Contacts of the helix formed by residues 205 - 224 (chain A) in PDB entry 1UD8
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 HIS 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PHE* 2.8 30.0 + - + -
159A HIS* 3.9 14.3 - + + -
160A PHE 4.6 2.2 + - - -
180A THR* 5.9 4.7 - - + +
202A ASP* 3.5 37.1 + - + +
203A PHE 3.0 4.8 - - - +
204A SER* 1.3 82.1 + - - +
206A PRO* 1.3 69.7 - - - +
207A GLU* 3.3 15.5 + - + +
208A VAL* 3.0 25.1 + - + +
209A GLN 3.2 9.0 + - - -
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Residues in contact with PRO 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A SER 3.2 10.5 - - - +
205A HIS* 1.3 84.6 - - - +
207A GLU* 1.3 71.5 + - - +
209A GLN* 3.4 15.2 + - + +
210A ASP* 2.8 36.9 + - - +
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PHE* 3.7 15.4 - - + -
159A HIS* 4.4 19.5 - - + +
205A HIS* 3.3 17.1 + - + +
206A PRO* 1.3 91.6 - - - +
208A VAL* 1.3 64.9 + - - +
210A ASP* 4.1 5.4 - - - +
211A GLU* 3.2 23.7 + - - +
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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
----------------------------------------------------------
153A PHE* 5.1 3.1 - - + -
155A TRP* 4.1 13.0 - - + -
159A HIS* 4.1 29.2 - - + +
201A ILE* 3.5 29.8 - - + -
202A ASP 3.7 11.9 - - - +
203A PHE* 4.3 12.1 - - + -
205A HIS* 3.0 31.6 + - + +
207A GLU* 1.3 77.0 - - - +
209A GLN* 1.3 67.1 - - - +
211A GLU* 2.9 16.9 + - - +
212A LEU* 3.0 16.9 + - + +
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Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE* 2.6 29.3 + - + +
204A SER* 3.7 15.8 + - - +
205A HIS 3.2 5.5 + - - +
206A PRO* 3.4 15.7 + - + +
208A VAL* 1.3 79.4 - - - +
210A ASP* 1.3 61.4 + - - +
213A LYS* 3.0 30.3 + - - +
239A TRP* 3.3 25.8 - - - -
240A TYR* 2.8 46.4 + - + -
243A ASP* 4.9 1.4 - - - +
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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
----------------------------------------------------------
206A PRO* 2.8 24.9 + - - +
207A GLU* 4.5 4.5 - - - +
209A GLN* 1.3 79.0 - - - +
211A GLU* 1.3 56.1 + - - +
213A LYS* 3.6 18.8 + - - +
214A ASP* 2.7 49.4 + - - +
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR* 3.0 36.3 + - - -
151A SER* 3.9 3.7 + - - -
153A PHE* 3.5 52.1 - - + +
155A TRP* 4.3 14.5 + - + +
207A GLU 3.2 19.2 + - - +
208A VAL* 2.9 5.6 + - - +
210A ASP* 1.3 79.2 - - - +
212A LEU* 1.3 59.7 + - + +
214A ASP* 3.6 8.5 - - - +
215A TRP* 2.7 27.4 + - - +
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Residues in contact with LEU 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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61A LEU* 4.3 24.5 - - + -
103A MET* 4.1 26.0 - - + -
155A TRP* 4.2 21.3 - - + -
201A ILE* 4.3 12.3 - - + -
203A PHE* 3.3 36.6 - - + -
208A VAL* 3.0 20.9 + - + +
211A GLU* 1.3 76.6 - - + +
213A LYS* 1.3 60.0 + - - +
215A TRP* 3.7 8.8 - - + -
216A GLY 2.8 23.9 + - - -
240A TYR* 3.2 15.7 - - - +
244A TRP* 3.1 10.7 + - - -
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Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLN* 3.0 36.2 + - - +
210A ASP* 3.6 18.8 + - - +
211A GLU 3.2 0.2 - - - -
212A LEU* 1.3 77.1 - - - +
214A ASP* 1.3 63.4 + - - +
216A GLY 3.2 0.3 + - - -
217A SER* 3.1 6.9 + - - -
240A TYR* 3.5 22.2 - - - +
243A ASP* 3.8 26.8 + - - -
244A TRP* 3.9 12.6 - - + -
247A HIS* 3.2 46.5 - - + +
248A GLN* 2.9 22.0 + - - -
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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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62A TYR* 4.3 4.0 - - - +
210A ASP* 2.7 38.2 + - - +
211A GLU* 3.6 12.5 + - - +
213A LYS* 1.3 75.0 - - - +
215A TRP* 1.3 61.5 + - - +
217A SER* 3.4 6.1 + - - -
218A TRP* 3.0 21.8 + - - +
247A HIS* 5.0 6.5 + - - -
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Residues in contact with TRP 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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46A TYR* 3.9 20.6 - + - -
61A LEU* 2.9 55.5 + - + +
62A TYR* 3.3 37.4 + + + +
101A VAL* 3.8 33.4 - - + -
102A VAL 5.1 0.2 - - - -
103A MET* 4.2 8.5 - - + -
211A GLU* 2.7 25.2 + - - +
212A LEU* 3.7 17.3 - - + +
214A ASP* 1.3 74.2 - - - +
216A GLY* 1.3 73.1 + - - +
218A TRP* 2.8 17.9 + + - +
219A PHE* 2.6 67.8 + + + +
244A TRP* 4.4 1.1 - + - -
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Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU 2.8 19.1 + - - -
213A LYS 3.2 0.2 + - - -
215A TRP* 1.3 85.4 - - - +
217A SER* 1.3 58.1 + - - +
219A PHE* 3.4 3.0 - - - +
220A THR* 2.8 34.7 + - - -
244A TRP* 3.7 12.1 - - - -
248A GLN* 3.2 17.7 - - - -
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Residues in contact with SER 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS 3.1 7.4 + - - -
214A ASP* 3.7 9.4 - - - -
216A GLY* 1.3 73.0 - - - +
218A TRP* 1.3 67.9 + - - +
220A THR* 3.3 3.3 + - - -
221A ASP* 2.9 42.1 + - - +
247A HIS* 4.9 2.2 - - - -
248A GLN* 2.9 20.1 - - - +
251A GLU* 3.8 28.7 + - - +
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Residues in contact with TRP 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU 3.7 20.2 - - - -
62A TYR* 3.5 43.5 - + + +
64A LEU* 4.1 12.1 - - + -
80A LYS* 4.9 1.8 - - - -
150A TYR* 3.3 49.2 - + + -
214A ASP 3.0 13.4 + - - +
215A TRP* 2.8 19.2 + + - +
217A SER* 1.3 71.8 - - - +
219A PHE* 1.3 85.3 + + - +
221A ASP* 3.8 6.3 - - - +
222A GLU* 2.9 68.4 + - + +
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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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42A ILE* 5.8 0.9 - - + -
45A ALA* 5.1 6.1 - - + -
46A TYR* 3.9 17.3 - + - -
64A LEU* 3.8 18.8 - - + -
99A GLY* 4.8 7.0 - - - -
100A ASP 4.3 6.7 - - - -
101A VAL* 3.9 22.2 - - + -
215A TRP* 2.6 49.4 + + + +
216A GLY* 3.4 6.1 - - - +
218A TRP* 1.3 91.1 - + - +
220A THR* 1.3 64.5 + - - +
222A GLU* 3.0 4.3 + - - +
223A LEU* 3.0 54.2 + - + +
225A LEU* 3.7 24.7 - - + -
228A TYR* 5.1 1.1 - + - -
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Residues in contact with THR 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 GLY 2.8 25.9 + - - -
217A SER* 3.7 5.8 - - - -
219A PHE* 1.3 73.0 - - - +
221A ASP* 1.3 61.8 + - - +
224A ASP* 3.0 21.8 + - - -
225A LEU* 3.1 21.0 + - + -
228A TYR* 2.3 43.5 + - - +
248A GLN* 4.5 1.1 - - - -
252A ALA* 4.7 8.1 - - + -
254A GLN* 3.9 21.1 + - - +
256A LEU* 4.1 12.1 - - + -
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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
----------------------------------------------------------
217A SER* 2.9 35.7 + - - +
218A TRP* 3.9 4.9 + - - +
220A THR* 1.3 82.1 - - - +
222A GLU* 1.3 66.2 + - - +
224A ASP* 3.3 12.2 + - - +
251A GLU 5.3 3.8 - - - +
252A ALA* 5.2 7.4 - - - +
254A GLN* 5.4 3.5 + - - +
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Residues in contact with GLU 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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64A LEU* 4.4 7.4 - - + -
80A LYS* 3.3 30.1 + - - +
84A GLU* 3.6 12.7 - - - +
150A TYR* 4.0 9.0 - - - -
218A TRP* 2.9 59.9 + - + +
219A PHE* 3.0 5.4 + - - +
221A ASP* 1.3 78.2 - - - +
223A LEU* 1.3 62.1 + - + +
224A ASP* 5.3 0.3 - - - +
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 4.7 6.7 - - + -
45A ALA* 4.7 0.9 - - + -
64A LEU* 3.9 19.3 - - + -
83A LEU* 3.8 29.8 - - + -
84A GLU* 4.4 14.4 - - + -
87A ILE* 3.7 41.2 - - + +
219A PHE* 3.0 45.6 + - + +
222A GLU* 1.3 82.2 - - + +
224A ASP* 1.3 71.0 + - - +
225A LEU* 3.4 21.8 + - + -
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Residues in contact with ASP 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 5.2 1.5 - - + +
91A LYS* 2.9 38.5 + - - +
220A THR 3.0 12.0 + - - -
221A ASP* 3.3 10.8 + - - +
222A GLU 5.3 0.4 - - - +
223A LEU* 1.3 82.0 - - - +
225A LEU* 1.3 62.4 + - - +
226A ASP* 5.0 0.5 - - - +
254A GLN* 3.7 16.9 + - - +
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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