Contacts of the helix formed by residues 66 - 81 (chain E) in PDB entry 5IC4
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 66 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LYS* 4.8 4.4 - - - +
64E ARG 3.4 0.2 + - - -
65E SER* 1.3 73.1 - - - +
67E THR* 1.3 64.3 + - - +
68E ASP* 3.2 4.4 - - - +
69E VAL* 3.3 23.5 + - - +
70E ASP 3.4 1.9 + - - -
207F ARG* 4.6 1.3 - - - -
208F ASN 4.0 4.9 - - - -
209F SER 3.3 19.3 + - - -
212F GLY* 3.3 24.0 - - - -
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Residues in contact with THR 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ASN* 2.5 33.5 + - - +
53E LYS* 3.5 28.0 - - + -
64E ARG* 2.8 51.8 + - - +
65E SER 3.4 0.6 + - - -
66E GLY* 1.3 77.2 - - - +
68E ASP* 1.3 63.2 + - - +
69E VAL 3.3 0.2 - - - -
70E ASP* 3.2 12.1 + - - +
71E ALA* 2.9 23.2 + - - +
119E LEU* 3.8 6.6 - - - +
207F ARG* 4.3 2.4 - - - +
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Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ASN* 2.9 24.4 + - - +
53E LYS* 3.0 37.5 + - - +
66E GLY* 3.2 1.9 - - - +
67E THR* 1.3 77.8 - - - +
69E VAL* 1.3 65.1 + - + +
71E ALA* 3.4 2.9 + - - +
72E ALA* 3.0 26.5 + - - +
89E ASN* 4.8 2.1 - - - +
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Residues in contact with VAL 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E GLY* 3.4 17.7 - - - +
68E ASP* 1.3 80.0 - - + +
70E ASP* 1.3 56.0 + - - +
72E ALA* 3.9 4.3 - - - +
73E ASN* 3.0 32.2 + - + +
210F LYS 3.5 20.2 - - - +
211F ASP* 3.4 23.8 - - - +
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Residues in contact with ASP 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ARG* 4.9 1.9 + - - -
66E GLY 3.4 4.2 + - - +
67E THR* 3.2 16.1 + - - +
68E ASP 3.2 0.4 - - - -
69E VAL* 1.3 78.0 - - - +
71E ALA* 1.3 53.9 + - - +
73E ASN* 3.0 5.3 + - - +
74E LEU* 2.8 40.6 + - - +
119E LEU* 4.3 14.4 - - + +
161E GLN* 4.9 0.9 - - - +
207F ARG* 5.0 0.7 - - - +
211F ASP 4.2 2.8 - - - +
212F GLY* 3.3 9.0 - - - -
213F SER* 2.7 51.8 + - - +
216F ILE* 3.7 24.3 - - + +
217F GLN* 4.4 2.8 + - - +
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Residues in contact with ALA 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ILE* 4.4 1.3 - - + -
51E ASN* 3.9 27.6 - - + +
67E THR 2.9 15.8 + - - +
68E ASP* 3.4 5.1 + - - +
70E ASP* 1.3 76.4 - - - +
72E ALA* 1.3 56.8 + - - +
74E LEU* 3.8 5.1 - - - +
75E ARG* 3.0 28.4 + - - +
87E ASN* 3.7 22.1 + - - +
89E ASN* 5.5 1.1 - - - +
119E LEU* 4.1 10.3 - - + +
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Residues in contact with ALA 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ASP 3.0 16.9 + - - +
69E VAL* 3.9 4.9 - - - +
71E ALA* 1.3 75.5 - - - +
73E ASN* 1.3 65.5 + - - +
75E ARG* 3.4 8.3 + - - +
76E GLU* 3.1 24.4 + - - +
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Residues in contact with ASN 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 VAL* 3.0 23.1 + - + +
70E ASP* 3.5 6.6 + - - +
72E ALA* 1.3 75.6 - - - +
74E LEU* 1.3 55.8 + - - +
76E GLU* 3.5 5.7 + - - +
77E THR* 2.8 38.5 + - - -
216F ILE* 4.5 4.2 + - - +
217F GLN* 4.5 12.9 + - - +
220F CYS* 3.4 31.9 - - - +
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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
----------------------------------------------------------
49E ILE* 3.8 17.5 - - + -
70E ASP 2.8 23.9 + - - +
71E ALA* 3.8 2.9 - - - +
73E ASN* 1.3 71.0 - - - +
75E ARG* 1.3 63.7 + - - +
77E THR* 3.3 1.1 + - - -
78E PHE* 3.0 51.3 + - + +
117E VAL* 3.6 31.0 - - + -
119E LEU* 3.6 21.8 - - + -
216F ILE* 3.6 34.8 - - + -
219F LEU* 4.6 8.3 - - + -
220F CYS* 3.9 11.7 - - - -
223F LEU* 6.4 0.2 - - + -
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Residues in contact with ARG 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B GLU* 5.6 4.0 + - - +
249B SER 5.1 1.8 + - - -
250B PHE* 3.4 34.6 - - + +
257B HIS* 4.3 21.0 + - - +
49E ILE* 3.8 8.0 - - + +
71E ALA 3.0 18.4 + - - +
72E ALA* 3.7 8.7 - - - +
73E ASN 3.4 0.2 - - - -
74E LEU* 1.3 76.3 - - - +
76E GLU* 1.3 58.6 + - - +
79E ARG* 3.0 30.0 + - - +
85E VAL* 3.8 28.2 + - + +
86E ARG* 4.7 0.2 - - - +
87E ASN* 2.8 50.2 + - - +
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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
----------------------------------------------------------
257B HIS* 4.1 11.4 + - - -
72E ALA 3.1 14.5 + - - +
73E ASN* 4.0 6.7 - - - +
74E LEU 3.2 0.2 - - - -
75E ARG* 1.3 76.9 - - - +
77E THR* 1.3 66.9 + - - +
79E ARG* 2.6 45.9 + - - +
80E ASN* 3.0 24.7 + - + +
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Residues in contact with THR 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASN* 2.8 24.3 + - - -
74E LEU* 3.6 4.9 - - - -
76E GLU* 1.3 77.3 - - - +
78E PHE* 1.3 64.2 + - + +
80E ASN* 3.3 16.0 + - - +
81E LEU* 3.3 18.0 + - + +
220F CYS* 3.4 26.9 + - - +
223F LEU* 3.7 42.2 - - + -
224F LYS* 4.7 6.1 - - + +
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Residues in contact with PHE 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E CYS* 3.6 31.0 - - - -
74E LEU* 3.0 46.0 + - + +
77E THR* 1.3 77.3 - - + +
79E ARG* 1.3 61.7 + - - +
80E ASN 3.2 0.7 - - - -
81E LEU* 3.4 22.3 + - + +
83E TYR* 2.9 50.0 + + + +
85E VAL* 3.9 8.5 - - + -
115E VAL* 3.9 30.3 - - + -
117E VAL* 4.5 1.6 - - + -
157E LEU* 5.9 1.6 - - + -
159E ILE* 3.9 19.3 - - + -
219F LEU* 5.3 0.2 - - + -
220F CYS* 6.2 0.2 - - - -
223F LEU* 4.0 20.9 - - + -
232F PHE* 6.1 2.0 - + - -
275F PHE* 5.2 6.3 - + - -
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Residues in contact with ARG 79 (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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250B PHE* 3.9 19.5 - - + -
251B SER 2.8 39.7 + - - +
252B PHE* 2.9 34.7 + - + -
254B ALA* 3.6 30.3 - - - +
257B HIS* 3.5 31.7 - - - +
75E ARG* 3.0 22.1 + - + +
76E GLU* 2.6 37.0 + - - +
78E PHE* 1.3 78.5 - - - +
80E ASN* 1.3 71.9 + - - +
82E LYS* 3.0 19.6 + - - +
83E TYR 4.3 4.3 - - - -
85E VAL* 3.8 5.8 - - - +
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Residues in contact with ASN 80 (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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252B PHE 5.5 4.1 + - - -
76E GLU* 3.0 18.3 + - + +
77E THR* 3.5 7.9 - - - +
78E PHE 3.2 0.4 - - - -
79E ARG* 1.3 94.6 - - - +
81E LEU* 1.3 62.7 + - - +
82E LYS* 3.2 27.3 + - - +
224F LYS* 6.1 0.7 - - - -
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Residues in contact with LEU 81 (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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44E MET* 3.4 22.3 - - - +
77E THR* 3.3 16.5 + - + +
78E PHE* 3.8 25.6 - - + +
79E ARG 3.1 1.2 - - - -
80E ASN* 1.3 82.5 - - + +
82E LYS* 1.3 71.8 + - - +
83E TYR* 3.4 16.5 + - + -
223F LEU* 4.5 15.7 - - + +
227F ALA* 3.7 25.4 - - + -
275F PHE* 4.0 41.3 - - + +
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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