.7 - - - +
87F SER* 3.1 19.9 + - - -
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Residues in contact with GLU 84 (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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78E GLU* 4.1 27.5 - - + +
80F VAL* 3.3 30.6 + - - +
81F PHE* 3.8 0.4 - - - +
82F PHE 3.2 0.4 - - - -
83F ALA* 1.4 76.0 - - - +
85F VAL* 1.3 65.5 + - - +
87F SER* 3.3 16.0 + - - -
88F GLY 3.3 9.0 + - - -
300F THR* 2.7 44.5 + - - +
301F ARG* 3.4 35.6 + - + +
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Residues in contact with VAL 85 (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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72F LEU* 5.6 4.0 - - + -
81F PHE* 3.2 41.6 + - + +
82F PHE* 3.2 11.4 + - + +
84F GLU* 1.3 72.8 - - - +
86F ALA* 1.3 61.0 + - - +
88F GLY 3.0 3.3 + - - -
89F VAL* 2.9 30.2 + - + +
128F ILE* 5.7 0.2 - - + -
152F VAL* 4.4 23.1 - - + -
300F THR* 3.4 22.7 - - - +
303F ILE* 4.3 10.8 - - + -
304F GLY* 3.2 21.2 - - - +
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Residues in contact with ALA 86 (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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77E ILE* 5.1 4.0 - - + -
102E LEU* 4.7 12.7 - - + +
72F LEU* 3.7 29.9 - - + +
74F VAL* 5.1 0.9 - - + -
77F ILE* 4.2 16.6 - - + -
82F PHE 3.0 16.2 + - - +
83F ALA 3.6 6.1 - - - +
85F VAL* 1.3 76.5 - - - +
87F SER* 1.3 53.0 + - - +
89F VAL* 3.5 3.0 - - - +
90F GLU* 2.7 39.1 + - - +
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Residues in contact with SER 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E ILE* 3.9 9.8 - - - +
78E GLU* 2.5 35.3 + - - -
104E ASN* 3.3 20.1 + - - +
83F ALA 3.1 15.6 + - - -
84F GLU 3.3 10.8 - - - -
85F VAL 3.2 0.4 - - - -
86F ALA* 1.3 75.3 - - - +
88F GLY* 1.3 57.5 - - - +
90F GLU* 3.9 5.5 - - - +
91F SER* 3.0 30.3 + - - -
301F ARG* 4.5 2.8 - - - +
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Residues in contact with GLY 88 (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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84F GLU 3.3 4.2 + - - -
85F VAL 3.0 4.8 + - - -
87F SER* 1.3 76.8 - - - +
89F VAL* 1.3 65.7 + - - +
91F SER* 3.9 4.5 - - - -
92F GLU* 3.0 26.3 + - - +
301F ARG* 3.5 27.3 - - - +
305F GLN* 3.6 14.1 - - - +
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Residues in contact with VAL 89 (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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72F LEU* 4.4 18.4 - - + -
85F VAL* 2.9 26.1 + - + +
86F ALA* 3.5 10.8 - - - +
88F GLY* 1.3 78.0 - - - +
90F GLU* 1.3 65.1 + - - +
92F GLU* 3.7 1.4 - - - +
93F ALA* 2.9 21.8 + - - +
100F VAL* 4.5 7.2 - - + -
128F ILE* 3.8 24.2 - - + -
304F GLY* 3.3 26.6 - - - +
307F ALA* 5.0 0.2 - - + -
308F MET* 2.7 39.0 - - + +
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Residues in contact with GLU 90 (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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102E LEU* 3.6 30.7 - - + +
103E ALA* 3.0 12.3 - - - +
104E ASN* 2.8 49.4 + - + +
111E ARG* 4.6 2.6 + - - -
86F ALA 2.7 20.8 + - - +
87F SER* 3.9 5.1 - - - +
89F VAL* 1.3 73.9 - - - +
91F SER* 1.3 68.6 + - - +
93F ALA* 3.9 0.3 - - - +
94F ARG* 3.0 45.6 + - + +
100F VAL* 4.3 18.1 - - + +
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Residues in contact with SER 91 (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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104E ASN* 6.4 0.2 - - - -
111E ARG* 5.3 8.8 + - - +
87F SER* 3.0 21.3 + - - -
88F GLY* 3.9 5.2 - - - -
90F GLU* 1.3 85.7 + - - +
92F GLU* 1.3 63.6 + - - +
94F ARG* 3.7 5.2 - - - +
95F HIS* 3.2 22.5 + - - +
305F GLN* 6.2 2.0 - - - -
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Residues in contact with GLU 92 (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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88F GLY 3.0 17.7 + - - +
89F VAL 3.8 2.0 - - - +
91F SER* 1.3 75.6 - - - +
93F ALA* 1.3 65.7 + - - +
95F HIS* 3.3 15.7 + - - +
96F LYS* 2.8 63.1 + - - +
305F GLN* 3.3 43.7 + - + +
308F MET* 3.9 17.3 - - + -
309F ARG* 3.4 24.5 + - + +
312F ILE* 4.5 0.9 - - + -
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Residues in contact with ALA 93 (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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89F VAL 2.9 16.6 + - - +
90F GLU 3.9 0.9 - - - +
92F GLU* 1.3 74.6 - - - +
94F ARG* 1.3 57.3 + - - +
96F LYS* 2.9 6.8 + - - +
97F GLY 2.8 10.4 + - - -
98F TYR* 2.6 50.3 + - + +
100F VAL* 3.6 23.8 - - + -
308F MET* 3.6 18.9 - - + +
312F ILE* 4.8 0.7 - - - -
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Residues in contact with ARG 94 (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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103E ALA* 5.0 1.3 - - - +
104E ASN 2.9 30.3 + - - +
105E THR* 4.1 2.2 - - - +
111E ARG* 2.4 63.1 + - - +
114E GLU* 3.9 11.1 + - - +
115E ALA* 3.5 21.1 - - - +
118E GLN* 4.5 23.7 + - - +
90F GLU* 3.0 35.1 + - - +
91F SER* 3.7 5.4 - - - +
93F ALA* 1.3 77.5 - - - +
95F HIS* 1.4 57.1 + - - +
97F GLY* 3.0 17.8 + - - +
98F TYR 3.6 8.2 + - - +
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Residues in contact with HIS 95 (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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91F SER 3.2 15.1 + - - +
92F GLU* 3.7 22.2 + - - +
93F ALA 3.2 0.4 - - - -
94F ARG* 1.4 78.0 - - - +
96F LYS* 1.3 65.9 + - + +
97F GLY 3.4 0.6 + - - -
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Residues in contact with LYS 96 (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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68F ASN* 4.4 2.4 + - - -
92F GLU* 2.8 40.3 + - - +
93F ALA 2.9 7.1 + - - +
95F HIS* 1.3 88.7 - - + +
97F GLY* 1.3 62.4 + - - +
98F TYR* 3.5 23.5 - - + -
309F ARG* 3.8 15.8 + - - +
312F ILE* 3.7 34.4 - - + +
313F HIS* 5.7 6.6 + - - -
316F GLU* 5.3 2.5 - - - +
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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