Contacts of the strand formed by residues 210 - 221 (chain E) in PDB entry 6CU0
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 GLN 210 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133E LEU 3.6 1.4 - - - +
134E VAL* 3.5 1.8 - - - -
135E VAL* 2.9 38.7 + - + +
167E LEU* 3.9 37.7 - - + +
168E GLN 3.3 19.0 - - - +
169E PRO* 3.4 26.1 + - - +
205E HIS 4.9 1.6 + - - -
206E LEU* 4.4 11.0 - - + +
207E SER* 3.2 51.5 + - - +
208E ALA 3.3 2.0 - - - -
209E GLY* 1.3 76.4 - - - +
211E ARG* 1.3 62.5 + - - +
212E LEU* 3.9 1.7 + - + +
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Residues in contact with ARG 211 (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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127E LYS* 5.8 1.1 - - + +
132E GLU* 3.7 30.6 - - + +
133E LEU 3.2 8.5 - - - +
134E VAL* 4.5 10.5 - - + +
166E HIS 3.9 0.3 - - - +
168E GLN* 2.9 45.2 + - + +
209E GLY 3.7 3.9 + - - +
210E GLN* 1.3 72.7 - - - +
212E LEU* 1.3 63.0 + - - +
213E GLY 3.9 1.0 + - - -
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Residues in contact with LEU 212 (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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132E GLU* 3.3 4.3 - - - -
133E LEU* 2.8 55.2 + - + +
135E VAL* 5.6 5.8 - - + -
165E LEU* 4.0 20.9 - - + -
166E HIS 3.7 4.7 - - - -
167E LEU* 4.3 15.3 - - + -
206E LEU* 6.1 3.1 - - + -
210E GLN* 3.9 3.3 + - + -
211E ARG* 1.3 72.0 - - - +
213E GLY* 1.3 58.7 + - - +
214E VAL* 5.7 0.2 - - - -
235E LEU* 5.3 3.4 - - + +
237E LEU* 5.8 4.3 - - + -
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Residues in contact with GLY 213 (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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109E TRP* 5.9 0.4 - - - -
131E LYS 4.2 13.2 - - - -
132E GLU* 4.7 7.1 + - - +
164E ALA 3.8 0.3 - - - +
165E LEU* 3.5 2.8 - - - -
166E HIS* 2.8 40.1 + - - +
211E ARG 3.9 1.0 + - - -
212E LEU* 1.3 74.7 - - - +
214E VAL* 1.3 64.5 + - - -
215E HIS 4.3 0.2 + - - -
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Residues in contact with VAL 214 (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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106E PRO* 3.4 7.9 - - - +
107E LEU* 3.0 29.1 + - + +
109E TRP* 3.6 38.6 - - + +
131E LYS 4.8 2.0 + - - -
163E LEU* 4.2 38.4 - - + -
164E ALA 3.4 9.9 - - - +
165E LEU* 3.7 20.0 - - + -
213E GLY* 1.3 77.3 - - - -
215E HIS* 1.3 62.1 + - - +
235E LEU* 3.8 16.4 - - + -
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Residues in contact with HIS 215 (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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105E GLY* 5.0 1.8 - - - -
106E PRO* 4.1 12.3 - - + -
162E SER 3.5 1.2 - - - +
163E LEU* 3.5 5.3 - - - -
164E ALA* 2.8 39.4 + - + +
166E HIS* 4.2 20.4 - - + +
214E VAL* 1.3 77.0 - - - +
216E LEU* 1.3 61.3 + - - +
217E HIS* 4.0 0.9 + - - +
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Residues in contact with LEU 216 (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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99E ASN* 5.8 3.4 - - + -
101E LEU 4.5 3.8 - - - +
102E LEU* 4.1 13.0 - - + -
103E ILE 3.8 29.8 - - - +
104E ASP* 3.4 3.5 - - - +
105E GLY 3.1 37.0 + - - +
107E LEU* 5.0 8.0 - - + +
161E VAL* 3.5 29.2 - - + -
162E SER 3.3 4.3 - - - +
163E LEU* 3.5 25.8 - - + -
214E VAL 4.3 0.6 + - - -
215E HIS* 1.3 73.4 - - - +
217E HIS* 1.3 63.6 + - - +
218E THR* 4.8 1.6 - - + -
228E LEU* 4.7 22.0 - - + -
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Residues in contact with HIS 217 (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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104E ASP* 3.4 25.6 + - - +
161E VAL* 3.5 2.6 - - - +
162E SER* 2.7 54.4 + - - +
215E HIS 4.0 1.1 + - - +
216E LEU* 1.3 74.7 + - - +
218E THR* 1.3 83.0 + - - +
219E GLU* 4.5 4.1 + - + +
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Residues in contact with THR 218 (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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102E LEU* 4.1 22.5 - - + +
103E ILE 4.4 1.1 - - - +
104E ASP* 2.9 25.0 + - - +
160E SER 3.4 11.5 + - - -
161E VAL* 4.2 13.7 - - - +
162E SER* 5.4 0.2 - - - -
185E LEU* 5.8 1.0 - - - +
216E LEU* 4.8 4.5 - - + -
217E HIS* 1.3 87.7 + - - +
219E GLU* 1.3 59.8 + - - +
220E ALA* 3.2 16.6 + - - +
223E ARG* 3.3 42.6 + - - +
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Residues in contact with GLU 219 (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 SER 4.0 0.9 - - - +
159E GLY* 3.7 8.2 - - - -
160E SER* 3.0 41.7 + - - +
185E LEU* 5.8 0.5 - - - +
217E HIS* 4.5 6.7 - - + +
218E THR* 1.3 68.2 + - - +
220E ALA* 1.3 62.9 + - - +
221E ARG* 3.5 2.8 + - - +
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Residues in contact with ALA 220 (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 SER 4.9 0.2 - - - -
218E THR* 3.2 8.3 + - - -
219E GLU* 1.3 70.9 - - - +
221E ARG* 1.3 60.9 + - - +
222E ALA 3.8 1.6 - - - +
223E ARG* 3.1 57.2 - - + +
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Residues in contact with ARG 221 (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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190C SER* 5.0 18.4 + - - -
191C GLU* 5.4 4.2 - - - +
157E GLY* 3.5 0.9 - - - -
158E SER* 3.1 55.0 + - - +
159E GLY* 5.3 1.3 - - - -
219E GLU 3.5 1.2 + - - +
220E ALA* 1.3 72.6 - - - +
222E ALA* 1.3 68.2 + - + +
223E ARG 4.2 0.6 - - - +
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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