Contacts of the helix formed by residues 118 - 131 (chain E) in PDB entry 6IY6
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 SER 118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66E GLY 5.6 0.4 - - - -
67E LEU* 3.4 18.2 - - - +
69E GLY* 5.2 2.7 - - - -
78E ILE* 3.9 15.9 - - - -
113E VAL* 3.6 25.8 + - - +
116E SER* 4.2 3.6 - - - -
117E LEU* 1.3 74.1 - - - +
119E LEU* 1.3 66.1 + - - +
120E ALA* 3.6 10.6 - - - +
121E ASP* 2.8 34.2 + - - +
122E LEU* 3.4 11.2 + - - +
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Residues in contact with LEU 119 (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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20E ALA* 4.6 5.4 - - + -
55E LEU* 3.3 52.0 - - + +
56E ARG* 3.9 4.5 - - - +
59E ALA* 3.4 27.8 - - + +
67E LEU* 2.9 22.8 + - + +
68E TYR* 3.9 16.2 - - + -
78E ILE* 3.9 15.0 - - + +
82E LEU* 4.5 10.5 - - + -
118E SER* 1.3 68.5 - - - +
120E ALA* 1.3 56.2 + - - +
122E LEU* 3.1 19.3 + - + +
123E CYS* 2.7 38.6 + - - +
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Residues in contact with ALA 120 (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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78E ILE* 4.2 11.8 - - + +
81E TRP* 3.7 35.4 - - + -
112E LEU* 3.7 12.8 - - + -
113E VAL* 4.0 7.2 - - + -
118E SER* 3.6 12.9 + - - +
119E LEU* 1.3 75.7 - - - +
121E ASP* 1.3 62.9 + - - +
123E CYS* 3.9 8.7 - - - -
124E VAL* 3.0 31.2 + - - +
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Residues in contact with ASP 121 (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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111E TYR* 3.5 21.6 - - - +
112E LEU* 2.8 26.7 + - - +
116E SER 3.5 3.1 - - - +
117E LEU* 3.6 14.8 - - + -
118E SER* 2.8 39.0 + - - +
120E ALA* 1.3 78.6 - - - +
122E LEU* 1.3 57.7 + - - +
125E TRP* 3.1 32.9 + - - +
150E TRP* 3.3 24.5 + - - -
154E LEU* 3.9 10.3 - - + -
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Residues in contact with LEU 122 (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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16E GLY* 4.5 10.8 - - - +
19E LEU* 4.3 13.4 - - + +
20E ALA* 3.8 36.3 - - + +
23E HIS* 4.9 4.3 - - + +
55E LEU* 5.7 1.6 - - + -
67E LEU* 4.3 18.4 - - + -
117E LEU* 3.8 26.2 - - + -
118E SER 3.7 9.9 - - - +
119E LEU* 3.1 14.0 + - + +
121E ASP* 1.3 72.8 - - - +
123E CYS* 1.3 57.4 + - - +
125E TRP* 3.2 4.5 + - - +
126E ALA* 2.8 38.2 + - - +
154E LEU* 5.8 0.2 - - + -
158E LEU* 4.2 27.1 - - + -
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Residues in contact with CYS 123 (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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16E GLY* 5.0 3.6 - - - -
52E ASN* 5.4 0.4 - - - +
55E LEU* 4.1 16.7 - - + +
81E TRP 3.6 16.8 - - - -
82E LEU* 3.7 26.2 - - + -
85E SER* 3.4 21.1 - - - +
119E LEU 2.7 18.9 + - - +
120E ALA* 3.4 15.9 - - - -
122E LEU* 1.3 71.5 - - - +
124E VAL* 1.3 62.7 + - - +
126E ALA* 4.0 4.9 - - - +
127E THR* 2.7 32.4 + - - -
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Residues in contact with VAL 124 (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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81E TRP* 4.0 25.8 - - + +
84E PHE* 4.6 2.9 - - + -
85E SER* 4.0 8.7 - - - -
89E LEU* 3.7 17.2 - - + +
102E LEU* 3.8 21.8 - - + -
112E LEU* 3.7 11.9 - - + -
120E ALA 3.0 18.2 + - - +
123E CYS* 1.3 88.7 - - - +
125E TRP* 1.3 52.7 + - - +
127E THR* 3.3 3.6 + - - -
128E LEU* 2.7 37.5 + - + +
150E TRP* 3.5 22.4 - - + -
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Residues in contact with TRP 125 (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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15E LEU* 6.0 2.0 - - + -
19E LEU* 3.7 24.7 - - + -
121E ASP 3.1 22.2 + - - +
122E LEU* 3.8 2.7 - - - +
124E VAL* 1.3 75.4 - - - +
126E ALA* 1.3 59.8 + - - +
128E LEU* 3.3 4.6 + - - +
129E LYS* 2.8 66.7 + - + +
150E TRP* 3.8 9.9 - + + -
151E PHE* 3.2 55.1 + + - -
154E LEU* 3.5 25.1 - - + +
155E GLU* 3.8 27.6 - - + -
158E LEU* 3.7 19.3 - - + -
159E GLU* 3.5 20.2 - - - -
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Residues in contact with ALA 126 (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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15E LEU* 3.6 20.5 - - + +
16E GLY* 3.3 35.9 - - - +
19E LEU* 4.4 3.1 - - + -
122E LEU 2.8 21.2 + - - +
123E CYS* 4.0 4.9 - - - +
125E TRP* 1.3 83.5 - - - +
127E THR* 1.3 57.5 + - - +
129E LYS* 3.4 3.3 + - - +
130E GLY* 3.0 22.9 + - - -
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Residues in contact with THR 127 (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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85E SER* 3.3 33.0 + - - +
89E LEU* 3.7 8.3 - - + +
90E SER* 3.6 26.4 + - - +
123E CYS 2.7 22.1 + - - -
124E VAL 3.3 4.1 + - - -
126E ALA* 1.3 76.4 - - - +
128E LEU* 1.3 56.7 + - - +
130E GLY* 3.3 2.9 + - - +
131E ASN* 2.9 27.0 + - - +
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Residues in contact with LEU 128 (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 LEU* 3.6 31.2 - - + +
95E PHE* 4.0 6.3 - - + -
99E ILE* 3.8 17.0 - - + -
102E LEU* 4.2 6.1 - - + -
124E VAL 2.7 20.8 + - - +
125E TRP 3.5 5.4 - - - +
127E THR* 1.3 70.4 - - - +
129E LYS* 1.3 63.2 + - - +
131E ASN* 3.3 14.6 + - - +
134E TRP* 3.0 43.6 - - + +
147E VAL* 3.9 18.8 - - + -
150E TRP* 3.8 27.4 - - + -
151E PHE* 3.8 15.0 - - + -
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Residues in contact with LYS 129 (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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15E LEU* 4.9 9.9 - - + -
125E TRP* 2.8 49.5 + - + +
126E ALA* 3.6 5.2 - - - +
128E LEU* 1.3 70.9 - - - +
130E GLY* 1.3 61.8 + - - +
131E ASN 3.4 5.9 + - - +
134E TRP* 4.4 1.8 - - - -
135E GLN* 3.4 34.8 + - - +
151E PHE* 3.9 20.5 - - + -
155E GLU* 4.8 8.0 + - - -
159E GLU* 3.0 32.7 + - - -
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Residues in contact with GLY 130 (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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15E LEU* 4.4 12.5 - - - +
126E ALA 3.0 14.4 + - - -
127E THR* 3.6 5.8 - - - -
128E LEU 3.3 0.2 - - - -
129E LYS* 1.3 72.2 - - - +
131E ASN* 1.3 61.9 + - - +
132E ALA 3.9 0.7 + - - -
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Residues in contact with ASN 131 (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 LEU* 3.0 24.7 + - + +
90E SER 5.1 1.4 + - - -
91E SER 3.8 6.1 + - - -
92E CYS* 4.1 10.0 - - - +
95E PHE* 3.3 26.7 - - + -
127E THR 2.9 12.9 + - - +
128E LEU* 3.4 17.8 - - - +
129E LYS 3.2 10.1 - - - +
130E GLY* 1.3 78.8 - - - +
132E ALA* 1.3 60.7 + - - +
133E ALA* 2.7 34.0 + - - +
134E TRP* 2.9 12.1 + - + -
135E GLN* 3.6 15.1 + - - +
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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