Contacts of the helix formed by residues 189 - 199 (chain D) in PDB entry 2E52
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 189 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLN* 3.5 29.6 - - - +
197A LYS* 2.7 27.3 + - - -
101D PHE* 4.7 6.1 - - - +
102D ASN 5.1 0.5 + - - -
103D TYR* 3.6 28.5 + - + +
138D TYR* 2.5 35.3 + - + +
187D SER* 3.0 18.0 + - - +
188D PHE* 1.3 76.5 - - - +
190D GLN* 1.3 69.2 + - + +
191D LEU 3.1 0.2 - - - -
192D TRP* 3.2 11.2 + - - +
193D ASN* 3.1 22.3 + - - +
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Residues in contact with GLN 190 (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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101A PHE* 6.5 0.7 - - + -
138A TYR* 4.6 0.6 + - - -
189A GLU* 3.5 29.3 + - - +
190A GLN* 3.7 19.6 - - - +
138D TYR* 4.9 0.2 + - - -
187D SER* 5.0 2.0 + - - +
188D PHE 3.2 1.0 - - - -
189D GLU* 1.3 82.7 - - + +
191D LEU* 1.3 62.9 + - - +
193D ASN* 2.9 32.6 + - - +
194D PHE 3.2 7.1 + - - -
197D LYS* 3.0 26.2 + - - +
218D TYR* 2.6 36.7 + - + +
222D LEU* 4.1 16.5 - - + +
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Residues in contact with LEU 191 (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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165D LEU* 3.5 11.0 - - + +
167D PHE* 4.1 14.8 - - + -
175D LEU* 4.1 7.4 - - + -
188D PHE* 2.9 15.1 + - + +
190D GLN* 1.3 77.8 - - - +
192D TRP* 1.3 96.7 + - + +
194D PHE* 3.2 19.3 + - + +
215D PHE* 3.8 32.1 - - + -
218D TYR* 4.4 4.5 - - + -
219D PHE* 4.4 3.4 - - + -
222D LEU* 3.6 18.5 - - + +
223D PHE* 3.7 31.2 - - + -
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Residues in contact with TRP 192 (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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75D PHE* 3.7 31.2 - + - -
78D LEU* 4.2 14.8 - - + -
80D LEU* 4.5 5.8 - - + +
103D TYR* 2.9 48.2 + + - -
105D LEU* 3.9 12.3 - - + +
138D TYR* 3.6 34.8 - + + +
139D ALA 4.9 1.2 - - - +
140D VAL* 3.6 20.9 - - + -
163D ASN* 4.1 3.8 - - - +
165D LEU* 3.7 26.0 + - + +
167D PHE* 4.2 13.0 - + - -
188D PHE* 3.5 36.7 + + + +
189D GLU 3.2 6.1 + - - +
191D LEU* 1.3 96.8 - - + +
193D ASN* 1.3 57.1 + - - +
194D PHE 3.3 1.3 + - - -
195D PRO* 3.6 10.6 - - - +
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Residues in contact with ASN 193 (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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138A TYR* 4.5 6.9 + - - -
193A ASN* 6.1 1.4 - - - +
138D TYR* 3.4 21.9 + - + -
163D ASN* 3.1 24.4 + - - -
189D GLU 3.1 14.5 + - - +
190D GLN* 2.9 35.5 + - - +
191D LEU 3.1 0.4 - - - -
192D TRP* 1.3 75.3 - - - +
194D PHE* 1.3 64.3 + - - +
195D PRO* 3.1 5.2 - - - -
196D LYS* 3.2 21.9 + - - +
197D LYS* 3.2 22.5 + - - +
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Residues in contact with PHE 194 (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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165D LEU* 3.8 11.2 - - + -
166D LEU 6.0 0.2 - - - -
190D GLN 3.2 9.5 + - - -
191D LEU 3.2 14.3 + - - +
193D ASN* 1.3 76.6 - - - +
195D PRO* 1.4 65.8 - - + +
197D LYS* 3.1 3.1 + - - +
198D GLN* 2.7 73.7 + - + +
211D PHE* 4.0 29.8 - + - -
214D ASP 4.4 0.2 - - - -
215D PHE* 3.7 45.5 - + + -
218D TYR* 3.4 48.7 - + + -
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Residues in contact with PRO 195 (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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159D SER* 3.4 32.5 - - - +
160D LEU* 3.4 13.7 - - + +
163D ASN* 3.3 13.0 - - - +
164D VAL 3.4 30.1 - - - +
165D LEU* 3.6 8.1 - - + +
166D LEU 5.0 0.2 - - - +
192D TRP 3.6 8.1 - - - +
193D ASN 3.3 5.2 - - - -
194D PHE* 1.4 104.0 - - + +
196D LYS* 1.3 55.0 + - - +
199D SER* 2.8 32.4 + - - -
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Residues in contact with LYS 196 (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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137A ASP* 5.7 1.8 - - - +
196A LYS* 4.2 26.6 - - - +
160D LEU 5.0 2.7 - - - -
163D ASN* 3.0 34.3 + - + +
193D ASN* 3.2 25.7 + - - +
195D PRO* 1.3 74.8 - - - +
197D LYS* 1.3 63.1 + - + +
199D SER* 2.6 27.0 + - - +
200D LYS* 3.6 17.1 + - + +
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Residues in contact with LYS 197 (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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102A ASN* 2.9 31.4 + - - +
103A TYR* 4.0 0.2 - - - -
137A ASP* 3.4 32.5 - - + +
138A TYR* 4.7 1.8 - - - +
189A GLU* 2.7 33.4 + - - +
190D GLN* 3.0 31.0 + - - +
193D ASN* 3.2 18.6 + - - +
194D PHE 3.1 6.8 + - - +
196D LYS* 1.3 77.4 - - + +
198D GLN* 1.3 62.5 + - - +
200D LYS* 3.2 18.7 + - - +
201D LYS* 3.5 16.5 - - - +
218D TYR* 3.7 23.1 + - + +
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Residues in contact with GLN 198 (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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160D LEU* 3.7 18.6 - - + -
194D PHE* 2.7 55.1 + - + +
195D PRO 3.7 3.8 - - - +
197D LYS* 1.3 70.6 - - - +
199D SER* 1.3 63.7 + - - +
201D LYS* 3.1 32.4 + - - +
202D THR* 2.9 32.0 + - - +
211D PHE* 3.9 15.3 - - + +
214D ASP* 3.0 36.5 + - - +
218D TYR* 5.5 0.5 - - - -
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Residues in contact with SER 199 (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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160D LEU* 3.9 31.2 + - - +
195D PRO 2.8 18.8 + - - -
196D LYS* 2.6 27.7 + - - +
198D GLN* 1.3 71.8 - - - +
200D LYS* 1.3 67.6 + - - +
202D THR* 3.3 24.7 + - - +
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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