Contacts of the helix formed by residues 154 - 166 (chain D) in PDB entry 1EQB
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 154 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D GLY 4.7 3.0 + - - -
147D ILE* 5.2 0.6 - - - +
148D ASP* 3.4 27.1 - - - +
152D HIS 3.5 2.0 + - - -
153D ILE* 1.3 75.0 - - - +
155D TYR* 1.3 63.0 + - - +
156D ALA* 3.0 20.0 + - - +
157D ASP* 3.0 31.7 + - + +
158D LEU* 3.0 19.9 + - - +
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Residues in contact with TYR 155 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D HIS* 6.4 0.2 - - + -
153D ILE* 3.5 34.5 - - + +
154D ASP* 1.3 71.6 + - - +
156D ALA* 1.3 61.2 + - - +
157D ASP 3.4 0.2 - - - -
158D LEU* 3.8 20.0 - - + -
159D GLU* 3.2 24.1 + - - +
177D TYR* 5.4 0.7 + - - -
180D VAL 3.8 4.9 + - - -
181D VAL* 3.4 15.8 - - + +
182D ASP* 2.9 40.6 + - + +
185D LYS* 3.9 35.7 - - + -
186D MET* 4.1 19.1 - - + -
189D ILE* 3.7 7.0 - - + +
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ASP* 3.0 17.1 + - - +
155D TYR* 1.3 78.9 - - - +
157D ASP* 1.3 61.6 + - - +
159D GLU* 3.4 9.8 + - - +
160D LYS* 3.2 36.3 + - - +
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Residues in contact with ASP 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D TYR* 5.7 0.3 - - - +
154D ASP* 3.0 26.8 + - + +
156D ALA* 1.3 76.2 - - - +
158D LEU* 1.3 67.2 + - - +
160D LYS* 3.2 16.0 + - - +
161D GLN* 2.9 46.3 + - - +
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 3.6 20.8 - - + +
145D TYR* 3.4 44.2 - - + -
153D ILE* 4.9 8.1 - - + -
154D ASP 3.0 15.7 + - - +
155D TYR* 3.8 16.6 - - + +
157D ASP* 1.3 77.3 + - - +
159D GLU* 1.3 57.9 + - - +
161D GLN* 3.3 10.0 + - - +
162D ALA* 2.9 28.9 + - - +
170D ILE* 5.0 3.1 - - + -
186D MET* 3.9 31.2 - - + -
189D ILE* 3.8 22.2 - - + -
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Residues in contact with GLU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TYR 3.2 16.0 + - - +
156D ALA* 3.5 8.7 - - - +
157D ASP 3.2 0.2 - - - -
158D LEU* 1.3 80.5 - - - +
160D LYS* 1.3 57.1 + - + +
162D ALA* 3.2 1.7 + - - +
163D LYS* 2.9 63.8 + - + +
185D LYS* 4.0 20.1 + - - -
189D ILE* 3.9 30.9 - - + +
192D SER* 5.3 1.3 - - - +
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Residues in contact with LYS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLU* 5.6 0.4 - - - -
156D ALA* 3.2 23.7 + - - +
157D ASP* 3.2 19.3 + - - +
159D GLU* 1.3 78.8 - - + +
161D GLN* 1.3 57.6 + - + +
163D LYS* 3.3 8.2 + - + +
164D GLU* 2.9 35.1 + - - +
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Residues in contact with GLN 161 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D LEU* 4.2 14.0 - - + +
143D VAL* 4.0 9.9 - - - +
144D PRO 2.7 27.4 + - - -
145D TYR* 3.4 21.9 - - - +
157D ASP* 2.9 38.5 + - - +
158D LEU* 3.5 11.6 - - - +
160D LYS* 1.3 77.2 - - + +
162D ALA* 1.3 59.1 + - - +
164D GLU* 4.6 2.2 - - - -
165D HIS* 2.9 48.5 + - + +
167D PRO* 4.6 0.4 - - - +
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 4.1 13.4 - - + +
158D LEU 2.9 17.3 + - - +
159D GLU 3.2 4.9 + - - +
161D GLN* 1.3 78.0 - - - +
163D LYS* 1.3 57.1 + - + +
166D LYS* 2.8 28.2 + - - -
167D PRO* 3.2 14.0 - - - +
170D ILE* 4.1 0.9 - - + -
189D ILE* 3.6 24.2 - - + -
193D ILE* 3.6 20.4 - - + +
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Residues in contact with LYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLN* 5.8 5.5 - - - +
164A GLU* 2.9 44.0 + - - +
165A HIS* 3.5 29.2 + - + +
159D GLU* 2.9 50.6 + - + +
160D LYS* 3.8 7.2 - - + +
162D ALA* 1.3 76.8 - - + +
164D GLU* 1.3 61.9 + - - +
166D LYS* 4.1 5.2 + - - +
192D SER* 3.7 27.3 + - - +
193D ILE* 4.2 14.5 - - + +
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Residues in contact with GLU 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLU* 4.9 0.4 + - - -
160D LYS* 2.9 19.9 + - - +
161D GLN* 4.0 4.0 - - - +
162D ALA 3.3 0.2 - - - -
163D LYS* 1.3 79.7 - - - +
165D HIS* 1.3 79.1 + - + +
166D LYS* 5.2 1.1 - - - +
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Residues in contact with HIS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D THR* 4.3 11.3 + - + +
117D LEU* 6.2 0.9 - - + -
143D VAL* 3.7 44.9 - - + +
161D GLN* 2.9 38.4 + - + +
164D GLU* 1.3 92.5 + - + +
166D LYS* 1.3 73.5 + - - +
167D PRO* 3.3 8.1 - - + +
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Residues in contact with LYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ASN* 2.8 44.7 + - - +
142A ILE 2.9 27.3 + - - +
143A VAL* 4.1 5.8 - - + +
165A HIS* 5.0 11.9 - - + +
115D THR* 4.7 3.1 - - - -
162D ALA 2.8 15.4 + - - -
163D LYS 4.1 4.2 + - - +
164D GLU 3.5 1.7 - - - +
165D HIS* 1.3 79.3 - - - +
167D PRO* 1.3 73.5 - - - +
168D LYS* 3.8 1.7 + - - -
193D ILE* 2.8 43.1 - - + +
194D GLY 5.3 0.9 - - - -
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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