Contacts of the helix formed by residues 182 - 197 (chain P) in PDB entry 6F0X
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 SER 182 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P SER 4.0 0.2 + - - -
181P LEU* 1.3 80.5 - - - +
183P THR* 1.3 61.4 + - - +
184P ALA* 4.2 6.8 - - - +
185P ALA* 2.9 45.5 + - - +
186P CYS 3.4 3.6 + - - -
188P ARG* 4.2 4.9 + - - -
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Residues in contact with THR 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67P GLU 5.7 0.2 - - - -
68P GLY* 4.3 13.4 - - - +
71P GLN* 4.1 21.3 - - + +
72P PHE* 3.6 25.8 - - + -
179P GLN* 4.3 16.1 + - - +
181P LEU* 3.8 4.9 + - - -
182P SER* 1.3 70.7 - - - +
184P ALA* 1.3 63.1 + - - +
186P CYS* 3.0 8.2 + - - +
187P LEU* 2.9 27.2 + - + +
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Residues in contact with ALA 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182P SER* 3.2 7.1 - - - +
183P THR* 1.3 79.2 - - - +
185P ALA* 1.3 57.9 + - - +
187P LEU* 3.3 17.9 + - + +
188P ARG* 2.9 52.9 + - - +
144Z LEU* 6.0 1.6 - - + -
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Residues in contact with ALA 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181P LEU* 5.0 6.1 - - + -
182P SER* 2.9 33.2 + - - +
184P ALA* 1.3 76.4 - - - +
186P CYS* 1.3 57.4 + - - +
188P ARG* 3.1 21.0 - - - +
189P ARG* 2.9 31.7 + - - +
205Z ASP 4.8 12.8 - - - +
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Residues in contact with CYS 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60P PHE* 3.2 51.1 - - + -
61P PRO* 6.3 0.4 - - - -
62P GLY 5.2 2.5 - - - -
63P PRO 5.8 0.4 - - - -
72P PHE* 3.8 18.6 - - + -
179P GLN* 4.9 3.1 - - - -
181P LEU* 3.5 34.8 - - - -
182P SER 3.4 0.6 + - - -
183P THR* 3.0 9.2 + - - +
185P ALA* 1.3 79.9 - - - +
187P LEU* 1.3 64.0 + - - +
189P ARG* 4.3 1.1 - - - +
190P LEU* 2.9 23.0 + - - +
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Residues in contact with LEU 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P GLN* 4.0 16.8 - - + +
72P PHE* 3.4 38.8 - - + +
75P GLU* 4.5 6.7 - - + -
183P THR* 2.9 22.9 + - + +
184P ALA* 3.4 24.9 - - + +
186P CYS* 1.3 77.0 - - - +
188P ARG* 1.3 57.7 + - - +
190P LEU* 3.3 2.3 + - - +
191P PHE* 2.9 60.4 + - + -
140Z THR 5.5 0.2 - - - +
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Residues in contact with ARG 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182P SER* 4.2 3.8 + - - -
184P ALA* 2.9 36.2 + - - +
185P ALA* 3.1 41.3 - - - +
187P LEU* 1.3 71.0 - - - +
189P ARG* 1.3 63.8 + - + +
192P ARG* 2.8 30.5 + - - +
140Z THR 3.6 12.1 - - - +
141Z PHE* 3.1 35.0 - - - +
143Z PRO* 4.3 24.6 - - - +
144Z LEU* 4.2 24.5 - - + +
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Residues in contact with ARG 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58P VAL* 5.6 0.9 - - + -
59P VAL* 2.8 35.7 + - - +
60P PHE* 3.5 21.9 - - + -
61P PRO* 4.3 16.2 - - - +
185P ALA 2.9 18.4 + - - +
186P CYS* 3.7 4.0 - - - +
188P ARG* 1.3 79.8 - - + +
190P LEU* 1.3 59.4 + - - +
192P ARG* 3.4 37.4 + - - +
193P ALA* 2.9 27.3 + - + +
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Residues in contact with LEU 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58P VAL* 3.6 24.0 - - + +
60P PHE* 3.8 12.8 - - + -
72P PHE* 5.6 13.9 - - + -
76P LEU* 5.2 4.0 - - + -
167P LEU* 5.9 3.1 - - + -
186P CYS 2.9 17.1 + - - +
187P LEU* 3.7 2.9 - - - +
189P ARG* 1.3 77.5 - - - +
191P PHE* 1.3 82.0 + - + +
193P ALA* 3.2 8.9 - - - +
194P ILE* 2.8 44.7 + - + +
243P VAL* 4.7 8.5 - - + -
245P LEU* 3.5 31.0 - - + -
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Residues in contact with PHE 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P PHE 4.7 2.9 - - - -
75P GLU* 3.2 41.3 - - + -
76P LEU* 4.2 17.3 - - + -
79P HIS* 5.6 5.2 - + + -
187P LEU* 2.9 42.4 + - + +
188P ARG 4.0 0.4 - - - +
189P ARG 3.2 0.2 - - - -
190P LEU* 1.3 91.6 - - + +
192P ARG* 1.3 61.6 + - - +
193P ALA 3.1 1.1 - - - -
194P ILE* 3.1 25.2 + - + +
195P PHE* 2.9 29.1 + - - +
140Z THR* 3.1 49.8 + - + +
141Z PHE* 4.0 3.7 - - - -
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Residues in contact with ARG 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188P ARG* 2.8 18.9 + - - +
189P ARG* 3.6 46.0 + - - +
191P PHE* 1.3 75.7 - - - +
193P ALA* 1.3 57.6 + - - +
195P PHE* 3.5 2.8 + - + +
196P MET* 2.9 42.6 + - + +
141Z PHE* 3.3 36.6 - - + +
179Z GLU* 4.1 20.0 + - - +
181Z VAL* 5.2 4.7 - - + -
199Z TYR* 4.0 18.8 + - - -
202Z PRO* 5.9 6.3 - - - +
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Residues in contact with ALA 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P VAL* 5.2 3.5 - - + +
57P PRO 5.3 3.8 - - - +
58P VAL* 4.8 15.7 - - + -
189P ARG* 2.9 14.7 + - + +
190P LEU* 3.2 13.7 - - - +
192P ARG* 1.3 74.5 - - - +
194P ILE* 1.3 53.0 - - - +
196P MET* 2.8 8.2 + - - +
197P ALA* 2.1 41.4 + - - +
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Residues in contact with ILE 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58P VAL* 5.8 1.3 - - + -
76P LEU* 3.7 22.4 - - + -
79P HIS* 4.1 23.6 - - + +
190P LEU* 2.8 31.3 + - + +
191P PHE* 3.4 36.6 - - + +
193P ALA* 1.3 72.4 - - + +
195P PHE* 1.3 65.0 + - - +
197P ALA* 2.9 23.3 + - + +
198P ASP 2.9 8.8 + - - -
199P ALA* 3.7 10.6 + - + -
200P PHE* 4.6 15.0 - - + -
241P LEU* 5.9 2.5 - - + -
243P VAL* 5.1 15.5 - - + -
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Residues in contact with PHE 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191P PHE 2.9 12.9 + - - +
192P ARG* 3.5 8.3 - - + +
194P ILE* 1.3 78.1 - - - +
196P MET* 1.3 70.4 + - + +
198P ASP* 2.8 21.5 + - - +
199P ALA 5.5 0.2 - - - +
134Z GLN* 3.4 29.6 + - + -
137Z ALA* 5.6 4.5 - - + -
138Z THR* 3.5 26.9 - - + -
141Z PHE* 3.9 22.4 - + + -
181Z VAL* 4.3 18.2 - - + -
182Z ARG 3.1 31.0 - - - -
183Z LEU* 3.5 21.3 - - + -
184Z ARG* 6.0 0.4 - - - -
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Residues in contact with MET 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192P ARG* 2.9 28.5 + - + +
193P ALA* 2.8 10.7 + - - +
195P PHE* 1.3 87.1 - - + +
197P ALA* 1.3 56.8 + - - +
198P ASP* 2.9 14.4 + - - +
181Z VAL* 4.7 18.2 - - + -
182Z ARG 5.1 4.3 - - - +
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Residues in contact with ALA 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P CYS* 4.9 7.6 - - - -
56P VAL* 3.6 45.0 - - + +
193P ALA 2.1 26.4 + - - +
194P ILE* 2.9 18.6 + - + +
196P MET* 1.3 66.2 - - - +
198P ASP* 1.3 58.1 + - - +
199P ALA* 2.7 19.6 + - - +
241P LEU* 4.9 9.5 - - + +
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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
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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