Contacts of the helix formed by residues 201 - 214 (chain A) in PDB entry 1D1T
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 GLY 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLY 3.3 6.5 + - - -
200A LEU* 1.3 76.6 - - - +
202A GLY* 1.3 65.3 + - - -
203A VAL 3.4 2.5 - - - -
204A GLY 4.0 0.8 - - - +
205A LEU* 3.0 27.8 + - - +
228A LYS* 4.8 2.0 - - - -
268A VAL 5.3 0.4 + - - -
368A ILE* 4.3 10.3 - - - -
1377A NAD 3.2 33.9 + - - -
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Residues in contact with GLY 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLY* 5.0 2.4 - - - -
201A GLY* 1.3 73.8 - - - +
203A VAL* 1.3 54.7 + - - +
205A LEU* 3.8 0.4 + - - -
206A SER* 2.7 30.5 + - - -
345A LEU* 4.1 7.0 - - - +
368A ILE* 3.7 23.2 - - - +
369A ARG* 4.2 22.6 - - - +
1377A NAD 3.0 13.4 + - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLY* 3.9 15.9 - - - -
178A THR* 3.6 25.8 - - + -
179A GLY* 3.6 12.8 - - - +
202A GLY* 1.3 70.7 - - - -
204A GLY* 1.3 65.6 + - - +
206A SER* 3.0 7.8 + - - -
207A VAL* 2.9 19.9 + - - +
268A VAL* 3.3 24.0 - - + -
292A VAL* 3.9 2.9 - - + -
369A ARG* 4.4 1.3 - - - +
1377A NAD 2.8 58.3 + - + +
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Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 3.9 11.4 - - - -
199A GLY 3.2 26.4 + - - -
200A LEU* 5.1 0.2 - - - -
201A GLY 3.5 4.2 + - - +
202A GLY 3.4 0.2 - - - -
203A VAL* 1.3 77.0 - - - +
205A LEU* 1.3 62.9 + - - +
207A VAL* 2.8 15.9 + - - +
208A ILE* 2.9 17.0 + - - +
268A VAL* 3.6 12.4 + - - +
1377A NAD 4.3 0.8 + - - -
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Residues in contact with LEU 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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199A GLY 4.5 0.4 + - - -
200A LEU* 3.5 18.8 - - + +
201A GLY 3.0 22.2 + - - +
204A GLY* 1.3 74.5 - - - +
206A SER* 1.3 56.5 + - - +
208A ILE* 3.4 11.3 + - + +
209A MET* 3.0 29.5 + - - +
228A LYS 5.0 0.2 - - - +
231A LYS* 3.5 26.2 - - + -
232A ALA* 3.6 38.4 - - + +
235A VAL* 3.8 11.7 - - + +
345A LEU* 3.6 19.5 - - + -
368A ILE* 3.7 24.7 - - + -
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Residues in contact with SER 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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175A GLY 3.7 1.7 + - - -
176A PHE* 3.4 43.9 + - - -
179A GLY* 3.6 4.0 - - - -
180A TYR* 3.5 11.3 - - - +
202A GLY 2.7 21.9 + - - -
203A VAL 3.0 7.8 + - - -
205A LEU* 1.3 76.2 - - - +
207A VAL* 1.3 60.2 + - - +
209A MET* 3.2 13.7 + - - +
210A GLY 2.9 23.0 + - - -
345A LEU* 4.0 9.6 - - - +
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY* 3.1 30.9 - - - +
182A ALA* 4.0 11.0 - - + -
183A ALA* 3.7 1.4 - - + +
197A VAL* 3.6 23.6 - - + -
203A VAL* 2.9 14.1 + - + +
204A GLY 2.8 8.8 + - - +
206A SER* 1.3 74.3 - - - +
208A ILE* 1.3 53.2 + - - +
210A GLY* 2.8 4.7 + - - -
211A CYS* 2.7 39.0 + - - -
266A PHE* 3.7 28.7 - - + -
268A VAL* 4.1 19.5 - - + -
292A VAL* 4.8 1.1 - - + -
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Residues in contact with ILE 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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197A VAL* 3.7 20.4 - - + -
200A LEU* 3.8 28.9 - - + -
204A GLY 2.9 16.3 + - - +
205A LEU* 3.4 10.8 - - + +
207A VAL* 1.3 76.1 - - - +
209A MET* 1.3 56.9 + - - +
211A CYS* 3.2 7.6 + - - +
212A LYS* 2.8 27.5 + - - +
219A ILE* 3.8 12.6 - - + +
221A GLY* 4.9 2.0 - - - -
232A ALA* 4.2 14.8 - - + -
235A VAL* 3.6 22.2 - - + -
236A GLY* 3.8 7.0 - - - -
237A ALA* 3.6 26.9 - - + +
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Residues in contact with MET 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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176A PHE* 3.6 22.9 - - + -
180A TYR* 4.0 9.1 - - + -
205A LEU 3.0 19.0 + - - +
206A SER* 3.2 9.6 + - - +
208A ILE* 1.3 77.4 - - - +
210A GLY* 1.3 57.8 + - - +
212A LYS* 3.4 9.3 + - + +
213A SER* 3.0 27.5 + - - -
235A VAL* 4.0 26.7 - - + +
340A PHE* 3.6 21.8 - - + -
341A ASP 3.6 27.1 - - - +
342A LEU* 5.0 0.2 - - + -
344A GLN* 5.9 0.2 - - - -
345A LEU* 4.2 25.1 - - + -
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Residues in contact with GLY 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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180A TYR* 3.6 24.2 - - - -
183A ALA* 3.5 15.0 - - - -
184A VAL* 3.5 8.7 - - - +
206A SER 2.9 8.9 + - - -
207A VAL 2.8 9.0 + - - -
209A MET* 1.3 75.1 - - - +
211A CYS* 1.3 56.9 + - - -
213A SER* 2.9 18.8 + - - -
214A ALA* 3.0 12.3 + - - +
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Residues in contact with CYS 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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183A ALA* 3.9 7.6 - - - -
189A VAL* 4.4 1.8 - - - -
195A CYS* 3.7 25.6 - - - -
197A VAL* 4.7 3.1 - - - -
207A VAL* 2.7 28.1 + - - -
208A ILE* 3.7 4.7 - - - +
210A GLY* 1.3 72.7 - - - +
212A LYS* 1.3 59.6 + - - +
214A ALA* 3.2 12.2 + - - +
215A GLY 3.3 0.2 + - - -
216A ALA* 3.0 27.0 + - - +
219A ILE* 3.7 19.7 - - + -
266A PHE* 3.7 31.2 - - - -
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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 ILE 2.8 17.6 + - - +
209A MET* 3.6 7.0 - - + +
210A GLY 3.2 0.2 - - - -
211A CYS* 1.3 79.1 - - - +
213A SER* 1.3 60.9 + - - +
215A GLY* 3.4 10.6 + - - -
216A ALA 4.8 3.1 - - - +
219A ILE* 3.7 13.0 - - + +
234A ALA 5.3 2.8 + - - -
235A VAL* 3.4 24.5 + - - +
236A GLY* 4.1 11.0 - - - +
994A CAC 5.2 9.0 - - + +
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Residues in contact with SER 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TYR* 3.7 21.0 + - - -
184A VAL* 3.6 14.8 - - - +
209A MET 3.0 14.0 + - - -
210A GLY* 2.9 16.3 + - - -
212A LYS* 1.3 74.0 - - - +
214A ALA* 1.3 60.1 + - - +
215A GLY 3.0 7.1 + - - -
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Residues in contact with ALA 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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184A VAL* 4.6 10.5 - - + -
189A VAL* 3.5 39.1 - - + +
191A PRO* 3.5 26.9 - - - +
210A GLY 3.0 13.8 + - - +
211A CYS 3.2 10.0 + - - +
213A SER* 1.3 77.5 + - - +
215A GLY* 1.3 59.8 + - - +
216A ALA 3.5 0.2 - - - -
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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