Contacts of the helix formed by residues 189 - 205 (chain F) in PDB entry 6M04
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 189 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F TRP 5.5 2.7 - - - +
184F PHE* 5.3 4.7 - - + -
186F TYR* 3.4 29.0 + - - -
188F LYS* 1.3 80.2 + - - +
190F CYS* 1.3 64.0 + - - +
191F SER 3.3 2.9 - - - -
192F LYS* 3.3 41.9 - - + +
193F VAL* 3.5 13.1 - - + +
303F LEU* 4.0 25.7 - - + +
304F ILE* 5.6 6.7 - - + +
307F LEU* 4.5 12.2 - - + +
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Residues in contact with CYS 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F TYR* 4.3 8.1 - - - -
184F PHE* 4.0 18.2 - - - +
185F LYS* 5.7 2.7 - - - -
186F TYR 3.6 6.4 + - - +
187F PRO* 3.7 22.8 - - + -
188F LYS 3.7 0.8 - - - -
189F THR* 1.3 78.7 - - - +
191F SER* 1.3 57.8 + - - +
193F VAL* 3.3 7.5 + - - +
194F GLU* 3.0 43.5 + - - +
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Residues in contact with SER 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187F PRO 4.7 6.7 + - - -
188F LYS 4.8 4.7 + - - -
190F CYS* 1.3 79.6 - - - +
192F LYS* 1.3 75.1 + - - +
194F GLU* 3.4 6.3 + - - +
195F HIS* 2.9 27.6 + - - +
297F HIS* 5.9 2.6 - - - -
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Residues in contact with LYS 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F LYS 3.6 9.1 + - - -
189F THR* 3.3 46.2 - - + +
191F SER* 1.3 86.3 + - - +
193F VAL* 1.3 61.3 + - + +
195F HIS* 3.3 8.7 - - - +
196F PHE* 2.9 28.2 + - - +
294F PHE* 4.6 8.1 - - + -
297F HIS* 4.9 17.0 - - + -
298F VAL* 4.1 32.1 - - + -
303F LEU* 4.4 14.1 - - + +
304F ILE* 6.3 2.9 - - + -
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Residues in contact with VAL 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F TYR* 3.5 32.1 - - + +
20F LEU* 3.8 23.6 - - + -
184F PHE* 4.9 14.6 - - + -
189F THR* 3.5 21.1 - - + +
190F CYS* 3.3 9.3 + - - +
191F SER 3.2 0.6 - - - -
192F LYS* 1.3 81.0 - - + +
194F GLU* 1.3 59.7 + - - +
196F PHE* 3.2 7.3 + - - +
197F VAL* 2.9 28.2 + - - +
304F ILE* 6.1 5.2 - - + -
419F LEU* 6.1 2.7 - - + -
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Residues in contact with GLU 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F PRO* 6.0 1.4 - - - +
16F THR* 5.4 3.9 - - - +
17F TYR* 2.6 36.0 + - - +
190F CYS* 3.0 31.9 + - - +
191F SER* 3.8 5.6 - - - +
193F VAL* 1.3 75.5 - - - +
195F HIS* 1.3 56.7 + - - +
197F VAL* 3.3 9.0 + - - +
198F SER* 3.0 36.3 + - - -
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Residues in contact with HIS 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F SER 2.9 18.1 + - - +
192F LYS* 3.3 11.7 - - - +
194F GLU* 1.3 76.8 - - - +
196F PHE* 1.3 56.0 + - - +
198F SER* 3.4 5.7 + - - -
199F ILE* 3.0 59.0 + - + +
290F LYS* 3.4 30.7 + - + +
293F LYS* 4.8 8.6 - - - +
294F PHE* 3.3 39.9 - + + -
297F HIS* 6.5 0.4 - + - -
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Residues in contact with PHE 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LEU* 3.9 20.6 - - + -
192F LYS 2.9 17.0 + - - +
193F VAL* 3.2 7.4 + - - +
195F HIS* 1.3 76.3 + - - +
197F VAL* 1.3 56.4 + - - +
199F ILE* 3.4 12.1 + - + +
200F LEU* 2.9 56.8 + - + +
294F PHE* 4.1 26.7 - + + -
415F ASP* 5.8 3.6 - - - -
419F LEU* 3.5 36.1 - - + -
420F LEU* 4.4 13.9 - - + -
423F VAL* 3.6 17.9 - - + -
434F PHE* 5.0 17.5 - + - -
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Residues in contact with VAL 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F THR* 6.2 2.0 - - + +
17F TYR* 3.7 33.4 - - + -
19F ILE* 5.7 10.8 - - + +
20F LEU* 4.3 23.1 - - + -
193F VAL 2.9 21.6 + - - +
194F GLU* 3.6 11.4 - - - +
196F PHE* 1.3 78.2 - - - +
198F SER* 1.3 60.0 - - - +
200F LEU* 3.4 3.4 + - - +
201F GLY* 2.9 26.7 + - - -
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Residues in contact with SER 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F GLU* 3.0 20.0 + - - +
195F HIS* 3.8 5.8 - - - -
197F VAL* 1.3 77.7 - - - +
199F ILE* 1.3 62.9 + - - +
201F GLY* 3.5 1.2 + - - -
202F LYS* 3.0 34.1 + - - +
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Residues in contact with ILE 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F HIS* 3.0 48.8 + - + +
196F PHE* 3.6 11.9 - - + +
197F VAL 3.3 0.2 - - - -
198F SER* 1.3 77.0 - - - +
200F LEU* 1.3 59.0 + - + +
202F LYS* 3.7 3.2 - - - +
203F CYS* 2.8 34.3 + - + +
287F LEU* 4.4 12.2 - - + +
290F LYS* 3.9 25.6 - - + +
291F VAL* 4.9 7.6 - - + +
294F PHE* 3.6 26.0 - - + -
434F PHE* 4.2 25.6 - - + -
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Residues in contact with LEU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ILE* 5.2 11.2 - - + -
196F PHE* 2.9 50.5 + - + +
197F VAL* 4.2 3.6 - - - +
199F ILE* 1.3 80.0 - - + +
201F GLY* 1.3 59.0 + - - +
203F CYS* 3.9 4.9 - - - -
204F PHE* 2.9 25.3 + - + +
420F LEU* 5.5 1.6 - - + -
423F VAL* 4.0 16.8 - - + -
430F TYR* 3.5 52.5 - - + +
433F ARG* 3.7 11.8 + - - +
434F PHE* 5.1 7.6 - - + -
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Residues in contact with GLY 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ILE* 6.6 0.2 - - - -
197F VAL 2.9 16.9 + - - -
198F SER* 3.9 1.1 - - - -
200F LEU* 1.3 78.8 - - - +
202F LYS* 1.3 61.3 + - - +
204F PHE* 3.4 2.2 + - - +
205F GLU* 3.0 38.1 + - - +
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Residues in contact with LYS 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F SER* 3.0 21.9 + - - +
199F ILE* 4.2 2.0 - - - +
201F GLY* 1.3 76.5 - - - +
203F CYS* 1.3 59.5 + - - +
205F GLU* 3.2 37.4 + - - +
206F SER* 3.6 10.7 + - - -
283F GLN* 5.8 5.8 - - - +
287F LEU* 3.3 28.1 - - + +
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Residues in contact with CYS 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F ILE* 2.8 23.5 + - + +
200F LEU* 3.8 6.1 - - - +
201F GLY 3.2 0.2 - - - -
202F LYS* 1.3 76.7 - - - +
204F PHE* 1.3 61.0 + - - +
206F SER* 5.3 0.4 - - - -
209F THR* 3.7 14.0 - - - +
287F LEU* 4.0 11.9 - - + -
433F ARG* 2.7 49.2 + - - +
434F PHE* 3.7 16.8 - - + -
437F PHE* 3.6 36.8 - - - -
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Residues in contact with PHE 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293E LYS* 4.7 33.7 - - + -
297E HIS* 4.7 11.2 - + - -
200F LEU* 2.9 13.1 + - + +
201F GLY* 4.1 2.5 - - - +
203F CYS* 1.3 76.6 - - - +
205F GLU* 1.3 64.1 + - + +
206F SER 3.2 14.4 + - - +
209F THR* 4.3 3.1 + - - -
429F LEU* 3.6 35.0 - - + -
430F TYR* 3.4 39.3 - + + -
433F ARG* 3.3 34.9 - - + +
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Residues in contact with GLU 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293E LYS* 5.9 4.3 - - - +
201F GLY* 3.0 21.6 + - - +
202F LYS* 3.2 36.7 + - - +
203F CYS 3.6 0.2 - - - -
204F PHE* 1.3 82.9 - - + +
206F SER* 1.3 59.6 + - - +
207F PRO* 3.7 6.4 - - - +
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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
------------------------------------------------------------
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