Contacts of the helix formed by residues 152 - 170 (chain E) in PDB entry 4XCS
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 SER 152 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E PHE* 4.8 0.7 - - - -
150E GLY 3.7 1.2 + - - -
151E ARG* 1.3 72.9 - - - +
153E VAL* 1.3 63.7 + - - +
154E ASP* 3.5 7.4 + - - +
155E GLU* 2.9 45.6 + - - +
156E THR* 3.0 22.8 + - - -
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Residues in contact with VAL 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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58E ALA* 3.7 38.6 - - + +
59E PHE* 3.8 27.8 - - + +
62E ARG* 3.6 39.9 - - + +
66E PHE* 3.8 16.6 - - + -
151E ARG 3.7 2.5 + - - +
152E SER* 1.3 68.9 - - - +
154E ASP* 1.3 65.6 + - - +
156E THR* 3.0 3.1 + - - -
157E LEU* 2.9 32.5 + - + +
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Residues in contact with ASP 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ARG* 2.9 37.3 + - - +
152E SER* 3.3 6.0 + - - +
153E VAL* 1.3 78.2 - - - +
155E GLU* 1.3 64.5 + - - +
157E LEU* 3.2 9.0 + - - +
158E ARG* 3.0 49.1 + - - +
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Residues in contact with GLU 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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151E ARG* 6.1 0.7 - - - +
152E SER* 2.9 32.8 + - - +
154E ASP* 1.3 78.1 - - - +
156E THR* 1.3 58.0 + - - +
158E ARG* 3.4 27.1 + - - +
159E LEU* 3.0 27.5 + - - +
155F GLU* 3.3 41.0 - - + +
158F ARG* 4.3 11.6 + - - +
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Residues in contact with THR 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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40E VAL* 4.0 29.4 - - + -
59E PHE* 3.7 22.5 - - + -
66E PHE* 4.2 7.2 - - + -
130E LEU* 4.5 14.1 - - + +
132E ILE* 4.6 7.0 - - + -
151E ARG* 4.1 13.3 - - - +
152E SER 3.0 12.8 + - - -
153E VAL 3.0 8.7 + - - -
155E GLU* 1.3 78.3 - - - +
157E LEU* 1.3 62.7 + - - +
159E LEU* 3.2 8.1 + - + +
160E VAL* 3.0 22.7 + - - +
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Residues in contact with LEU 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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62E ARG* 3.4 29.6 - - - +
65E GLU* 3.6 25.6 - - + +
66E PHE* 3.5 42.1 - - + -
69E LEU* 3.7 18.2 - - + +
153E VAL* 2.9 22.1 + - + +
154E ASP* 3.5 8.3 - - - +
156E THR* 1.3 77.9 - - - +
158E ARG* 1.3 57.5 + - + +
160E VAL* 3.2 4.8 + - - +
161E GLN* 2.9 40.4 + - - +
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Residues in contact with ARG 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 ASP* 3.0 41.4 + - - +
155E GLU* 3.5 38.6 - - - +
157E LEU* 1.3 76.2 - - - +
159E LEU* 1.3 58.1 + - - +
161E GLN* 3.3 15.1 + - - +
162E ALA* 2.8 30.5 + - - +
155F GLU* 4.2 9.9 + - - +
158F ARG* 5.3 5.5 - - - +
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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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130E LEU* 4.5 8.7 - - + -
132E ILE* 3.8 26.0 - - + -
141E GLN* 3.3 35.4 - - - +
155E GLU 3.0 14.1 + - - +
156E THR* 3.4 11.9 - - - +
158E ARG* 1.3 78.8 - - - +
160E VAL* 1.3 63.1 + - - +
162E ALA* 3.1 5.7 + - - +
163E PHE* 2.9 51.0 + - + -
145F ASN* 5.0 0.4 - - - +
147F LEU* 3.7 18.8 - - + -
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Residues in contact with VAL 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E TYR* 4.3 12.8 - - + -
40E VAL* 3.8 27.4 - - + -
66E PHE* 4.4 5.2 - - + -
69E LEU* 4.2 13.9 - - + -
71E CYS* 4.3 15.0 - - + -
132E ILE* 4.4 14.1 - - + -
156E THR 3.0 15.1 + - - +
157E LEU 3.6 6.7 - - - +
159E LEU* 1.3 75.7 - - - +
161E GLN* 1.3 63.0 + - - +
163E PHE* 3.1 10.3 + - - +
164E GLN* 3.0 45.9 + - - +
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Residues in contact with GLN 161 (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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69E LEU* 3.8 30.4 - - + +
157E LEU* 2.9 26.6 + - - +
158E ARG* 3.4 21.6 + - - +
160E VAL* 1.3 75.2 - - - +
162E ALA* 1.3 59.5 + - - +
164E GLN* 3.3 8.9 + - - +
165E PHE* 2.8 34.3 + - - +
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Residues in contact with ALA 162 (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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158E ARG 2.8 17.4 + - - +
159E LEU* 3.5 6.5 - - - +
161E GLN* 1.3 76.8 - - - +
163E PHE* 1.3 60.7 + - - +
165E PHE* 4.0 4.2 - - - +
166E THR* 2.8 31.8 + - - +
147F LEU* 3.8 23.3 - - + -
149F VAL* 4.3 13.0 - - + -
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Residues in contact with PHE 163 (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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38E TYR* 3.4 21.3 - + + +
132E ILE* 4.0 21.3 - - + -
140E ARG* 3.6 62.5 + - + -
141E GLN* 3.9 7.2 - - + -
159E LEU* 2.9 49.7 + - + -
160E VAL 3.6 5.8 - - - +
162E ALA* 1.3 76.4 - - - +
164E GLN* 1.3 54.1 + - - +
166E THR* 3.1 4.8 + - - -
167E ASP* 2.7 38.8 + - - +
145F ASN* 4.1 7.6 - - + -
146F ASP* 3.9 4.9 - - - -
147F LEU* 3.7 30.3 - - + -
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Residues in contact with GLN 164 (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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38E TYR* 3.5 42.7 - - + +
69E LEU* 2.8 42.8 + - - +
70E ASN* 4.6 4.2 + - - +
160E VAL* 3.0 24.2 + - - +
161E GLN* 3.8 8.7 - - - +
163E PHE* 1.3 73.1 - - - +
165E PHE* 1.3 69.1 + - - +
167E ASP* 3.1 10.8 + - - +
168E LYS* 3.0 24.5 + - - +
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Residues in contact with PHE 165 (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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161E GLN 2.8 19.1 + - - +
162E ALA* 4.0 4.7 - - - +
164E GLN* 1.3 77.0 - - - +
166E THR* 1.3 59.5 + - + +
168E LYS* 3.1 3.6 + - - -
169E HIS* 2.8 69.8 + + + +
170E GLY 4.9 0.7 - - - -
172E VAL* 3.6 31.9 - - + -
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Residues in contact with THR 166 (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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140E ARG* 5.4 1.6 + - - -
162E ALA 2.8 22.5 + - - +
163E PHE* 3.1 12.8 + - - -
165E PHE* 1.3 73.6 - - + +
167E ASP* 1.3 62.6 + - - +
170E GLY* 2.8 44.1 + - - +
172E VAL* 3.9 13.9 - - + -
147F LEU* 3.7 6.8 - - - +
148F PRO* 3.8 24.0 - - + +
149F VAL* 3.8 24.9 - - + -
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Residues in contact with ASP 167 (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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38E TYR* 2.6 31.9 + - - -
134E ASP* 4.5 2.3 - - - +
135E ASP* 4.3 4.9 - - - +
136E LYS* 5.6 7.7 - - - -
140E ARG* 2.3 30.5 + - - -
163E PHE 2.7 23.2 + - - +
164E GLN* 3.1 12.9 + - - +
166E THR* 1.3 75.8 - - - +
168E LYS* 1.3 60.2 + - + +
170E GLY 4.6 0.5 + - - -
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Residues in contact with LYS 168 (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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164E GLN 3.0 14.2 + - - +
165E PHE* 3.7 7.0 - - - +
167E ASP* 1.3 80.5 - - + +
169E HIS* 1.3 94.8 + - + +
170E GLY 4.0 0.2 + - - -
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Residues in contact with HIS 169 (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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165E PHE* 2.8 65.9 + + + +
168E LYS* 1.3 112.3 + - + +
170E GLY* 1.3 59.6 + - - +
171E GLU 4.0 2.1 + - - +
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Residues in contact with GLY 170 (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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166E THR* 2.8 41.5 + - - +
167E ASP 4.5 0.4 + - - -
168E LYS 3.7 1.2 - - - -
169E HIS* 1.3 78.2 - - - +
171E GLU* 1.3 65.2 + - - -
172E VAL* 3.5 4.5 + - - +
148F PRO* 4.5 2.7 - - - -
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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