Contacts of the helix formed by residues 145 - 159 (chain E) in PDB entry 4QAE
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 145 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B SER* 5.4 3.8 - - - -
117E GLN* 4.6 15.0 - - - +
144E LEU* 1.3 78.5 - - - +
146E SER* 1.3 64.6 + - - +
147E GLU* 3.6 22.5 + - - +
148E LEU* 3.2 29.1 + - - +
149E LYS* 3.1 20.3 + - - +
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Residues in contact with SER 146 (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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144B LEU 5.5 2.6 + - - -
145B THR* 5.6 2.1 - - - -
146B SER* 4.6 16.4 + - - -
144E LEU 3.9 0.4 + - - -
145E THR* 1.3 69.2 - - - +
147E GLU* 1.3 65.4 + - - +
149E LYS* 3.3 15.6 + - - +
150E GLU* 2.7 53.3 + - - +
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Residues in contact with GLU 147 (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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145E THR* 3.6 18.1 - - - +
146E SER* 1.3 90.6 + - - +
148E LEU* 1.3 59.4 + - + +
150E GLU* 3.4 12.1 + - - +
151E ASN* 2.9 29.3 + - - +
154E ARG* 4.5 3.2 + - - +
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Residues in contact with LEU 148 (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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117E GLN* 3.7 23.1 - - - +
118E HIS* 3.5 53.2 - - + +
120E MET* 5.6 0.2 - - - +
137E LEU* 4.2 9.2 - - + +
144E LEU* 4.2 19.5 - - + -
145E THR* 3.2 22.7 + - - +
147E GLU* 1.3 77.9 - - + +
149E LYS* 1.3 60.2 + - - +
151E ASN* 3.4 11.7 + - + +
152E PHE* 3.0 27.9 + - - +
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Residues in contact with LYS 149 (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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143B GLU* 5.6 3.4 + - - -
149B LYS* 5.0 11.3 - - - +
34E VAL* 4.4 10.5 - - + -
137E LEU* 4.0 16.6 - - + -
143E GLU* 4.9 8.3 + - - -
144E LEU* 3.9 25.0 + - + +
145E THR 3.1 11.0 + - - +
146E SER* 3.3 17.7 + - - +
148E LEU* 1.3 77.2 - - - +
150E GLU* 1.3 57.8 + - + +
152E PHE* 3.2 4.9 + - - +
153E ILE* 3.0 33.8 + - + +
168E PHE* 3.9 35.0 - - + -
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Residues in contact with GLU 150 (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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146E SER* 2.7 37.1 + - - +
147E GLU* 3.8 10.7 - - - +
149E LYS* 1.3 73.2 - - + +
151E ASN* 1.3 56.9 + - - +
153E ILE* 3.3 15.6 + - + +
154E ARG* 3.0 48.3 + - - +
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Residues in contact with ASN 151 (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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120E MET* 3.5 25.9 - - - +
147E GLU 2.9 16.4 + - - +
148E LEU* 3.8 13.6 + - + +
150E GLU* 1.3 76.1 - - - +
152E PHE* 1.3 57.8 + - - +
154E ARG* 3.4 30.9 + - - +
155E PHE* 2.9 29.8 + - - +
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Residues in contact with PHE 152 (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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35E GLY* 3.6 15.9 - - - -
36E LEU 3.5 30.5 - - - -
37E ALA* 3.7 7.6 - - + -
120E MET* 3.8 25.1 - - - -
135E VAL* 3.7 26.2 - - + -
137E LEU* 3.7 27.1 - - + -
148E LEU 3.0 14.7 + - - +
149E LYS 3.2 5.6 + - - +
151E ASN* 1.3 74.0 - - - +
153E ILE* 1.3 61.9 + - - +
155E PHE* 3.9 0.7 - + - +
156E SER* 2.8 44.2 + - - -
166E ILE* 3.7 20.6 - - + -
167E VAL 4.4 0.2 - - - -
168E PHE* 3.8 22.4 - + - -
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Residues in contact with ILE 153 (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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149E LYS* 3.0 21.0 + - + +
150E GLU* 3.6 17.5 - - + +
152E PHE* 1.3 75.1 - - - +
154E ARG* 1.3 64.6 + - + +
156E SER* 3.2 3.9 + - - -
157E LYS* 3.0 48.9 + - + +
163E GLU* 5.0 12.6 - - + +
166E ILE* 4.1 23.7 - - + +
168E PHE* 4.0 26.0 - - + -
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Residues in contact with ARG 154 (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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147E GLU 4.5 3.2 + - - -
150E GLU* 3.0 30.4 + - - +
151E ASN* 3.4 45.2 + - - +
153E ILE* 1.3 78.7 - - + +
155E PHE* 1.3 58.1 + - - +
157E LYS* 3.3 8.3 + - + +
158E SER* 3.0 27.6 + - - -
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Residues in contact with PHE 155 (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 LYS 4.2 1.8 - - - -
16E VAL* 4.3 5.4 - - + -
17E PRO* 3.7 27.6 - - + -
111E VAL* 3.8 31.2 - - + -
120E MET* 4.1 27.8 - - + -
135E VAL* 4.1 23.3 - - + -
151E ASN* 2.9 19.0 + - - +
152E PHE 3.9 3.4 - - - +
153E ILE 3.3 0.2 - - - -
154E ARG* 1.3 76.3 - - - +
156E SER* 1.3 63.0 + - - +
158E SER* 2.6 29.6 + - - -
159E LEU* 3.2 43.1 + - + +
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Residues in contact with SER 156 (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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37E ALA* 3.4 30.4 - - - +
135E VAL* 4.8 4.0 - - - +
152E PHE* 2.8 35.0 + - - -
153E ILE 3.6 4.0 - - - -
155E PHE* 1.3 77.7 - - - +
157E LYS* 1.3 62.6 + - - +
159E LEU* 3.0 18.7 + - - +
161E LEU* 3.2 25.8 + - - +
166E ILE* 3.9 14.1 - - - -
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Residues in contact with LYS 157 (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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153E ILE* 3.0 37.8 + - + +
154E ARG* 3.8 6.5 - - + +
156E SER* 1.3 72.6 - - - +
158E SER* 1.3 62.0 + - - +
160E GLY* 2.8 22.5 + - - -
161E LEU 3.4 22.2 - - - +
162E PRO* 5.3 0.7 - - + -
163E GLU* 3.2 39.7 + - - +
166E ILE* 4.2 6.7 - - + -
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Residues in contact with SER 158 (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 LYS* 4.9 15.2 + - - +
154E ARG 3.0 14.5 + - - -
155E PHE* 2.6 33.1 + - - -
157E LYS* 1.3 76.6 - - - +
159E LEU* 1.3 63.5 + - - +
160E GLY 3.2 2.7 + - - -
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Residues in contact with LEU 159 (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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8E ILE* 4.8 1.0 - - - +
9E PRO 4.7 4.9 - - - +
11E PRO* 4.1 32.2 - - + +
15E LYS* 3.7 26.0 - - + +
16E VAL* 4.4 2.9 - - + -
122E PHE* 4.3 13.9 - - + -
133E PHE* 4.0 26.3 - - + -
135E VAL* 3.9 19.3 - - + -
155E PHE* 3.4 39.9 - - + +
156E SER* 3.0 9.7 + - - +
157E LYS 3.0 1.6 - - - -
158E SER* 1.3 87.2 - - - +
160E GLY* 1.3 58.4 + - - +
161E LEU* 3.4 2.0 + - - -
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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