Contacts of the helix formed by residues 204 - 224 (chain A) in PDB entry 5HAN
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 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PRO* 4.1 11.2 - - + -
199A ASN* 3.5 11.2 - - - +
200A GLN 3.2 4.0 - - - +
201A VAL* 3.9 11.7 - - - +
202A PHE 3.6 7.2 - - - +
203A ALA* 1.3 87.2 - - - +
205A PHE* 1.4 63.9 + - - +
206A LYS* 3.4 1.1 - - + +
207A ASP* 3.4 23.8 + - - +
208A THR* 2.9 25.3 + - - -
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Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLY* 3.4 26.4 + - - +
199A ASN* 2.9 21.0 + - + +
203A ALA 3.4 1.8 + - - -
204A PRO* 1.4 71.1 - - - +
206A LYS* 1.3 68.4 + - + +
208A THR* 3.3 4.2 + - - -
209A VAL* 2.9 45.3 + - + +
231A PHE* 5.2 3.4 - + - -
232A ASN 4.3 7.9 - - - -
243A ALA 5.0 0.2 - - - -
244A ARG* 3.5 61.5 - - + -
247A PHE* 3.9 21.3 - + + -
248A ILE* 3.6 17.3 - - + -
95B VAL* 3.6 24.9 - - + -
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Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASN* 4.9 0.2 + - - -
204A PRO* 3.4 1.9 - - + +
205A PHE* 1.3 84.3 - - + +
207A ASP* 1.3 58.1 + - - +
209A VAL* 3.5 1.2 + - - +
210A ARG* 3.0 52.0 + - - +
243A ALA 6.0 0.2 - - - -
247A PHE* 3.7 55.8 - - + -
95B VAL* 4.0 24.9 - - + +
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Residues in contact with ASP 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO* 3.9 19.2 - - + +
204A PRO* 3.4 29.5 + - + +
205A PHE 3.4 0.2 - - - -
206A LYS* 1.3 75.9 - - - +
208A THR* 1.3 58.6 + - - +
210A ARG* 3.4 22.0 + - - +
211A ALA* 3.0 29.3 + - - +
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Residues in contact with THR 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO* 3.6 21.3 - - + +
177A PHE* 3.8 42.8 - - + -
193A ASN* 5.6 2.9 - - - +
198A GLY 5.2 3.1 - - - +
203A ALA* 3.7 16.0 + - + +
204A PRO 2.9 18.8 + - - -
205A PHE* 3.3 5.4 + - - -
207A ASP* 1.3 73.1 - - - +
209A VAL* 1.3 60.1 + - - +
211A ALA* 3.2 2.1 + - - +
212A VAL* 2.9 36.3 + - + +
231A PHE* 5.5 4.5 - - + -
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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
----------------------------------------------------------
205A PHE* 2.9 53.4 + - + +
206A LYS 3.8 3.8 - - - +
208A THR* 1.3 76.2 - - - +
210A ARG* 1.4 57.9 + - - +
212A VAL* 3.4 1.9 + - - +
213A ALA* 2.9 28.2 + - - +
231A PHE* 3.8 23.3 - - + -
247A PHE* 3.7 23.8 - - + -
248A ILE* 3.8 17.0 - - + -
251A THR* 4.1 11.9 - - + -
252A PHE* 3.8 11.8 - - + -
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Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LYS* 3.0 37.1 + - - +
207A ASP* 3.4 29.5 + - - +
209A VAL* 1.4 76.7 - - - +
211A ALA* 1.3 61.2 + - - +
213A ALA* 3.4 2.9 + - - +
214A ASP* 3.1 22.3 + - - +
247A PHE* 3.8 29.9 - - + -
251A THR* 4.2 21.8 - - + -
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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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174A PRO* 3.7 18.8 - - + +
175A GLN* 4.3 15.3 - - - +
178A ALA* 3.4 26.2 - - + +
207A ASP 3.0 17.4 + - - +
208A THR 3.2 2.7 + - - +
210A ARG* 1.3 73.2 - - - +
212A VAL* 1.3 60.3 + - - +
214A ASP* 3.3 8.6 + - - +
215A ALA 3.0 22.9 + - - -
218A ARG* 5.3 0.2 + - - -
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 3.6 37.5 - - + -
178A ALA* 4.3 3.1 - - + -
181A CYS* 4.1 5.2 - - - -
185A TRP* 3.9 12.0 - - + -
208A THR* 2.9 23.2 + - + +
209A VAL 3.8 3.6 - - - +
211A ALA* 1.3 74.8 - - - +
213A ALA* 1.3 59.8 + - - +
215A ALA* 3.2 7.2 + - - +
216A MET* 2.8 27.9 + - - +
229A PHE* 3.6 29.6 - - + -
231A PHE* 3.8 18.8 - - + -
252A PHE* 4.0 4.7 - - + -
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A VAL 2.9 18.0 + - - +
210A ARG 3.7 5.4 - - - +
211A ALA 3.3 0.2 - - - -
212A VAL* 1.3 76.4 - - - +
214A ASP* 1.3 61.0 + - - +
216A MET* 3.4 2.8 + - - +
217A ARG* 3.1 31.1 + - - +
251A THR* 4.0 20.9 - - + +
252A PHE* 3.4 34.6 - - + -
255A ASN* 5.3 0.7 + - - -
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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
----------------------------------------------------------
175A GLN* 5.3 6.1 + - - +
210A ARG 3.1 13.6 + - - +
211A ALA* 3.6 10.6 - - - +
212A VAL 3.2 0.2 - - - -
213A ALA* 1.3 74.5 - - - +
215A ALA* 1.4 60.1 + - - +
217A ARG* 3.3 10.6 + - - +
218A ARG* 3.0 61.3 + - - +
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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
----------------------------------------------------------
178A ALA* 3.4 28.5 - - + +
181A CYS* 4.5 0.4 - - + -
182A TYR* 3.8 12.4 - - + +
185A TRP* 4.0 7.4 - - + -
211A ALA 3.0 14.4 + - - +
212A VAL* 3.2 8.7 + - - +
214A ASP* 1.4 77.2 + - - +
216A MET* 1.4 54.8 + - - +
218A ARG* 3.4 21.6 + - - +
219A ALA* 2.9 31.7 + - - +
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Residues in contact with MET 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TRP* 3.5 24.6 - - + -
212A VAL 2.8 16.4 + - - +
213A ALA 3.6 5.4 - - - +
214A ASP 3.3 0.2 - - - -
215A ALA* 1.4 76.1 - - - +
217A ARG* 1.4 56.0 + - - +
219A ALA* 3.9 0.9 - - - +
220A GLN* 2.9 50.7 + - - +
227A LYS* 3.3 33.2 - - + +
229A PHE* 3.9 20.6 - - + +
252A PHE* 3.7 32.8 - - + -
255A ASN* 3.8 20.2 - - - +
258A HIS* 3.9 12.3 - - + +
259A ILE* 4.5 0.7 - - + -
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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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213A ALA* 3.1 19.8 + - - +
214A ASP* 3.6 12.6 - - - +
216A MET* 1.4 75.3 - - - +
218A ARG* 1.3 59.6 + - + +
220A GLN* 3.8 6.7 - - - +
221A ASP* 2.9 41.5 + - - +
251A THR 4.9 2.4 + - - -
252A PHE 3.3 20.8 + - - -
253A ALA* 4.1 6.5 - - - +
254A ASP* 2.7 40.8 + - - -
255A ASN* 3.7 16.5 - - - +
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Residues in contact with ARG 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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175A GLN* 4.6 6.9 + - - -
178A ALA* 4.6 1.6 + - - +
179A ASN* 4.3 15.0 + - - -
182A TYR* 3.5 48.4 - - + +
211A ALA 5.3 0.2 + - - -
214A ASP* 3.0 44.0 + - - +
215A ALA* 3.8 23.4 - - - +
217A ARG* 1.3 77.7 - - + +
219A ALA* 1.4 56.0 + - - +
221A ASP* 3.4 8.7 + - - +
222A LYS* 3.0 29.3 + - - +
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Residues in contact with ALA 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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182A TYR* 3.5 19.7 - - + +
185A TRP* 3.7 37.0 - - + -
186A LEU* 4.8 1.8 - - - +
215A ALA 2.9 18.1 + - - +
216A MET 3.9 3.1 - - - +
218A ARG* 1.4 75.4 - - - +
220A GLN* 1.4 54.5 + - - +
222A LYS* 4.4 1.8 - - - -
223A THR* 2.7 42.1 + - - +
227A LYS* 4.3 4.7 - - + -
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Residues in contact with GLN 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 MET* 2.9 26.5 + - - +
217A ARG* 3.8 4.9 - - - +
219A ALA* 1.4 73.3 - - - +
221A ASP* 1.3 61.9 + - - +
224A GLY* 2.8 30.8 + - - -
225A GLU 3.2 20.8 + - - +
226A ALA* 4.2 2.7 - - - -
227A LYS* 2.8 23.5 + - + +
255A ASN* 3.0 34.6 + - - +
258A HIS* 2.8 30.7 + - - -
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Residues in contact with ASP 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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217A ARG* 2.9 28.6 + - - +
218A ARG* 3.8 8.1 - - - +
219A ALA 3.4 0.2 - - - -
220A GLN* 1.3 79.1 - - - +
222A LYS* 1.3 62.6 + - - +
224A GLY* 4.0 3.8 + - - -
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Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TYR* 3.6 23.3 - - - +
186A LEU* 3.8 17.5 - - + -
218A ARG 3.0 18.2 + - - +
219A ALA 3.8 3.4 - - - +
221A ASP* 1.3 79.3 - - - +
223A THR* 1.3 60.0 + - + +
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Residues in contact with THR 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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185A TRP 4.0 6.1 - - - +
186A LEU* 3.9 44.0 - - + +
219A ALA 2.7 24.8 + - - +
222A LYS* 1.3 77.0 - - + +
224A GLY* 1.3 61.1 + - - +
225A GLU* 3.1 33.4 + - - +
227A LYS* 3.5 13.9 - - - +
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Residues in contact with GLY 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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220A GLN 2.8 20.0 + - - -
221A ASP 4.0 3.8 + - - -
222A LYS 3.6 1.6 - - - -
223A THR* 1.3 72.3 - - - +
225A GLU* 1.3 59.8 + - - +
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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
------------------------------------------------------------
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