Contacts of the helix formed by residues 160 - 172 (chain B) in PDB entry 2E7Y
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 ASP 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158B GLY 3.7 2.3 + - - +
159B LEU* 1.3 74.2 - - - +
161B SER* 1.3 59.0 + - - +
162B LYS* 2.8 13.3 + - - +
163B GLU* 2.8 48.6 + - - +
164B ILE* 2.9 28.5 + - - +
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Residues in contact with SER 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ASP* 1.3 75.0 - - - +
162B LYS* 1.3 62.5 + - - +
164B ILE* 3.1 11.7 - - - +
165B SER* 3.0 27.4 + - - -
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ASP* 2.8 14.8 + - - +
161B SER* 1.3 73.4 - - - +
163B GLU* 1.3 60.9 + - + +
165B SER* 3.3 7.1 + - - -
166B ARG* 2.9 56.0 + - - +
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLY 4.3 2.1 - - - +
159B LEU* 3.3 27.4 - - + +
160B ASP* 2.8 54.7 + - - +
162B LYS* 1.3 75.7 - - + +
164B ILE* 1.3 60.7 + - - +
166B ARG* 3.4 14.2 + - - +
167B LEU* 3.2 22.7 + - - +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 4.1 14.4 - - + -
156B PHE* 4.0 24.7 - - + +
159B LEU* 4.1 15.0 - - + +
160B ASP 2.9 16.1 + - - +
161B SER* 3.1 25.8 - - - +
163B GLU* 1.3 76.7 - - - +
165B SER* 1.3 61.3 + - - +
167B LEU* 3.2 3.7 + - + +
168B VAL* 3.0 37.6 + - + +
176B VAL* 3.4 35.0 - - + -
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Residues in contact with SER 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B SER* 3.0 18.1 + - - -
162B LYS* 3.9 8.1 - - - -
164B ILE* 1.3 82.2 - - - +
166B ARG* 1.3 56.8 + - - +
168B VAL* 3.8 7.3 - - - +
169B LYS* 2.9 29.8 + - - +
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Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LYS* 2.9 47.2 + - + +
163B GLU* 3.7 11.8 - - - +
165B SER* 1.3 77.1 - - - +
167B LEU* 1.3 62.4 + - - +
169B LYS* 3.5 11.3 + - + +
170B GLU* 3.2 33.3 + - + +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B PHE* 3.5 37.9 - - + -
159B LEU* 4.1 12.8 - - + -
163B GLU 3.2 11.3 + - - +
164B ILE* 3.6 9.4 - - + +
166B ARG* 1.3 79.3 - - - +
168B VAL* 1.3 56.0 + - - +
170B GLU* 4.6 8.5 - - - +
171B LYS* 2.7 64.1 + - + +
175B PHE* 4.3 9.6 - - + -
176B VAL* 3.6 21.5 - - + -
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ILE* 3.0 26.0 + - + +
165B SER* 3.8 7.2 - - - +
167B LEU* 1.3 75.2 - - - +
169B LYS* 1.3 60.4 + - - +
172B GLY* 2.6 35.8 + - - +
173B ARG* 3.6 33.9 - - + +
176B VAL* 3.8 25.6 - - + -
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Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B SER 2.9 17.9 + - - +
166B ARG* 3.7 11.7 - - + +
168B VAL* 1.3 81.3 - - - +
170B GLU* 1.3 63.0 + - + +
172B GLY* 4.5 1.2 + - - -
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ARG* 3.2 25.0 + - + +
167B LEU* 4.0 8.6 - - - +
169B LYS* 1.3 85.7 - - + +
171B LYS* 1.3 90.8 + - + +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B LEU* 2.7 28.7 + - + +
170B GLU* 1.3 107.5 + - + +
172B GLY* 1.3 59.0 + - - +
175B PHE* 3.3 63.9 + - + +
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Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL* 2.6 31.7 + - - -
169B LYS 4.4 1.0 + - - -
170B GLU 3.8 0.4 - - - -
171B LYS* 1.3 75.0 - - - +
173B ARG* 1.3 65.4 + - - +
174B ASP* 3.2 3.6 - - - -
175B PHE* 3.1 15.7 + - - +
176B VAL* 3.7 4.2 + - - +
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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