Contacts of the helix formed by residues 206 - 224 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17K GLY 5.8 0.2 - - - -
18K ARG* 3.3 48.0 - - + +
201K THR* 4.3 1.3 - - - -
205K VAL* 1.3 76.7 - - - +
207K PRO* 1.3 75.7 - - - +
208K LEU* 3.8 6.4 + - - +
209K GLU* 3.1 37.1 + - - +
210K ALA* 2.9 22.0 + - - +
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Residues in contact with PRO 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K THR* 6.2 1.8 - - + -
17K GLY 5.1 1.1 - - - +
18K ARG* 3.0 20.4 - - - +
19K GLU 3.2 20.9 - - - +
20K TYR 3.3 20.6 - - - +
21K GLY* 3.5 2.9 - - - +
23K PHE* 3.7 21.8 - - + -
199K ILE* 3.5 27.1 - - + +
201K THR* 3.7 6.2 - - + +
206K THR* 1.3 84.7 - - - +
208K LEU* 1.3 57.3 + - - +
210K ALA* 3.2 4.1 + - + +
211K LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K PHE* 4.8 12.8 - - + -
13K VAL* 4.9 11.4 - - + -
15K THR* 5.7 5.8 - - + -
23K PHE* 3.4 32.2 - - + -
206K THR* 3.2 6.2 + - - +
207K PRO* 1.3 80.5 - - - +
209K GLU* 1.3 63.1 + - + +
211K LEU* 3.2 6.5 + - + +
212K ASN* 2.8 54.5 + - - +
228L PRO* 6.3 0.4 - - + -
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Residues in contact with GLU 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ARG* 4.4 5.8 + - - -
88K ARG* 5.4 2.3 + - - -
205K VAL* 3.8 18.4 - - + +
206K THR* 3.1 40.4 + - - +
208K LEU* 1.3 78.2 - - + +
210K ALA* 1.3 64.8 + - - +
212K ASN* 3.2 10.0 + - - +
213K GLN* 3.0 37.9 + - - +
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Residues in contact with ALA 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44K LEU* 3.7 16.6 - - + -
48K ILE* 3.7 6.5 - - + +
174K VAL* 4.5 15.0 - - + -
199K ILE* 4.7 2.5 - - + -
201K THR* 4.6 3.6 - - + -
205K VAL* 4.4 10.5 - - + +
206K THR 2.9 12.4 + - - +
207K PRO* 3.2 13.9 - - + +
209K GLU* 1.3 77.2 - - - +
211K LEU* 1.3 63.1 + - - +
213K GLN* 3.2 13.8 + - - +
214K ALA* 2.9 23.9 + - - +
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Residues in contact with LEU 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K PHE* 4.4 5.2 - - + -
23K PHE* 3.6 43.5 - - + -
40K LEU* 3.8 20.2 - - + -
44K LEU* 3.9 10.5 - - + +
197K LEU* 3.7 24.7 - - + -
199K ILE* 4.1 9.0 - - + -
207K PRO 2.9 12.7 + - - +
208K LEU* 3.5 11.0 - - + +
210K ALA* 1.3 74.6 - - - +
212K ASN* 1.3 62.8 + - - +
214K ALA* 3.3 1.3 + - + +
215K VAL* 2.9 41.4 + - + +
225L PHE* 3.9 20.6 - - + -
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Residues in contact with ASN 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K PHE* 5.8 0.3 - - - -
208K LEU* 2.8 51.7 + - - +
209K GLU* 3.6 7.9 - - - +
211K LEU* 1.3 80.7 - - - +
213K GLN* 1.3 56.8 + - - +
215K VAL* 3.5 6.3 + - - +
216K GLU* 2.9 28.1 + - - +
225L PHE* 4.6 15.2 - - - +
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Residues in contact with GLN 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48K ILE* 3.7 21.7 - - + +
49K PRO* 4.1 18.0 - - + +
205K VAL* 4.4 16.0 - - - +
209K GLU* 3.0 39.8 + - - +
210K ALA* 3.3 14.3 - - - +
212K ASN* 1.3 74.8 - - - +
214K ALA* 1.3 59.6 + - - +
216K GLU* 3.6 8.7 - - + +
217K ILE* 2.9 37.1 + - + +
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Residues in contact with ALA 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K LEU* 4.4 11.4 - - + -
43K ILE* 3.7 25.8 - - + +
44K LEU* 3.8 26.2 - - + -
48K ILE* 3.7 3.8 - - + +
210K ALA 2.9 17.5 + - - +
211K LEU* 3.4 5.6 - - - +
213K GLN* 1.3 75.5 - - - +
215K VAL* 1.3 65.1 + - - +
217K ILE* 3.1 4.7 + - - +
218K LEU* 2.9 23.6 + - - +
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Residues in contact with VAL 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K LEU* 4.0 16.6 - - + -
211K LEU* 2.9 38.5 + - + +
212K ASN* 3.7 7.4 - - - +
214K ALA* 1.3 73.2 - - - +
216K GLU* 1.3 64.6 + - - +
218K LEU* 3.2 5.2 + - - +
219K ARG* 2.9 23.9 + - + +
222L LEU* 3.5 37.9 - - + +
225L PHE* 3.9 23.8 - - + -
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Residues in contact with GLU 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K ASN 2.9 19.0 + - - +
213K GLN* 3.6 10.1 - - + +
214K ALA 3.2 0.2 - - - -
215K VAL* 1.3 76.4 - - - +
217K ILE* 1.3 64.1 + - + +
219K ARG* 2.5 41.6 + - - +
220K GLU* 2.9 44.3 + - - +
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Residues in contact with ILE 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K ILE* 3.8 26.2 - - + -
47K SER* 3.6 29.2 - - - +
48K ILE* 4.3 5.8 - - + -
49K PRO* 5.1 4.3 - - + -
213K GLN* 2.9 30.4 + - + +
214K ALA 3.1 4.5 + - - +
216K GLU* 1.3 74.3 - - + +
218K LEU* 1.3 54.2 - - - +
220K GLU* 3.5 13.3 - - - +
221K HIS* 2.7 58.7 + - + +
32L PHE* 3.9 9.6 - - + -
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Residues in contact with LEU 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K LEU* 5.4 2.2 - - + +
39K PRO* 3.9 25.1 - - + -
40K LEU* 4.1 11.4 - - + -
43K ILE* 3.6 20.6 - - + -
214K ALA 2.9 7.9 + - - +
215K VAL* 3.5 9.0 - - - +
216K GLU 3.2 0.2 - - - -
217K ILE* 1.3 75.6 - - - +
219K ARG* 1.3 59.9 + - - +
221K HIS* 3.0 7.7 + - + +
222K LEU* 2.9 32.6 + - + +
35L THR* 4.6 8.5 - - + +
36L LEU* 3.8 25.8 - - + -
218L LEU* 4.9 13.5 - - + -
222L LEU* 3.6 29.8 - - + -
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Residues in contact with ARG 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K VAL* 2.9 14.0 + - + +
216K GLU* 2.5 47.2 + - - +
218K LEU* 1.3 75.3 - - - +
220K GLU* 1.3 66.6 + - - +
222K LEU* 2.8 23.5 + - - +
223K THR* 2.9 32.2 + - - -
219L ARG* 3.7 34.3 - - + +
222L LEU* 3.5 18.3 - - + +
223L THR* 6.3 1.3 - - + -
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Residues in contact with GLU 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216K GLU* 2.9 36.9 + - - +
217K ILE* 3.5 13.4 - - - +
219K ARG* 1.3 83.4 - - - +
221K HIS* 1.3 58.9 + - - +
223K THR* 3.0 29.0 - - + +
224K TYR* 3.4 30.8 + - + +
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Residues in contact with HIS 221 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217K ILE* 2.7 37.9 + - + +
218K LEU* 3.0 10.5 + - - +
220K GLU* 1.3 74.3 - - - +
222K LEU* 1.3 66.1 + - - +
223K THR 3.0 1.6 - - - -
224K TYR* 2.9 53.2 + + - +
225K PHE* 4.0 7.1 - - - -
28L LEU* 4.8 6.6 - - + +
29L GLU* 5.3 5.2 + - + +
32L PHE* 3.3 52.3 - + + +
36L LEU* 3.8 26.6 - - + +
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Residues in contact with LEU 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218K LEU* 2.9 16.2 + - + +
219K ARG* 2.8 11.0 + - + +
221K HIS* 1.3 75.2 - - - +
223K THR* 1.3 62.3 + - - +
225K PHE* 3.2 29.7 + - + +
226K SER 4.3 0.7 + - - -
36L LEU* 4.6 14.4 - - + -
40L LEU* 4.8 4.9 - - + -
215L VAL* 3.7 32.5 - - + +
218L LEU* 3.8 30.1 - - + -
219L ARG* 3.5 41.1 - - + +
222L LEU* 4.1 11.0 - - + -
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Residues in contact with THR 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219K ARG* 2.9 33.0 + - - -
220K GLU* 3.0 17.2 + - + +
221K HIS 3.0 0.2 - - - -
222K LEU* 1.3 77.0 - - - +
224K TYR* 1.3 59.2 + - + +
226K SER* 2.7 50.0 + - - +
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Residues in contact with TYR 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220K GLU* 3.4 39.1 + - + +
221K HIS* 2.9 56.7 + + - +
223K THR* 1.3 81.3 - - + +
225K PHE* 1.3 58.8 + - - +
226K SER* 3.1 3.6 + - - -
227K ASN* 4.3 3.6 + - - +
7L LYS 4.9 5.6 + - - -
8L ALA* 5.0 10.5 - - + -
9L PRO* 3.6 46.2 - - + +
11L PHE* 3.5 19.4 + - - +
25L LEU* 3.7 10.6 - - + +
28L LEU* 4.7 5.4 - - + -
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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