Contacts of the helix formed by residues 155 - 166 (chain E) in PDB entry 6XAV
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 GLU 155 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149E ARG* 3.8 14.4 - - - +
153E SER* 3.1 14.0 + - - +
154E THR* 1.3 96.2 + - - +
156E ASP* 1.3 59.2 + - - +
157E LEU 3.1 3.5 + - - -
158E THR* 3.6 1.9 + - - -
190E ASN* 2.3 41.5 + - - +
193E GLN* 4.8 10.5 - - - +
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Residues in contact with ASP 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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147E MET 3.8 0.5 - - - +
148E GLU* 3.5 10.2 - - - +
149E ARG* 3.0 49.9 + - - +
150E GLY* 3.2 13.9 + - - -
151E ASN* 4.0 11.1 + - - +
152E GLY* 4.9 2.3 + - - +
153E SER 3.1 14.7 + - - +
155E GLU* 1.3 76.0 - - - +
157E LEU* 1.3 57.5 + - - +
158E THR 3.2 0.9 - - - -
159E ALA* 3.2 20.9 + - - +
160E ARG* 2.9 33.9 + - + +
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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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153E SER 4.0 4.9 + - - +
154E THR* 3.4 34.3 - - - +
155E GLU 3.1 1.4 - - - -
156E ASP* 1.3 78.7 - - - +
158E THR* 1.3 63.0 + - - +
160E ARG* 3.3 31.2 + - - +
161E VAL* 3.1 31.9 + - + +
355E PHE 6.0 2.2 - - - +
356E PRO* 4.9 8.3 - - + -
400E ILE* 6.4 2.0 - - + -
403E LEU* 4.9 18.1 - - + +
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Residues in contact with THR 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 THR 4.9 0.2 + - - -
155E GLU 3.6 1.6 + - - -
156E ASP 3.2 0.8 - - - -
157E LEU* 1.3 80.5 - - - +
159E ALA* 1.3 62.2 + - - +
161E VAL* 3.5 2.3 + - - +
162E LEU* 3.1 25.8 + - + +
187E LEU* 3.9 35.4 - - + +
190E ASN* 3.4 29.7 + - + +
191E ILE* 6.0 1.8 - - + -
355E PHE* 5.6 2.1 - - - +
356E PRO* 4.3 26.4 - - + +
358E ILE* 4.9 3.0 - - + +
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Residues in contact with ALA 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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147E MET* 3.4 32.0 - - + +
148E GLU 4.7 0.2 - - - -
155E GLU 4.4 1.0 + - - -
156E ASP* 3.2 24.4 + - - +
158E THR* 1.3 78.5 - - - +
160E ARG* 1.3 57.8 + - - +
162E LEU* 3.4 6.7 + - - +
163E ASP* 3.0 36.4 + - - +
190E ASN* 4.4 4.4 + - - +
191E ILE* 6.4 1.6 - - + -
194E SER* 3.8 13.0 - - - +
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Residues in contact with ARG 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E GLU* 3.7 20.0 - - + -
156E ASP* 2.9 31.0 + - - +
157E LEU* 3.7 25.7 - - - +
158E THR 3.3 0.2 - - - -
159E ALA* 1.3 76.8 - - - +
161E VAL* 1.3 64.6 + - + +
163E ASP* 3.3 5.4 + - - +
164E LEU* 3.1 29.2 + - - +
403E LEU* 3.4 38.2 + - + +
406E THR* 4.3 3.8 + - - +
407E LYS* 2.5 35.9 + - - +
408E THR 3.3 20.3 + - - -
409E ASN* 2.6 46.3 + - - +
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Residues in contact with VAL 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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157E LEU* 3.1 18.8 + - + +
158E THR 4.0 1.1 - - - +
160E ARG* 1.3 74.5 - - - +
162E LEU* 1.3 57.8 + - - +
164E LEU* 3.4 8.0 + - - +
165E ALA* 2.9 27.7 + - - +
356E PRO* 3.8 24.0 - - + +
358E ILE* 3.9 26.5 - - + -
360E TYR* 4.9 9.4 - - + -
396E MET* 6.0 1.6 - - + -
399E LEU* 3.7 33.9 - - + -
403E LEU* 3.9 15.9 - - + -
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Residues in contact with LEU 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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147E MET* 3.8 23.8 - - + -
158E THR* 3.1 20.0 + - + +
159E ALA* 3.7 6.5 - - - +
160E ARG 3.2 0.2 - - - -
161E VAL* 1.3 77.9 - - - +
163E ASP* 1.3 57.7 + - - +
165E ALA* 4.6 3.8 - - - -
166E SER* 2.8 56.3 + - - +
168E ILE* 3.7 23.3 - - + -
176E ILE* 5.6 0.2 - - + -
187E LEU* 4.8 5.6 - - + -
191E ILE* 4.0 30.5 - - + -
343E LEU* 4.2 22.2 - - + -
358E ILE* 4.6 9.8 - - + +
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Residues in contact with ASP 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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144E ARG* 3.5 24.0 + - - +
145E LEU 4.4 1.6 - - - +
146E ARG* 4.2 2.9 - - + +
147E MET* 3.2 29.7 + - - +
148E GLU* 2.7 38.0 + - + +
159E ALA 3.0 18.3 + - - +
160E ARG* 3.7 5.2 - - - +
161E VAL 3.3 0.2 - - - -
162E LEU* 1.3 77.9 - - - +
164E LEU* 1.3 65.9 + - + +
165E ALA 3.5 0.2 + - - -
167E PRO* 3.3 30.2 - - - +
168E ILE 5.0 0.3 + - - -
380E MET* 3.4 6.9 - - - +
409E ASN* 5.1 2.9 - - - +
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Residues in contact with LEU 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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160E ARG 3.1 16.4 + - - +
161E VAL* 4.0 6.7 - - - +
163E ASP* 1.3 80.4 - - + +
165E ALA* 1.3 59.5 + - - +
360E TYR* 2.9 30.1 + - + +
376E GLU* 5.4 2.2 - - - +
380E MET* 3.8 27.4 - - + +
383E LEU* 4.5 11.7 - - + -
384E ARG* 5.0 1.7 + - - -
399E LEU* 5.3 5.8 - - + -
403E LEU* 4.9 12.1 - - + -
409E ASN* 4.0 32.3 - - + +
412E PHE* 5.1 3.1 - - + -
413E PHE* 3.6 39.5 - - + -
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Residues in contact with ALA 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 VAL 2.9 17.5 + - - +
162E LEU* 4.1 2.9 - - - +
164E LEU* 1.3 79.7 - - - +
166E SER* 1.3 63.0 + - - +
167E PRO* 4.0 6.0 - - - +
343E LEU* 5.1 1.8 - - + -
358E ILE* 4.8 10.3 - - + -
360E TYR* 3.7 25.8 - - + -
363E SER* 4.3 17.5 - - - +
364E GLY* 4.3 5.5 - - - -
365E THR* 4.5 0.2 + - - -
368E GLU* 4.9 3.6 - - - +
380E MET* 5.6 0.5 - - - +
384E ARG* 3.3 22.1 + - - +
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Residues in contact with SER 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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162E LEU* 2.8 35.3 + - - +
165E ALA* 1.3 76.3 - - - +
167E PRO* 1.3 69.0 - - - +
168E ILE* 3.5 4.7 + - - +
341E MET* 4.0 19.9 - - - +
342E GLU 5.8 0.7 - - - -
343E LEU* 3.9 22.6 - - - +
363E SER* 5.1 0.4 - - - -
364E GLY 4.1 12.1 - - - -
365E THR* 3.3 16.2 - - - -
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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