Contacts of the helix formed by residues 143 - 155 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G LYS* 5.3 9.6 - - - -
141H SER 3.7 2.6 + - - -
142H CYS* 1.3 76.5 - - - +
144H VAL* 1.3 54.7 - - - +
145H PHE* 3.1 8.3 - - - -
146H GLU* 3.1 12.2 + - - +
147H LYS* 2.7 33.7 + - - +
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Residues in contact with VAL 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G ALA* 5.0 16.3 + - + +
32G VAL* 6.4 2.0 - - + -
33G LYS* 5.4 5.6 - - + +
65H ILE* 5.1 13.5 - - + +
66H LEU* 6.2 5.2 - - + +
142H CYS 4.0 0.2 + - - -
143H THR* 1.3 72.9 - - - +
145H PHE* 1.3 57.9 + - - +
147H LYS* 3.2 8.2 + - - +
148H ILE* 2.9 29.8 + - - +
172H TYR* 5.0 17.3 - - + -
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Residues in contact with PHE 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H THR* 3.1 6.3 - - - -
144H VAL* 1.3 78.7 - - - +
146H GLU* 1.3 58.2 + - - +
148H ILE* 3.4 6.5 + - - +
149H PHE* 2.9 28.6 + - - +
173H PHE* 5.8 7.4 - - + -
177H GLU* 5.1 15.0 - - + -
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Residues in contact with GLU 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H CYS* 4.3 10.5 - - + -
143H THR* 3.1 22.2 + - - +
145H PHE* 1.3 78.8 - - - +
147H LYS* 1.3 57.5 + - - +
149H PHE* 3.8 7.4 - - - +
150H GLU* 2.9 28.8 + - - +
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Residues in contact with LYS 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H ILE* 4.8 18.6 - - + +
66H LEU* 5.5 4.7 - - + -
139H THR* 5.9 6.1 - - - -
142H CYS* 4.6 10.3 - - + +
143H THR 2.7 20.3 + - - +
144H VAL* 3.5 10.3 - - - +
145H PHE 3.2 0.2 - - - -
146H GLU* 1.3 70.6 - - - +
148H ILE* 1.3 60.3 + - - +
150H GLU* 3.3 7.1 + - - +
151H ILE* 2.9 27.2 + - - +
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Residues in contact with ILE 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H ILE* 5.6 8.2 - - + +
144H VAL 2.9 16.6 + - - +
145H PHE* 3.9 5.2 - - - +
147H LYS* 1.3 75.9 - - - +
149H PHE* 1.3 57.8 + - - +
151H ILE* 3.2 8.3 + - - +
152H LEU* 2.9 28.1 + - - +
169H SER* 6.5 1.1 - - - -
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Residues in contact with PHE 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H PHE 2.9 17.9 + - - +
146H GLU* 3.8 8.7 - - - +
148H ILE* 1.3 77.7 - - - +
150H GLU* 1.3 57.5 + - - +
152H LEU* 3.2 8.6 + - - +
153H GLN* 2.9 27.1 + - - +
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Residues in contact with GLU 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E LEU* 6.2 3.6 - - + +
118E ASP* 5.9 7.4 - - + +
70H ILE* 5.9 8.3 - - + -
137H ILE* 5.9 7.0 - - + -
146H GLU 2.9 19.0 + - - +
147H LYS* 3.7 6.5 - - - +
149H PHE* 1.3 75.5 - - - +
151H ILE* 1.3 56.5 + - - +
153H GLN* 3.3 8.0 + - - +
154H ILE* 2.9 30.3 + - - +
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Residues in contact with ILE 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H ILE* 6.0 4.7 - - + -
147H LYS 2.9 14.1 + - - +
148H ILE* 3.2 11.6 + - - +
150H GLU* 1.3 78.3 - - - +
152H LEU* 1.3 56.9 + - - +
154H ILE* 3.4 4.6 + - - +
155H PHE* 3.0 29.1 + - - +
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Residues in contact with LEU 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H ILE 2.9 13.1 + - - +
149H PHE* 3.2 10.7 + - - +
151H ILE* 1.3 76.3 - - - +
153H GLN* 1.3 60.9 + - - +
155H PHE* 3.8 15.2 + - - +
156H LYS* 4.4 3.3 + - - +
184H TYR* 6.3 3.8 - - + -
185H THR* 6.3 3.8 - - - -
188H SER* 4.8 15.4 - - - -
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Residues in contact with GLN 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E GLU* 5.8 3.6 - - + +
117E LEU* 4.7 21.8 - - + +
149H PHE 2.9 15.7 + - - +
150H GLU* 3.6 9.2 - - - +
151H ILE 3.2 0.2 - - - -
152H LEU* 1.3 78.6 - - - +
154H ILE* 1.3 60.2 + - - +
155H PHE 3.6 0.3 + - - -
156H LYS* 3.9 13.3 + - - +
157H TYR* 4.4 2.1 + - - +
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Residues in contact with ILE 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H ILE* 5.3 13.7 - - + +
75H VAL* 5.5 8.0 - - + +
150H GLU 2.9 17.4 + - - +
151H ILE* 3.8 4.7 - - - +
153H GLN* 1.3 73.4 - - - +
155H PHE* 1.3 59.5 + - - +
156H LYS 3.2 2.7 - - - -
157H TYR* 3.0 27.7 + - + +
158H LEU* 3.1 12.1 + - - +
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Residues in contact with PHE 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H ILE 3.0 17.0 + - - +
152H LEU* 3.9 11.7 - - - +
153H GLN 3.3 0.8 - - - -
154H ILE* 1.3 78.1 - - - +
156H LYS* 1.3 59.6 + - - +
158H LEU* 3.3 24.1 + - - +
161H LYS* 5.3 3.5 - - - +
164H LEU* 5.3 13.7 - - + -
190H ALA* 5.0 14.6 - - + -
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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