Contacts of the helix formed by residues 197 - 213 (chain A) in PDB entry 5JQE
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 ASN 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A GLY 2.8 26.5 + - - +
178A GLY* 4.0 4.5 - - - -
179A TYR* 4.2 10.9 - - - -
194A GLY* 4.1 11.9 + - - -
196A ASP* 1.3 81.9 - - - +
198A ALA* 1.3 62.0 + - - +
199A GLY 3.1 4.0 + - - -
200A ALA* 2.8 27.3 + - - +
201A LYS* 3.0 27.5 + - - +
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Residues in contact with ALA 198 (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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176A ASP* 3.9 2.2 - - - +
197A ASN* 1.3 75.5 - - - +
199A GLY* 1.3 57.5 + - - +
201A LYS* 3.8 10.8 - - - +
202A ALA* 3.0 28.9 + - - +
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Residues in contact with GLY 199 (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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173A ILE 3.3 10.7 - - - +
176A ASP* 3.3 40.2 + - - +
177A GLY* 4.0 2.7 - - - -
178A GLY 4.2 2.0 - - - -
197A ASN* 3.1 6.6 + - - -
198A ALA* 1.3 75.8 - - - +
200A ALA* 1.3 65.2 + - - +
202A ALA 3.3 0.5 + - - -
203A GLY 3.0 19.6 + - - -
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Residues in contact with ALA 200 (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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170A TRP* 5.3 0.2 - - + -
173A ILE* 3.5 27.9 + - + +
178A GLY* 4.1 6.6 - - - +
195A VAL* 4.0 24.9 - - - +
197A ASN* 2.8 19.8 + - - +
199A GLY* 1.3 72.7 - - - -
201A LYS* 1.3 57.2 + - - +
204A LEU* 3.1 29.5 + - - +
373A LEU* 3.6 19.3 - - + +
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Residues in contact with LYS 201 (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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196A ASP* 3.2 28.5 + - - -
197A ASN* 3.0 26.3 + - - +
198A ALA* 3.9 8.3 - - + +
199A GLY 3.1 0.6 - - - -
200A ALA* 1.3 74.7 - - - +
202A ALA* 1.3 57.2 + - - +
204A LEU* 3.2 1.7 + - - +
205A THR* 2.6 39.8 + - - +
369A VAL* 4.3 14.1 - - + +
370A ASP* 3.4 40.1 + - - +
373A LEU* 3.9 15.7 - - + -
374A ALA* 6.2 0.6 - - - +
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Residues in contact with ALA 202 (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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176A ASP* 3.2 26.7 - - - +
198A ALA 3.0 13.8 + - - +
199A GLY 3.8 1.1 - - - +
201A LYS* 1.3 75.7 - - - +
203A GLY* 1.3 62.4 + - - +
205A THR* 4.0 5.5 - - - -
206A PHE* 3.3 15.9 + - - +
262A PHE* 3.2 21.0 - - + -
263A LYS* 3.7 18.6 - - - +
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Residues in contact with GLY 203 (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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172A LEU* 3.5 33.6 - - - +
173A ILE* 4.1 7.2 - - - -
199A GLY 3.0 14.7 + - - -
202A ALA* 1.3 77.5 - - - +
204A LEU* 1.3 61.6 + - - +
206A PHE* 3.6 1.6 + - - +
207A LEU* 3.1 21.5 + - - +
262A PHE* 3.6 12.5 - - - -
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Residues in contact with LEU 204 (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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173A ILE* 3.7 19.2 - - + +
200A ALA 3.1 19.4 + - - +
201A LYS* 3.9 2.9 - - - +
203A GLY* 1.3 74.5 - - - +
205A THR* 1.3 55.7 + - - +
207A LEU* 3.0 28.0 + - + -
208A VAL* 2.6 52.6 + - + +
358A ALA 4.1 5.4 - - - +
359A VAL* 4.2 17.3 - - + +
362A ALA* 3.6 20.2 - - + -
363A ALA* 6.0 0.4 - - + -
369A VAL* 4.3 7.9 - - + -
373A LEU* 3.3 31.6 - - + -
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Residues in contact with THR 205 (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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201A LYS* 2.6 25.5 + - - +
202A ALA* 4.0 5.6 - - - -
204A LEU* 1.3 76.7 - - - +
206A PHE* 1.3 57.3 + - - +
208A VAL* 3.7 4.0 - - + +
209A ASP* 2.9 34.3 + - + +
369A VAL* 3.4 29.1 - - + +
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Residues in contact with PHE 206 (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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141A TRP* 3.5 51.1 - + + -
142A GLU* 3.9 17.9 - - + -
145A PRO* 4.2 20.0 - - + -
172A LEU* 4.2 13.9 - - + -
202A ALA 3.3 7.4 + - - +
203A GLY 3.9 3.4 - - - +
204A LEU 3.2 0.4 - - - -
205A THR* 1.3 77.6 - - - +
207A LEU* 1.3 60.1 + - - +
209A ASP* 2.6 35.2 - - - +
210A LEU* 3.2 22.9 - - + +
262A PHE* 3.6 34.3 - + + -
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Residues in contact with LEU 207 (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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141A TRP* 5.8 0.2 - - + -
161A PHE* 4.5 12.1 - - + -
163A LEU* 4.7 3.4 - - + -
169A THR* 3.9 35.4 - - + +
172A LEU* 3.7 20.1 - - + +
173A ILE* 4.7 1.3 - - + -
203A GLY 3.1 14.3 + - - +
204A LEU* 3.0 28.1 + - + +
206A PHE* 1.3 75.0 - - - +
208A VAL* 1.3 65.4 + - + +
210A LEU* 3.3 17.4 + - + +
211A ILE* 3.4 21.3 + - + +
216A MET* 3.5 31.2 - - + -
359A VAL* 5.3 4.7 - - + -
363A ALA* 5.8 3.6 - - + -
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Residues in contact with VAL 208 (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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204A LEU* 2.6 29.8 + - + +
205A THR* 3.7 8.7 - - + +
207A LEU* 1.3 72.1 - - - +
209A ASP* 1.3 58.9 + - + +
211A ILE* 3.3 7.2 + - - +
212A LYS* 2.9 54.1 + - + +
362A ALA* 3.5 41.5 - - + +
363A ALA* 3.9 10.4 - - + +
369A VAL* 3.9 13.9 - - + -
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Residues in contact with ASP 209 (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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205A THR* 2.9 21.4 + - + +
206A PHE* 2.6 31.3 - - - +
208A VAL* 1.3 74.9 - - + +
210A LEU* 1.3 80.2 + - - +
211A ILE 3.0 1.8 - - - -
212A LYS* 3.2 11.4 - - + +
213A ASN* 2.6 49.3 + - - +
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Residues in contact with LEU 210 (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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141A TRP* 4.2 20.4 - - + -
144A ILE* 5.2 6.1 - - + -
145A PRO* 3.7 33.4 - - + -
159A LEU* 5.3 1.3 - - + -
172A LEU* 5.2 0.2 - - + -
206A PHE* 3.2 33.9 - - + +
207A LEU* 3.3 13.3 + - + +
209A ASP* 1.3 85.5 + - - +
211A ILE* 1.3 62.7 + - - +
213A ASN* 3.3 1.9 + - - +
214A LYS 3.1 3.6 + - - -
215A HIS* 3.0 42.9 + - + -
216A MET* 3.7 31.1 + - + -
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Residues in contact with ILE 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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163A LEU* 3.6 25.1 - - + -
207A LEU* 3.6 17.9 - - + +
208A VAL 3.3 7.1 + - - +
209A ASP 3.0 0.2 - - - -
210A LEU* 1.3 76.2 - - - +
212A LYS* 1.3 65.9 + - + +
214A LYS* 3.2 12.5 + - - +
216A MET* 3.4 31.9 - - + +
218A ALA* 3.2 30.5 - - + +
363A ALA* 3.6 39.0 - - + +
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Residues in contact with LYS 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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208A VAL* 2.9 42.1 + - + +
209A ASP* 2.8 15.8 + - + +
211A ILE* 1.3 77.5 - - + +
213A ASN* 1.3 66.8 + - - +
214A LYS* 3.6 4.5 + - - +
362A ALA 4.0 2.6 + - - -
363A ALA 4.8 6.3 + - - +
364A SER 5.7 0.7 - - - -
365A GLY* 3.8 28.9 - - - +
367A GLN 5.3 2.2 + - - -
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Residues in contact with ASN 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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145A PRO* 5.9 3.0 - - - +
149A LYS* 5.9 1.0 + - - -
209A ASP* 2.6 33.8 + - - +
210A LEU* 5.0 1.8 - - - +
212A LYS* 1.3 81.1 - - - +
214A LYS* 1.3 67.4 + - - +
215A HIS* 2.9 37.8 + - + +
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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