Contacts of the helix formed by residues 205 - 226 (chain A) in PDB entry 1D7K
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 PRO 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A CYS* 3.9 9.8 - - - -
203A THR 3.8 6.7 - - - +
204A ASP* 1.3 90.5 - - - +
206A GLU* 1.3 60.2 + - - +
207A THR 3.2 0.2 - - - -
208A PHE* 3.1 25.2 + - + +
209A VAL 3.7 1.0 + - - -
246A LEU* 3.9 22.2 - - + -
250A GLU* 4.3 14.6 - - + +
251A ILE* 4.3 19.3 - - + -
254A VAL* 3.4 36.4 - - + +
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Residues in contact with GLU 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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204A ASP* 3.1 26.1 + - - +
205A PRO* 1.3 74.8 - - + +
207A THR* 1.3 57.2 + - - +
209A VAL* 2.7 50.8 + - - +
210A GLN* 2.8 14.5 + - - +
254A VAL* 4.3 14.6 - - - +
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Residues in contact with THR 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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157A THR* 5.0 1.8 - - - -
158A ASP* 3.5 36.4 + - + +
159A ASP* 3.7 23.8 + - + +
198A VAL* 4.0 25.6 - - + -
204A ASP* 2.8 24.2 + - - +
206A GLU* 1.3 76.7 - - - +
208A PHE* 1.3 55.4 + - - +
210A GLN* 3.4 6.9 + - - +
211A ALA* 3.0 26.7 + - - +
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Residues in contact with PHE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 4.2 10.3 - + - -
198A VAL* 3.8 29.6 - - + -
199A GLY 5.4 0.9 - - - -
202A CYS* 3.9 26.7 - - + -
205A PRO* 3.1 16.1 + - + +
207A THR* 1.3 72.4 - - - +
209A VAL* 1.4 66.5 + - + +
211A ALA* 3.1 4.9 + - - +
212A ILE* 2.9 34.3 + - + +
234A ILE* 4.1 14.6 - - + -
236A GLY 4.3 9.2 - - - -
237A GLY* 5.6 3.8 - - - -
238A PHE* 4.0 26.0 - + - -
251A ILE* 3.9 22.4 - - + -
254A VAL* 4.9 1.1 - - + -
255A ILE* 3.6 36.8 - - + -
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Residues in contact with VAL 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 PRO 4.2 4.0 - - - +
206A GLU* 2.7 42.4 + - - +
208A PHE* 1.4 80.1 - - + +
210A GLN* 1.3 64.8 + - - +
212A ILE* 3.8 1.7 - - - +
213A SER* 3.1 21.3 + - - -
254A VAL* 4.1 26.2 - - + +
255A ILE* 5.7 0.2 - - - -
258A ALA* 4.2 20.6 - - + -
262A TYR* 4.6 13.4 - - + +
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Residues in contact with GLN 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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158A ASP* 4.9 18.8 - - - +
206A GLU 2.8 10.7 + - - +
207A THR* 3.8 9.9 - - + +
208A PHE 3.4 0.2 - - - -
209A VAL* 1.3 81.7 - - - +
211A ALA* 1.3 57.4 + - - +
213A SER* 3.5 10.4 + - - -
214A ASP* 3.0 56.1 + - - +
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Residues in contact with ALA 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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155A ILE* 3.9 4.7 - - + +
156A ALA 5.7 2.5 - - - +
157A THR* 4.3 13.0 - - + +
196A PHE* 3.5 43.3 - - + -
198A VAL* 4.9 0.4 - - + -
207A THR 3.0 17.3 + - - +
208A PHE* 3.1 2.2 + - - +
210A GLN* 1.3 75.1 - - - +
212A ILE* 1.3 61.5 + - - +
214A ASP* 3.4 8.6 + - - +
215A ALA* 2.8 30.0 + - - +
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Residues in contact with ILE 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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196A PHE* 3.8 22.0 - - + -
208A PHE* 2.9 26.1 + - + +
209A VAL* 3.8 4.0 - - - +
211A ALA* 1.3 76.2 - - - +
213A SER* 1.3 60.9 + - - +
215A ALA* 3.1 5.5 + - - +
216A ARG* 3.0 19.2 + - - +
232A LEU* 5.0 1.6 - - + -
234A ILE* 4.6 4.0 - - + -
255A ILE* 4.4 18.8 - - + +
258A ALA* 4.0 34.3 - - + +
259A LEU* 3.8 26.0 - - + -
262A TYR* 4.1 6.7 - - + -
263A PHE* 3.6 24.7 - - + -
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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
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209A VAL* 3.1 17.7 + - - -
210A GLN* 3.6 12.5 + - - -
212A ILE* 1.3 77.8 - - - +
214A ASP* 1.3 63.9 + - - +
216A ARG* 3.3 5.4 + - - +
217A CYS* 3.1 19.8 + - - +
262A TYR* 3.7 38.8 + - - -
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Residues in contact with ASP 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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155A ILE* 3.7 15.5 - - + -
156A ALA 4.6 9.4 - - - +
174A LEU* 4.2 26.7 - - + +
210A GLN* 3.0 44.6 + - - +
211A ALA* 3.6 7.3 - - - +
213A SER* 1.3 73.8 + - - +
215A ALA* 1.3 67.4 + - - +
217A CYS* 3.0 10.2 + - - +
218A VAL* 3.0 24.8 + - - +
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Residues in contact with ALA 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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155A ILE* 3.7 8.5 - - + +
194A VAL* 3.8 19.2 - - + +
196A PHE* 4.6 2.9 - - + -
211A ALA 2.8 20.9 + - - +
212A ILE* 3.1 7.4 + - - +
214A ASP* 1.3 72.8 - - - +
216A ARG* 1.4 57.8 + - - +
218A VAL* 3.2 4.1 + - - +
219A PHE* 3.0 30.7 + - - -
232A LEU* 3.7 30.1 - - + -
263A PHE* 3.9 3.6 - - + -
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Residues in contact with ARG 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 ILE 3.0 12.9 + - - +
213A SER 3.6 7.4 - - - +
214A ASP 3.2 0.2 - - - -
215A ALA* 1.4 75.8 - - - +
217A CYS* 1.4 62.0 + - - +
219A PHE* 3.3 25.3 + - - +
220A ASP* 3.0 54.4 + - - +
262A TYR* 2.8 53.8 + - + +
263A PHE* 3.4 41.6 - - + +
264A PRO* 5.0 3.0 - - - +
267A SER* 5.1 7.3 + - - -
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Residues in contact with CYS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 4.0 28.3 - - + -
213A SER 3.1 11.4 + - - +
214A ASP* 3.0 13.4 + - - +
216A ARG* 1.4 76.6 - - - +
218A VAL* 1.3 62.0 + - - +
220A ASP* 3.3 9.5 + - - +
221A MET* 3.0 33.0 + - - +
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Residues in contact with VAL 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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153A LEU* 4.3 15.0 - - + -
155A ILE* 3.9 19.5 - - + -
174A LEU* 3.8 19.7 - - + -
177A SER* 4.1 4.0 - - - +
181A LEU* 4.1 9.0 - - + -
194A VAL* 3.5 23.3 - - + -
214A ASP 3.0 14.4 + - - +
215A ALA 3.2 6.0 + - - +
217A CYS* 1.3 73.6 - - - +
219A PHE* 1.3 68.3 + - - +
221A MET* 3.2 28.1 + - + -
222A GLY* 2.8 20.8 + - - -
229A MET* 3.9 4.3 - - + +
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Residues in contact with PHE 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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193A GLY* 4.2 2.7 - - - -
194A VAL* 3.9 23.1 - - + -
215A ALA 3.0 18.9 + - - +
216A ARG* 3.3 28.7 + - - +
218A VAL* 1.3 78.4 - - - +
220A ASP* 1.3 62.1 + - - +
222A GLY* 3.2 2.4 + - - -
223A ALA* 3.1 19.4 + - - +
229A MET* 3.7 44.7 - - + +
230A TYR* 4.1 5.2 - - - -
231A LEU 3.5 36.8 - - - -
232A LEU* 4.2 6.3 - - + -
263A PHE* 3.6 33.2 - + - -
269A VAL* 4.3 5.2 - - + -
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Residues in contact with ASP 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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216A ARG* 3.0 46.2 + - - +
217A CYS* 3.7 8.8 - - - +
218A VAL 3.2 0.4 - - - -
219A PHE* 1.3 74.0 - - - +
221A MET* 1.3 63.6 + - - +
223A ALA* 3.3 8.9 + - - +
224A GLU* 3.1 28.9 + - + +
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Residues in contact with MET 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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174A LEU* 3.8 13.5 - - - +
177A SER* 3.6 12.1 - - - -
178A ARG* 3.0 61.0 + - - +
181A LEU* 3.6 15.5 - - + -
217A CYS* 3.0 27.2 + - - +
218A VAL* 3.3 45.8 - - + -
220A ASP* 1.3 75.2 - - - +
222A GLY* 1.3 63.4 + - - +
224A GLU* 3.1 18.2 + - - +
225A VAL* 3.3 4.7 + - - +
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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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181A LEU* 3.7 6.4 - - - +
218A VAL 2.8 11.5 + - - -
219A PHE 3.5 2.0 - - - -
221A MET* 1.3 76.6 - - - +
223A ALA* 1.3 60.8 + - - +
225A VAL* 3.1 5.8 + - - +
226A GLY 3.0 17.2 + - - -
227A PHE* 3.0 18.2 + - - -
229A MET* 3.3 29.8 - - - -
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Residues in contact with ALA 223 (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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219A PHE 3.1 11.9 + - - +
220A ASP* 3.6 12.1 - - - +
221A MET 3.3 0.2 - - - -
222A GLY* 1.3 74.1 - - - +
224A GLU* 1.3 64.2 + - - +
226A GLY* 3.1 11.6 + - - -
227A PHE 3.6 15.3 + - - +
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Residues in contact with GLU 224 (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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178A ARG* 3.4 26.1 + - - +
220A ASP* 3.1 16.9 + - - +
221A MET* 3.1 19.6 + - - +
223A ALA* 1.3 80.5 - - + +
225A VAL* 1.3 59.7 + - - +
226A GLY 3.7 0.2 + - - -
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Residues in contact with VAL 225 (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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178A ARG* 3.7 26.7 - - - +
181A LEU* 4.4 19.7 - - + +
182A GLU* 4.3 17.3 - - + +
185A LYS* 3.7 25.9 - - + +
221A MET 3.3 7.5 + - - +
222A GLY 3.1 10.9 + - - +
224A GLU* 1.3 76.9 - - - +
226A GLY* 1.3 56.4 - - - +
227A PHE* 4.2 20.4 - - + -
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Residues in contact with GLY 226 (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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185A LYS* 3.1 21.7 + - - -
222A GLY 3.0 2.4 + - - -
223A ALA 3.1 11.4 + - - -
224A GLU 3.4 0.4 + - - -
225A VAL* 1.3 77.9 - - - +
227A PHE* 1.3 62.2 + - - +
228A SER 3.9 1.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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