Contacts of the helix formed by residues 205 - 222 (chain A) in PDB entry 6XYY
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 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLY 3.4 8.8 + - - -
187A PHE* 3.8 14.8 + - - +
204A GLY* 1.3 71.2 - - - +
206A VAL* 1.3 54.2 + - - +
207A GLY 3.0 4.0 - - - -
208A LEU* 2.6 43.4 + - + +
209A TRP* 3.1 14.5 + - + -
334A PRO* 3.4 9.9 - - - +
335A THR* 2.7 56.4 + - - -
337A ASP* 2.8 29.4 + - - +
340A PHE* 4.5 4.0 - - + -
341A LEU* 4.1 4.0 - - - +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 3.5 24.2 - - - +
45A ARG 3.5 20.2 - - - +
46A LYS* 3.6 11.9 - - + +
181A ARG* 3.6 17.9 + - - +
185A PHE 3.6 21.1 - - - +
186A GLY* 2.8 17.0 + - - +
188A LEU 6.0 1.1 - - - +
203A PRO* 3.8 20.9 - - + -
204A GLY* 4.0 3.8 - - - +
205A ASN* 1.3 77.4 - - - +
207A GLY* 1.3 56.0 + - - +
209A TRP* 3.1 10.3 + - + +
210A ASP* 2.8 33.1 + - - +
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Residues in contact with GLY 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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180A TYR* 3.6 6.0 - - - +
181A ARG 3.6 24.7 - - - -
186A GLY* 3.0 12.8 + - - -
187A PHE* 4.3 4.5 - - - -
206A VAL* 1.3 80.7 - - - +
208A LEU* 1.3 62.1 + - - +
210A ASP* 3.4 13.0 - - - +
211A GLN* 3.2 26.2 + - - +
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Residues in contact with LEU 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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152A PHE* 4.5 12.3 - - + -
187A PHE* 4.1 20.6 - - + -
205A ASN* 2.6 31.0 + - + +
207A GLY* 1.3 70.8 - - - +
209A TRP* 1.3 62.1 + - - +
211A GLN* 3.3 25.5 + - - +
212A ALA* 3.0 20.3 + - - +
243A SER* 4.6 4.7 - - - +
246A ALA* 4.5 8.7 - - + -
247A GLN* 3.0 11.6 + - - +
334A PRO* 3.9 13.2 - - + -
340A PHE* 3.7 26.2 - - + -
341A LEU* 3.5 31.9 - - + -
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Residues in contact with TRP 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 4.0 42.1 - - + +
47A PRO* 3.6 19.8 - - + +
203A PRO* 5.8 0.4 - - - +
204A GLY 4.0 10.5 + - - -
205A ASN* 3.1 28.1 + - + +
206A VAL* 3.1 17.5 + - - +
208A LEU* 1.3 73.7 - - - +
210A ASP* 1.3 59.5 + - - +
212A ALA* 3.2 8.7 + - + +
213A LEU* 2.8 30.5 + - - +
252A VAL* 3.5 43.1 - - + -
337A ASP* 4.9 2.6 + - - -
339A ALA* 4.6 9.1 - - + +
340A PHE* 3.8 31.0 - + + +
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Residues in contact with ASP 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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34A TYR* 3.2 27.6 + - - +
47A PRO* 3.2 16.8 - - - +
94A LEU* 3.7 10.7 - - - +
180A TYR* 4.0 6.5 - - + -
181A ARG* 2.7 64.9 + - - +
206A VAL 2.8 18.1 + - - +
207A GLY* 3.4 8.4 - - - +
209A TRP* 1.3 71.3 - - - +
211A GLN* 1.3 57.0 + - - +
213A LEU 3.1 1.9 + - - -
214A ALA* 2.8 26.0 + - - +
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Residues in contact with GLN 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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147A ILE* 3.7 6.4 - - + +
178A PHE* 3.6 23.5 - - + -
180A TYR* 3.4 44.0 - - + -
207A GLY 3.2 14.1 + - - +
208A LEU* 3.3 11.5 + - - +
210A ASP* 1.3 73.7 - - - +
212A ALA* 1.3 54.7 + - - +
214A ALA* 3.1 1.2 + - - +
215A ILE* 2.7 41.5 + - + +
243A SER* 3.3 38.1 + - - -
247A GLN* 3.0 28.7 + - + +
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Residues in contact with ALA 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 LEU 3.0 13.8 + - - +
209A TRP* 3.2 15.2 + - + +
211A GLN* 1.3 75.7 - - - +
213A LEU* 1.3 58.1 + - - +
215A ILE* 3.2 4.6 + - - +
216A ARG* 2.8 37.4 + - - +
247A GLN* 3.7 18.1 - - - +
252A VAL* 5.3 1.8 - - + -
253A THR* 3.8 20.4 - - + -
256A LEU* 6.2 0.2 - - - +
340A PHE* 4.1 8.1 - - + -
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Residues in contact with LEU 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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34A TYR* 3.3 30.1 - - + +
35A ALA* 3.8 18.4 - - + -
47A PRO* 4.0 20.6 - - + +
49A PRO* 4.3 29.6 - - + -
209A TRP 2.8 17.1 + - - +
210A ASP 3.5 4.0 - - - +
212A ALA* 1.3 77.6 - - - +
214A ALA* 1.3 57.2 + - - +
216A ARG* 3.3 14.6 + - + +
217A TRP* 2.8 28.2 + - + +
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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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34A TYR* 3.5 28.4 - - + -
96A ILE* 3.7 12.8 - - + +
178A PHE* 3.7 31.9 - - + -
210A ASP 2.8 13.8 + - - +
211A GLN 3.7 3.6 - - - +
213A LEU* 1.3 73.3 - - - +
215A ILE* 1.3 62.9 + - - +
217A TRP* 3.3 3.6 + - - +
218A LEU* 3.1 27.9 + - - +
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Residues in contact with ILE 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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145A ILE* 4.4 11.7 - - + -
147A ILE* 4.7 7.2 - - + -
178A PHE* 4.6 4.5 - - + -
211A GLN* 2.7 25.8 + - + +
212A ALA* 3.6 4.7 - - - +
214A ALA* 1.3 70.0 - - - +
216A ARG* 1.3 67.1 + - - +
218A LEU* 3.1 10.1 + - - +
219A LYS* 3.0 21.0 + - + +
232A MET* 4.0 23.0 - - + +
234A LEU* 3.6 38.6 - - + -
247A GLN* 3.8 24.0 - - + +
256A LEU* 5.5 10.3 - - + -
257A VAL* 4.3 10.1 - - + -
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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
----------------------------------------------------------
212A ALA* 2.8 24.4 + - - +
213A LEU* 3.3 15.2 + - + +
215A ILE* 1.3 74.1 - - - +
217A TRP* 1.3 63.2 + - - +
219A LYS* 3.2 8.9 + - + +
220A ASP* 2.9 36.4 + - - +
252A VAL* 4.0 20.4 + - - +
253A THR* 4.5 8.9 - - - +
256A LEU* 3.9 39.9 - - + +
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Residues in contact with TRP 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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9A THR* 3.8 32.5 - - + -
10A SER* 4.0 3.6 + - - -
11A SER* 3.5 21.3 + - - -
32A ILE* 4.0 26.2 - - + -
33A PRO 4.6 6.5 + - - -
34A TYR* 4.3 18.2 - - + +
53A TRP* 5.3 0.4 - + - -
96A ILE* 3.7 32.3 - - + -
98A VAL* 4.7 1.1 - - + -
213A LEU* 2.8 14.5 + - + +
214A ALA* 3.4 9.4 - - - +
215A ILE 3.1 0.2 - - - -
216A ARG* 1.3 77.8 - - - +
218A LEU* 1.3 74.4 + - + +
220A ASP* 3.2 8.7 + - + +
221A ASN* 2.9 66.2 + - + +
225A PHE* 4.1 12.1 - + - -
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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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96A ILE* 4.3 9.0 - - + -
98A VAL* 3.9 20.9 - - + -
143A ILE* 5.4 8.2 - - + +
145A ILE* 3.7 34.8 - - + -
176A ALA* 3.6 35.4 - - + -
178A PHE* 5.0 5.4 - - + -
214A ALA 3.1 19.8 + - - +
215A ILE 3.1 4.9 + - - +
217A TRP* 1.3 89.8 - - + +
219A LYS* 1.3 56.9 + - - +
221A ASN 3.3 0.8 - - - +
222A ALA* 2.6 39.4 + - - +
225A PHE* 5.8 2.5 - - + -
232A MET* 4.7 3.8 - - - -
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Residues in contact with LYS 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 ILE* 3.0 14.8 + - + +
216A ARG* 3.7 10.1 - - + +
218A LEU* 1.3 77.0 - - - +
220A ASP* 1.3 65.3 + - - +
221A ASN 3.4 0.2 + - - -
222A ALA* 3.6 7.1 + - - -
229A PRO* 3.0 47.3 + - + +
230A GLU* 4.0 15.0 - - - +
232A MET* 3.2 40.1 - - + +
256A LEU* 3.7 49.7 + - + +
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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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10A SER* 4.9 10.9 - - - +
216A ARG* 2.9 31.1 + - - +
217A TRP* 3.5 11.7 - - - +
219A LYS* 1.3 80.1 - - - +
221A ASN* 1.3 65.8 + - - +
222A ALA 3.9 0.2 + - - -
223A HIS* 5.0 3.3 + - - +
224A ALA 5.6 0.2 + - - -
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Residues in contact with ASN 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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9A THR* 3.3 8.8 - - - -
10A SER* 2.7 43.8 + - - -
217A TRP* 2.9 69.1 + - + +
218A LEU* 3.3 2.9 - - + +
220A ASP* 1.3 78.4 - - - +
222A ALA* 1.3 68.0 + - - +
223A HIS 3.3 2.5 - - - -
224A ALA* 3.2 18.8 + - + +
225A PHE* 3.3 21.2 - - + -
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Residues in contact with ALA 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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143A ILE* 3.4 32.5 - - + -
218A LEU* 2.6 20.7 + - - +
219A LYS* 3.9 1.3 - - - +
220A ASP 3.5 2.0 - - - -
221A ASN* 1.3 72.9 - - - +
223A HIS* 1.3 63.9 + - - +
225A PHE* 2.9 13.4 + - - +
227A GLY* 2.9 22.3 + - - -
229A PRO* 3.6 27.1 - - + -
232A MET* 5.3 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
------------------------------------------------------------
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