Contacts of the helix formed by residues 125 - 142 (chain E) in PDB entry 3HYW
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 THR 125 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E ARG* 4.2 24.0 - - - +
45E PHE* 3.7 9.6 - - - -
109E LEU* 4.3 11.9 - - + -
123E ILE 3.9 0.5 - - - +
124E CYS* 1.3 82.9 - - - +
126E ALA* 1.3 59.5 + - - +
127E GLU* 3.5 16.5 + - - +
128E HIS* 2.8 42.7 + - + +
129E ALA* 2.9 30.3 + - - +
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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
----------------------------------------------------------
38E TYR* 3.7 20.1 + - - +
45E PHE* 3.6 25.5 - - + -
48E LEU* 3.7 12.8 - - + +
55E PHE* 3.7 27.6 - - + -
125E THR* 1.3 74.0 - - - +
127E GLU* 1.3 60.7 + - - +
129E ALA* 3.3 0.6 + - - -
130E LEU* 3.0 37.1 + - + +
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Residues in contact with GLU 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ARG* 3.2 28.1 + - - +
38E TYR* 2.6 33.8 + - - -
55E PHE* 5.3 0.9 - - - -
125E THR* 3.5 12.2 + - - +
126E ALA* 1.3 77.3 - - - +
128E HIS* 1.3 63.0 + - + +
130E LEU* 3.5 10.1 + - + +
131E GLU* 3.4 26.1 + - - +
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Residues in contact with HIS 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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109E LEU* 3.9 13.1 - - + +
111E PHE* 3.9 26.9 - + - -
117E GLU* 5.2 7.2 - - + -
122E SER* 3.1 32.2 + - - +
124E CYS 5.2 0.2 - - - -
125E THR* 2.8 44.4 + - + +
127E GLU* 1.3 74.8 - - + +
129E ALA* 1.3 64.0 + - - +
131E GLU* 3.2 11.5 + - - +
132E THR* 3.0 23.7 + - - -
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Residues in contact with ALA 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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45E PHE* 3.5 26.7 - - + +
48E LEU* 4.0 10.1 - - + -
49E ALA* 3.2 24.6 - - + +
122E SER 3.5 7.3 + - - -
123E ILE* 4.2 7.9 - - - +
125E THR 2.9 17.7 + - - +
126E ALA* 3.7 4.3 - - - +
128E HIS* 1.3 76.4 - - - +
130E LEU* 1.3 62.7 + - - +
132E THR* 3.2 3.9 + - - -
133E GLN* 3.2 17.7 + - - +
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Residues in contact with LEU 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LEU* 3.8 33.0 - - + +
55E PHE* 4.7 21.5 - - + +
126E ALA* 3.0 23.7 + - + +
127E GLU* 3.8 10.1 - - + +
128E HIS 3.3 0.2 - - - -
129E ALA* 1.3 75.2 - - - +
131E GLU* 1.3 65.4 + - - +
133E GLN* 3.5 10.1 + - + +
134E LYS* 3.5 26.8 + - - +
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Residues in contact with GLU 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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121E THR* 5.4 0.9 - - + -
127E GLU 3.4 14.6 + - - +
128E HIS* 3.2 12.7 + - - +
130E LEU* 1.3 77.7 - - - +
132E THR* 1.3 64.3 + - - +
134E LYS* 3.1 42.4 + - - +
135E LYS* 3.1 25.0 + - + +
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Residues in contact with THR 132 (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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49E ALA* 4.0 11.2 - - + -
121E THR* 3.4 36.1 - - - +
122E SER 2.7 27.8 + - - -
123E ILE* 4.3 3.6 - - + -
128E HIS 3.0 3.8 + - - -
129E ALA 3.2 9.6 + - - -
131E GLU* 1.3 75.9 - - - +
133E GLN* 1.3 56.6 + - - +
135E LYS* 3.1 2.9 + - - +
136E LEU* 2.8 28.0 + - + +
163E PHE* 3.9 28.3 - - + -
247E PHE* 3.9 4.9 - - + -
249E MET* 4.4 0.2 - - + -
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Residues in contact with GLN 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LEU 4.2 4.7 - - - +
49E ALA 3.0 26.9 + - - +
50E MET* 3.3 13.5 + - - +
51E GLY* 3.8 17.3 - - - -
129E ALA 3.2 9.8 + - - +
130E LEU* 3.7 13.5 - - + +
131E GLU 3.3 0.4 - - - -
132E THR* 1.3 70.8 - - - +
134E LYS* 1.3 66.7 - - + +
136E LEU* 3.1 9.8 + - - +
137E GLN* 2.8 56.7 + - + +
140E TYR* 5.2 2.6 + - - -
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Residues in contact with LYS 134 (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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130E LEU* 3.5 14.8 + - - +
131E GLU* 3.1 43.3 + - - +
133E GLN* 1.3 78.6 - - + +
135E LYS* 1.3 61.1 + - + +
137E GLN* 3.5 9.6 + - - +
138E GLU* 3.4 25.6 + - - +
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Residues in contact with LYS 135 (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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118E GLU 5.5 1.0 + - - -
119E ASN* 3.1 29.7 + - - +
120E SER 4.4 2.4 + - - +
121E THR* 3.3 24.0 - - + +
131E GLU* 3.1 13.9 + - + +
132E THR 3.1 8.8 + - - +
134E LYS* 1.3 77.2 - - + +
136E LEU* 1.3 63.4 + - - +
138E GLU* 3.3 26.9 + - - +
139E LEU* 3.1 19.6 + - - +
246E LYS 5.1 9.6 + - - -
247E PHE* 3.9 23.0 - - + -
248E THR 5.4 3.2 - - - +
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Residues in contact with LEU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ALA 3.3 25.6 - - - +
50E MET* 3.7 25.1 - - - -
132E THR* 2.8 16.8 + - + +
133E GLN* 3.1 11.6 + - - +
135E LYS* 1.3 70.5 - - - +
137E GLN* 1.3 59.8 + - - +
139E LEU* 3.0 14.7 + - + +
140E TYR* 2.9 49.8 + - + +
163E PHE* 3.9 8.7 - - + -
167E LEU* 3.8 26.9 - - + -
247E PHE* 3.5 29.6 - - + -
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Residues in contact with GLN 137 (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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133E GLN* 2.8 44.2 + - + +
134E LYS* 3.6 11.2 - - - +
135E LYS 3.3 0.2 - - - -
136E LEU* 1.3 77.8 - - - +
138E GLU* 1.3 57.0 + - + +
140E TYR* 3.4 23.8 + - - +
141E ALA* 3.0 29.3 + - - +
174E ARG* 4.0 12.5 + - - +
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Residues in contact with GLU 138 (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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134E LYS* 3.4 16.3 + - - +
135E LYS* 3.3 29.0 + - + +
136E LEU 3.2 0.2 - - - -
137E GLN* 1.3 77.4 - - + +
139E LEU* 1.3 55.8 + - - +
141E ALA* 3.5 6.8 + - - +
142E ASN* 3.0 25.9 + - - +
246E LYS* 3.8 20.6 + - - +
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Residues in contact with LEU 139 (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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135E LYS 3.1 11.1 + - - +
136E LEU* 3.0 32.1 + - + +
138E GLU* 1.3 74.5 - - - +
140E TYR* 1.3 72.5 + - + +
142E ASN 3.2 3.8 - - - -
143E PRO* 3.1 30.1 - - + +
144E GLY 3.8 31.4 - - - +
146E VAL* 3.8 26.0 - - + -
167E LEU* 4.3 12.6 - - + -
171E LEU* 4.6 6.3 - - + -
176E ILE* 5.2 1.5 - - + +
180E VAL* 4.7 5.6 - - + -
246E LYS* 4.6 9.2 - - + +
247E PHE* 4.0 20.4 - - + -
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Residues in contact with TYR 140 (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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50E MET* 3.8 18.0 + - - +
133E GLN* 5.2 2.5 - - - -
136E LEU* 2.9 43.3 + - + +
137E GLN* 3.4 22.0 + - - +
139E LEU* 1.3 80.7 - - + +
141E ALA* 1.3 62.4 - - - +
143E PRO* 3.9 10.7 - - - +
167E LEU* 3.8 10.3 - - + +
170E GLU* 3.4 21.5 - - + +
171E LEU* 3.7 30.1 - - + -
174E ARG* 3.4 51.8 - - - +
176E ILE* 4.3 12.2 - - + +
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Residues in contact with ALA 141 (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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137E GLN 3.0 17.6 + - - +
138E GLU* 3.7 7.6 - - - +
140E TYR* 1.3 78.7 - - - +
142E ASN* 1.3 71.5 + - - +
143E PRO* 3.5 7.0 - - - +
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Residues in contact with ASN 142 (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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138E GLU 3.0 8.5 + - - +
139E LEU 3.2 6.3 - - - +
141E ALA* 1.3 88.5 - - - +
143E PRO* 1.4 67.6 - - - +
144E GLY 3.6 1.0 + - - -
246E LYS* 3.1 35.9 + - - +
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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