Contacts of the helix formed by residues 210 - 222 (chain A) in PDB entry 4GEK
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A SER* 3.3 23.4 + - - -
168A PHE* 5.2 0.2 - - - -
169A GLU* 4.6 20.6 + - - +
209A ASP* 1.3 75.4 - - - +
211A VAL* 1.3 64.6 + - - +
212A GLU* 3.4 18.0 + - - +
213A THR* 3.0 28.7 + - - -
214A HIS* 2.9 26.1 + - - -
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 3.7 41.0 - - + -
167A SER 4.4 1.6 + - - -
168A PHE* 5.3 7.6 - - + -
209A ASP 4.1 0.2 + - - -
210A SER* 1.3 71.9 - - - +
212A GLU* 1.3 65.5 + - + +
214A HIS* 3.2 8.4 + - - +
215A LYS* 2.8 58.2 + - + +
228A LEU* 4.3 24.5 - - + -
231A GLN* 5.0 3.1 - - - +
238A LEU* 4.6 3.8 - - + -
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLU* 4.8 13.3 + - + +
210A SER* 3.4 20.6 - - - +
211A VAL* 1.3 83.7 + - + +
213A THR* 1.3 58.0 + - - +
215A LYS* 3.3 8.9 + - + +
216A ALA* 2.9 30.4 + - - +
215G LYS* 5.7 2.8 + - - -
227G GLU* 5.3 4.7 - - - +
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Residues in contact with THR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ASP* 3.7 22.4 - - + +
210A SER* 3.0 22.5 + - - -
212A GLU* 1.3 78.6 - - - +
214A HIS* 1.3 63.7 + - - +
216A ALA* 3.2 7.3 + - - +
217A ARG* 3.0 47.8 + - + +
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Residues in contact with HIS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 4.3 7.7 - - + +
147A LEU* 5.9 0.6 - - - +
162A LEU* 3.9 15.3 - - + +
164A GLU* 3.5 41.2 + - + +
166A PHE* 3.7 24.7 - + - -
209A ASP* 3.6 32.9 + - + +
210A SER 2.9 25.1 + - - -
211A VAL 3.6 5.4 - - - +
213A THR* 1.3 77.7 - - - +
215A LYS* 1.3 62.4 + - - +
217A ARG* 3.3 15.5 + - - +
218A LEU* 3.0 29.8 + - - +
238A LEU* 4.0 20.6 - - + -
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A VAL* 2.8 43.0 + - + +
212A GLU* 3.7 7.9 - - + +
214A HIS* 1.3 71.6 - - - +
216A ALA* 1.3 58.9 + - - +
218A LEU* 3.3 10.3 + - + +
219A HIS* 2.9 29.5 + - - +
226A SER* 5.4 9.5 - - - +
227A GLU* 3.0 34.9 + - - +
228A LEU* 4.0 12.0 - - - +
238A LEU* 3.7 13.0 - - + -
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLU 2.9 16.6 + - - +
213A THR* 3.6 7.6 - - - +
214A HIS 3.2 0.2 - - - -
215A LYS* 1.3 79.0 - - - +
217A ARG* 1.3 58.2 + - + +
219A HIS* 3.3 6.9 + - - +
220A LYS* 2.9 29.9 + - - +
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Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 4.5 2.8 - - - +
140A PRO* 4.2 13.7 + - - +
143A ARG* 3.9 27.6 - - - +
144A GLN* 3.0 46.6 + - - +
147A LEU* 3.7 24.5 - - + +
209A ASP* 2.9 42.6 + - - -
213A THR* 3.0 32.3 + - + +
214A HIS* 3.7 19.6 + - - +
216A ALA* 1.3 76.9 - - + +
218A LEU* 1.3 57.4 + - - +
220A LYS* 3.3 1.1 + - - -
221A ALA* 2.9 25.6 + - - +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 4.3 10.5 - - + -
160A LEU* 3.7 29.6 - - + -
162A LEU* 4.2 20.2 - - + -
214A HIS 3.0 21.1 + - - +
215A LYS* 3.7 4.5 - - - +
216A ALA 3.3 0.2 - - - -
217A ARG* 1.3 74.5 - - - +
219A HIS* 1.3 63.8 + - - +
221A ALA* 3.2 7.7 + - - -
222A GLY 3.3 0.3 + - - -
223A PHE* 3.2 41.0 + - + -
226A SER* 3.8 29.8 - - - +
238A LEU* 4.1 30.5 - - + -
240A ALA* 4.2 7.2 - - + -
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Residues in contact with HIS 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS 2.9 14.4 + - - +
216A ALA* 3.5 10.7 + - - +
218A LEU* 1.3 76.8 - - - +
220A LYS* 1.3 60.8 + - - +
222A GLY* 3.0 21.7 + - - -
223A PHE 4.2 15.3 - - - -
224A GLU* 6.0 1.1 - - - -
226A SER* 5.2 0.8 + - - -
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Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLN* 3.8 31.9 - - - +
148A ASP* 4.2 3.3 - - - +
216A ALA 2.9 16.8 + - - +
217A ARG* 3.6 5.8 - - - +
219A HIS* 1.3 81.9 + - - +
221A ALA* 1.3 61.2 + - - +
222A GLY* 3.3 1.0 + - - -
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLN* 3.5 1.5 - - - +
147A LEU* 3.5 31.2 - - + +
148A ASP* 3.2 25.5 - - - +
151A TYR* 3.2 25.6 - - + +
152A GLN* 4.7 2.6 - - - +
217A ARG 2.9 16.5 + - - +
218A LEU 3.6 6.1 - - - +
219A HIS 3.2 0.4 - - - -
220A LYS* 1.3 76.5 - - - +
222A GLY* 1.4 57.3 + - - +
223A PHE* 3.8 4.9 - - + -
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Residues in contact with GLY 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TYR* 3.2 23.1 + - - -
219A HIS 3.0 12.9 + - - -
220A LYS 3.2 1.3 - - - -
221A ALA* 1.4 79.1 - - - +
223A PHE* 1.4 67.5 + - - +
224A GLU* 3.1 15.2 + - - +
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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