Contacts of the helix formed by residues 116 - 129 (chain E) in PDB entry 5YWB
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 116 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C GLU* 6.0 2.4 - - - +
91E TRP* 4.0 8.4 - - - +
100E LEU* 4.6 3.7 - - - +
114E ILE* 4.6 2.1 - - - +
115E HIS* 1.3 83.6 + - - +
117E PHE* 1.3 76.2 + - - +
118E SER* 3.2 11.6 + - - -
119E SER* 3.5 6.9 + - - -
120E ALA* 3.1 21.5 + - - +
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Residues in contact with PHE 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E LEU* 4.8 19.7 - - + -
87E ALA* 4.3 8.7 - - + -
88E MET* 4.0 35.9 - - + -
91E TRP* 3.4 45.7 - + + +
116E SER* 1.3 82.9 + - - +
118E SER* 1.3 57.8 + - - +
120E ALA* 3.3 1.9 + - + +
121E PHE* 2.9 34.1 + + + +
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Residues in contact with SER 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLU* 4.0 26.0 + - - -
143C PRO* 5.7 5.6 - - - +
146C ILE* 5.2 12.2 - - - +
116E SER* 3.2 8.1 + - - -
117E PHE* 1.3 80.4 - - - +
119E SER* 1.3 57.7 + - - +
121E PHE* 3.3 7.6 + - - +
122E LEU* 2.9 27.5 + - - +
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Residues in contact with SER 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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140C GLU* 3.5 21.5 - - - +
113E SER 3.8 6.4 + - - -
114E ILE* 3.4 19.3 - - - +
115E HIS* 4.2 13.6 - - - -
116E SER 3.5 9.1 + - - -
118E SER* 1.3 77.6 - - - +
120E ALA* 1.3 58.5 + - - +
122E LEU* 3.3 7.6 + - - +
123E PHE* 2.9 23.9 + - - +
136E ARG* 3.1 27.4 + - - -
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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
----------------------------------------------------------
87E ALA* 4.5 6.1 - - - +
90E TRP* 4.9 6.0 - - + +
91E TRP* 3.9 36.3 - - + +
114E ILE* 3.5 15.8 - - + +
116E SER 3.1 15.8 + - - +
117E PHE* 3.5 9.2 - - + +
118E SER 3.2 0.2 - - - -
119E SER* 1.3 77.3 - - - +
121E PHE* 1.3 57.7 + - - +
123E PHE* 3.2 6.4 + - - +
124E SER* 2.9 26.7 + - - -
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Residues in contact with PHE 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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146C ILE* 4.2 23.1 - - + -
150C ILE* 3.8 34.3 - - + -
80E LEU* 6.5 0.9 - - + -
83E TRP* 4.4 11.9 - + + -
84E LEU* 3.6 39.7 - - + -
87E ALA* 3.5 29.1 - - + +
117E PHE* 2.9 27.3 + + + +
118E SER* 3.7 5.2 - - - +
120E ALA* 1.3 75.7 - - - +
122E LEU* 1.3 59.8 + - - +
124E SER* 3.2 2.3 + - - -
125E ILE* 2.9 31.9 + - + +
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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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138C VAL* 3.6 40.6 - - + +
139C THR 3.9 10.8 - - - +
140C GLU* 4.5 4.0 - - - +
146C ILE* 3.5 31.6 - - + +
149C LEU* 4.9 5.8 - - + -
118E SER 2.9 13.3 + - - +
119E SER* 3.5 9.6 - - - +
120E ALA 3.2 0.2 - - - -
121E PHE* 1.3 79.0 - - - +
123E PHE* 1.3 56.6 + - - +
125E ILE* 3.2 17.2 - - + +
126E GLU* 2.9 31.4 + - + +
131E ILE* 6.1 0.7 - - + -
133E PHE* 4.6 8.7 - - + -
136E ARG* 3.4 25.4 - - - +
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Residues in contact with PHE 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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90E TRP* 3.4 52.0 - + - -
111E VAL* 3.6 26.2 - - + -
114E ILE* 4.6 4.3 - - + -
119E SER 2.9 17.1 + - - +
120E ALA* 3.2 7.2 + - - +
122E LEU* 1.3 75.7 - - - +
124E SER* 1.3 59.6 + - - +
126E GLU* 3.2 6.6 + - + +
127E VAL* 2.9 31.1 + - + +
136E ARG* 3.3 49.0 - - + +
138E VAL* 4.2 10.1 - - + -
149E LEU* 5.3 0.2 - - + -
133G PHE* 3.8 27.6 - + - -
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Residues in contact with SER 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E TRP* 3.3 23.9 + - - +
86E PHE* 3.9 4.4 - - - +
87E ALA* 3.4 25.8 + - - -
90E TRP* 4.8 4.7 - - - -
120E ALA 2.9 14.2 + - - -
121E PHE* 3.2 8.9 + - - -
123E PHE* 1.3 80.2 - - - +
125E ILE* 1.3 58.4 + - - +
127E VAL* 3.5 7.9 - - - +
128E GLN* 2.9 33.5 + - - +
152E GLN* 4.0 9.4 + - - +
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Residues in contact with ILE 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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146C ILE* 6.3 1.3 - - + -
149C LEU* 4.1 24.9 - - + -
150C ILE* 3.7 19.3 - - + -
153C ASN* 4.5 7.2 - - + +
83E TRP* 3.5 55.0 - - + +
121E PHE* 2.9 24.7 + - + +
122E LEU* 3.2 26.2 - - + +
124E SER* 1.3 78.0 + - - +
126E GLU* 1.3 60.7 + - - +
128E GLN* 4.1 1.3 - - + -
129E VAL* 3.3 32.5 + - + +
131E ILE* 3.7 3.3 - - + +
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Residues in contact with GLU 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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122E LEU* 2.9 24.1 + - + +
123E PHE* 3.2 11.2 + - + +
125E ILE* 1.3 79.7 - - - +
127E VAL* 1.3 58.8 + - - +
130E THR* 4.1 0.5 - - - -
131E ILE* 3.3 26.7 + - + -
132E GLY* 2.9 26.8 + - - -
133E PHE* 4.3 21.3 - - + +
134E GLY 5.8 0.4 - - - +
136E ARG* 5.2 3.6 - - + +
131G ILE* 5.3 0.2 - - - +
133G PHE* 5.6 4.7 - - + -
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Residues in contact with VAL 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E TRP* 3.7 30.1 - - + -
123E PHE* 2.9 22.9 + - + +
124E SER* 3.5 5.6 - - - +
126E GLU* 1.3 77.2 - - - +
128E GLN* 1.3 69.7 + - - +
130E THR 3.8 4.0 + - - -
132E GLY* 5.6 0.2 - - - -
149E LEU* 4.1 32.3 - - + -
152E GLN* 3.8 8.4 - - + +
153E ASN* 4.0 10.9 - - - +
131G ILE* 3.9 25.2 - - + +
133G PHE* 4.3 20.2 - - + -
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Residues in contact with GLN 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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79E PHE* 5.8 1.7 - - - -
82E SER* 4.9 4.4 + - - -
83E TRP* 3.3 40.8 + - + +
86E PHE* 5.0 1.4 - - - -
124E SER* 2.9 21.0 + - - +
125E ILE* 4.6 2.0 - - - -
126E GLU 3.5 0.2 - - - -
127E VAL* 1.3 77.3 - - - +
129E VAL* 1.3 62.7 + - + +
130E THR* 3.0 17.9 + - - +
152E GLN* 2.5 54.4 + - - +
153E ASN* 4.5 4.1 - - - +
155E VAL* 5.1 0.6 - - - +
156E GLY* 3.3 27.0 - - - +
159E ILE* 4.7 5.0 - - - +
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Residues in contact with VAL 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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130C THR* 4.4 9.9 - - + +
153C ASN* 3.4 39.5 - - + +
157C LEU* 4.3 24.2 - - + -
83E TRP* 4.8 11.0 - - + +
125E ILE* 3.3 30.3 + - + +
128E GLN* 1.3 80.7 - - + +
130E THR* 1.3 73.7 + - - +
131E ILE* 3.9 11.0 - - + -
160E ASN* 5.9 1.3 - - - +
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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
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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