Contacts of the helix formed by residues 143 - 158 (chain E) in PDB entry 6QY3
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 143 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141E SER* 4.3 3.5 - - - -
142E CYS* 1.3 79.9 - - - +
144E VAL* 1.3 66.0 + - - +
145E PHE* 3.1 12.3 - - - -
146E GLU* 3.1 9.7 + - - +
147E LYS* 3.0 20.6 + - - +
29F ALA* 6.6 0.7 - - - -
33F LYS* 5.4 6.3 - - - -
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Residues in contact with VAL 144 (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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65E ILE* 5.0 14.0 - - + +
66E LEU* 5.9 5.4 - - + +
143E THR* 1.3 74.7 - - - +
145E PHE* 1.3 57.1 + - - +
147E LYS* 3.7 9.3 - - - +
148E ILE* 2.9 31.7 + - - +
172E TYR* 4.9 17.7 - - + -
29F ALA* 5.7 7.1 - - + +
33F LYS* 5.7 3.2 - - - +
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Residues in contact with PHE 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E THR* 3.1 9.2 - - - -
144E VAL* 1.3 79.4 - - - +
146E GLU* 1.3 59.1 + - - +
148E ILE* 3.9 4.7 + - - +
149E PHE* 3.4 18.9 + - - +
173E PHE* 5.9 3.1 - - + -
177E GLU* 5.1 15.3 - - + -
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Residues in contact with GLU 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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141E SER* 4.9 5.2 - - - -
142E CYS* 4.6 10.3 - - + +
143E THR* 3.1 16.1 + - - +
145E PHE* 1.3 77.2 - - - +
147E LYS* 1.3 61.7 + - - +
149E PHE* 3.1 8.5 + - - +
150E GLU* 2.9 27.4 + - - +
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Residues in contact with LYS 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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65E ILE* 4.7 20.5 - - + +
66E LEU* 5.3 5.4 - - + -
141E SER* 4.1 18.9 - - - -
143E THR 3.0 15.9 + - - +
144E VAL* 3.4 9.4 + - - +
146E GLU* 1.3 78.3 - - - +
148E ILE* 1.3 56.4 + - - +
150E GLU* 3.2 8.1 + - - +
151E ILE* 2.9 27.0 + - - +
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Residues in contact with ILE 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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65E ILE* 5.2 11.1 - - + +
144E VAL 2.9 18.2 + - - +
145E PHE* 4.2 5.6 - - - +
147E LYS* 1.3 76.8 - - - +
149E PHE* 1.3 57.5 + - - +
151E ILE* 3.3 9.1 + - - +
152E LEU* 2.9 27.5 + - - +
181E ILE* 6.5 0.7 - - + -
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Residues in contact with PHE 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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145E PHE 3.4 12.4 + - - +
146E GLU* 3.1 13.8 + - - +
148E ILE* 1.3 77.0 - - - +
150E GLU* 1.3 58.9 + - - +
152E LEU* 3.2 8.1 + - - +
153E GLN* 2.9 27.8 + - - +
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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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70E ILE* 5.7 8.5 - - + -
138E GLU 5.6 6.5 - - - +
146E GLU 2.9 12.6 + - - +
147E LYS* 3.2 10.7 + - - +
149E PHE* 1.3 76.9 - - - +
151E ILE* 1.3 57.6 + - - +
153E GLN* 3.2 8.2 + - - +
154E ILE* 2.9 30.7 + - - +
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Residues in contact with ILE 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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65E ILE* 6.6 0.2 - - + -
68E TYR* 6.4 1.8 - - + -
147E LYS 2.9 14.3 + - - +
148E ILE* 3.5 12.3 - - - +
149E PHE 3.2 0.4 - - - -
150E GLU* 1.3 76.1 - - - +
152E LEU* 1.3 58.1 + - - +
154E ILE* 4.1 4.7 - - - +
155E PHE* 2.9 30.1 + - - +
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Residues in contact with LEU 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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148E ILE 2.9 13.6 + - - +
149E PHE* 3.2 11.0 + - - +
151E ILE* 1.3 75.0 - - - +
153E GLN* 1.3 58.8 + - - +
155E PHE* 3.8 5.8 - - - +
156E LYS* 2.9 30.3 + - - +
184E TYR* 6.5 0.4 - - + -
185E THR* 6.6 0.2 - - - -
188E SER* 5.7 6.2 - - - -
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Residues in contact with GLN 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 PHE 2.9 13.8 + - - +
150E GLU* 3.2 11.2 + - - +
152E LEU* 1.3 74.5 - - - +
154E ILE* 1.3 59.7 + - - +
156E LYS* 3.3 6.3 + - - +
157E TYR* 2.9 28.3 + - - +
117H LEU* 6.1 7.0 - - + -
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Residues in contact with ILE 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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70E ILE* 5.7 11.4 - - + +
150E GLU 2.9 15.8 + - - +
151E ILE* 4.2 4.7 - - - +
153E GLN* 1.3 77.0 - - - +
155E PHE* 1.3 57.1 + - - +
157E TYR* 3.3 8.5 + - - +
158E LEU* 3.0 28.8 + - - +
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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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60E LEU* 6.1 3.1 - - + -
151E ILE 2.9 20.3 + - - +
152E LEU* 3.8 7.2 - - - +
154E ILE* 1.3 78.1 - - - +
156E LYS* 1.3 61.4 + - - +
158E LEU* 3.1 25.0 + - - +
161E LYS* 4.8 10.4 - - + +
164E LEU* 4.7 19.7 - - + -
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Residues in contact with LYS 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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152E LEU 2.9 18.9 + - - +
153E GLN* 3.8 5.4 - - - +
155E PHE* 1.3 77.4 - - - +
157E TYR* 1.3 61.3 + - - +
158E LEU 4.3 2.9 - - - +
159E VAL* 5.7 0.2 - - - -
188E SER* 5.1 15.0 - - - +
190E ALA* 4.9 16.5 - - + +
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Residues in contact with TYR 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 GLN 2.9 17.8 + - - +
154E ILE* 3.6 9.4 - - - +
155E PHE 3.2 0.2 - - - -
156E LYS* 1.3 79.2 - - - +
158E LEU* 1.3 60.7 + - - +
159E VAL* 3.4 4.5 + - - +
117H LEU* 5.7 9.2 - - + -
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Residues in contact with LEU 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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154E ILE 3.0 15.8 + - - +
155E PHE* 3.1 17.7 + - - +
156E LYS 4.3 3.3 - - - +
157E TYR* 1.3 74.6 - - - +
159E VAL* 1.3 63.2 + - - +
160E LYS* 3.7 5.8 + - + +
161E LYS* 3.8 22.4 - - + +
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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