Contacts of the helix formed by residues 206 - 224 (chain B) in PDB entry 5D4D
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 THR 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B GLY 5.4 1.1 - - - +
18B ARG* 3.3 51.8 - - + +
201B THR* 4.1 1.1 - - - -
205B VAL* 1.3 74.9 - - - +
207B PRO* 1.3 64.1 - - - +
208B LEU* 3.8 5.8 + - - +
209B GLU* 2.6 44.5 + - - +
210B ALA* 2.7 31.9 + - - +
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Residues in contact with PRO 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 6.4 0.9 - - - -
17B GLY 5.1 1.3 - - - +
18B ARG* 3.1 20.4 - - - +
19B GLU 3.8 3.4 - - - +
20B TYR* 3.5 30.3 - - - +
21B GLY* 3.5 13.7 - - - +
23B PHE* 3.8 9.9 - - + -
199B ILE* 3.5 28.4 - - + +
201B THR* 3.4 14.6 - - + +
206B THR* 1.3 86.7 - - - +
208B LEU* 1.3 57.0 + - - +
210B ALA* 3.3 2.7 + - + +
211B LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PRO* 4.7 20.4 - - + -
11B PHE* 4.6 13.5 - - + -
13B VAL* 4.8 14.1 - - + -
15B THR* 5.8 3.6 - - + -
23B PHE* 3.6 29.2 - - + -
206B THR* 3.2 6.8 + - - +
207B PRO* 1.3 75.0 - - - +
209B GLU* 1.3 67.5 + - - +
211B LEU* 3.2 4.4 + - + +
212B ASN* 2.9 48.3 + - - +
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 4.0 11.4 + - - -
88B ARG* 5.7 1.6 + - - -
204B SER 4.1 0.9 - - - +
205B VAL* 3.3 19.4 - - + +
206B THR* 2.6 53.6 + - - +
208B LEU* 1.3 78.8 - - + +
210B ALA* 1.3 58.2 - - - +
212B ASN* 3.1 10.6 + - - +
213B GLN* 2.9 35.5 + - - +
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.8 18.6 - - + -
48B ILE* 3.5 12.1 - - + +
174B VAL* 4.2 16.8 - - + -
199B ILE* 4.9 0.7 - - + -
201B THR* 4.5 3.1 - - + -
205B VAL* 3.6 14.3 - - + +
206B THR 2.7 19.0 + - - +
207B PRO* 3.6 8.5 - - + +
209B GLU* 1.3 72.5 - - - +
211B LEU* 1.3 57.7 + - - +
213B GLN* 3.3 5.6 + - - -
214B ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 4.0 13.0 - - + -
11B PHE* 3.6 31.4 - - + -
23B PHE* 3.7 26.0 - - + -
40B LEU* 3.9 29.6 - - + -
44B LEU* 4.1 14.7 - - + +
197B LEU* 4.3 12.6 - - + -
199B ILE* 4.1 6.5 - - + -
207B PRO 2.9 16.7 + - - +
208B LEU* 3.2 7.8 + - + +
210B ALA* 1.3 76.2 - - - +
212B ASN* 1.3 59.9 + - - +
214B ALA* 3.3 1.5 + - + +
215B VAL* 2.9 34.0 + - + +
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Residues in contact with ASN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A PHE* 4.4 14.4 - - - +
226A SER* 5.7 0.9 - - - -
11B PHE* 5.6 0.3 - - - -
208B LEU* 2.9 47.8 + - - +
209B GLU* 3.5 9.3 - - - +
211B LEU* 1.3 76.7 - - - +
213B GLN* 1.3 66.1 + - - +
215B VAL* 3.1 13.8 - - + +
216B GLU* 3.0 24.8 + - - +
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Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 3.7 13.4 - - + +
49B PRO* 3.3 30.8 + - - +
205B VAL* 3.6 33.9 - - - +
209B GLU* 2.9 19.9 + - - +
210B ALA 3.6 6.3 - - - +
212B ASN* 1.3 75.8 - - + +
214B ALA* 1.3 57.6 + - - +
216B GLU* 3.3 6.6 + - - +
217B ILE* 2.9 37.3 + - + +
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.4 13.7 - - + -
43B ILE* 3.8 28.2 - - + +
44B LEU* 4.0 20.4 - - + -
48B ILE* 3.8 4.2 - - + +
210B ALA 2.9 17.5 + - - +
211B LEU* 3.5 6.1 - - - +
213B GLN* 1.3 73.4 - - - +
215B VAL* 1.3 66.2 + - - +
217B ILE* 3.1 5.5 + - - +
218B LEU* 2.9 22.5 + - - +
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 4.0 26.2 - - + +
225A PHE* 4.1 30.1 - - + -
40B LEU* 3.7 26.2 - - + -
211B LEU* 2.9 22.4 + - + +
212B ASN* 3.1 27.1 - - + +
214B ALA* 1.3 74.9 - - - +
216B GLU* 1.3 56.4 + - + +
218B LEU* 3.3 4.7 + - - +
219B ARG* 2.9 29.5 + - - +
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B ASN 3.0 18.9 + - - +
213B GLN* 3.5 7.6 - - - +
215B VAL* 1.3 76.8 - - + +
217B ILE* 1.3 65.3 + - + +
219B ARG* 2.4 47.6 + - - -
220B GLU* 2.9 38.0 + - - +
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 3.9 16.6 - - + -
43B ILE* 4.0 13.2 - - + -
47B SER* 3.7 35.2 - - - +
48B ILE* 4.5 7.6 - - + -
49B PRO* 5.3 3.4 - - + -
213B GLN* 2.9 22.0 + - + +
214B ALA 3.4 7.0 - - - +
216B GLU* 1.3 75.7 - - + +
218B LEU* 1.3 58.5 + - - +
220B GLU* 3.4 10.2 - - - +
221B HIS* 2.9 55.9 + - + +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 5.5 0.7 - - + -
35A THR* 4.3 12.1 - - + +
36A LEU* 3.7 26.0 - - + -
218A LEU* 4.8 13.2 - - + -
222A LEU* 3.6 32.1 - - + -
36B LEU* 5.7 1.8 - - + +
39B PRO* 4.0 23.3 - - + -
40B LEU* 4.3 8.3 - - + -
43B ILE* 3.8 17.5 - - + -
214B ALA 2.9 13.0 + - - +
215B VAL* 3.6 8.7 - - - +
216B GLU 3.2 0.2 - - - -
217B ILE* 1.3 75.4 - - - +
219B ARG* 1.3 65.3 + - - +
221B HIS* 3.1 7.6 + - + +
222B LEU* 2.9 30.0 + - + +
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Residues in contact with ARG 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ARG* 3.9 30.5 - - + +
222A LEU* 3.8 16.7 - - + +
215B VAL 2.9 17.9 + - - +
216B GLU* 2.4 43.2 + - - +
218B LEU* 1.3 73.2 - - - +
220B GLU* 1.3 66.5 + - - +
222B LEU* 2.8 23.9 + - - +
223B THR* 3.0 36.8 + - + +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LYS* 3.9 20.0 + - - -
216B GLU* 2.9 32.1 + - - +
217B ILE* 3.4 11.3 - - - +
219B ARG* 1.3 82.9 - - - +
221B HIS* 1.3 61.5 + - - +
223B THR* 2.6 37.8 + - - +
224B TYR* 3.3 30.3 + - + +
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Residues in contact with HIS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 6.1 5.4 - - - -
28A LEU* 3.7 19.5 - - + +
29A GLU* 5.2 9.9 + - + +
32A PHE* 3.4 44.1 - + + -
36A LEU* 3.8 27.3 - - + +
217B ILE* 2.9 32.7 + - + +
218B LEU* 3.1 9.2 + - - +
220B GLU* 1.3 80.0 - - + +
222B LEU* 1.3 63.1 + - - +
224B TYR* 3.2 55.1 + + - +
225B PHE* 4.2 3.3 - - - -
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.2 16.8 - - + -
40A LEU* 4.6 7.9 - - + -
215A VAL* 3.5 35.8 - - + +
218A LEU* 3.7 34.5 - - + -
219A ARG* 3.5 41.5 - - + +
222A LEU* 3.8 12.6 - - + -
218B LEU* 2.9 14.4 + - + +
219B ARG* 2.8 12.4 + - - +
221B HIS* 1.3 76.8 - - - +
223B THR* 1.3 60.5 + - + +
224B TYR 3.2 0.9 + - - -
225B PHE* 3.4 18.6 + - + +
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ARG* 6.4 0.9 - - + -
219B ARG* 3.0 36.5 + - + +
220B GLU* 2.6 21.7 + - - +
222B LEU* 1.3 73.3 - - + +
224B TYR* 1.3 65.3 + - - +
225B PHE 2.9 9.4 + - - -
226B SER* 2.7 33.1 + - - -
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Residues in contact with TYR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 5.3 3.3 - - - -
6A LEU 5.1 2.9 + - - -
7A LYS* 4.7 3.4 - - - -
8A ALA* 3.7 31.4 + - + -
9A PRO* 3.4 35.8 - - + +
11A PHE* 3.5 10.2 - - - +
25A LEU* 3.5 25.5 - - + +
28A LEU* 4.3 2.9 - - + -
220B GLU* 3.3 40.7 + - + +
221B HIS* 3.3 55.1 - + - +
222B LEU 3.1 1.2 - - - -
223B THR* 1.3 82.5 + - - +
225B PHE* 1.3 56.8 + - - +
226B SER* 3.2 4.0 + - - -
227B ASN 5.0 0.5 + - - -
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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