Contacts of the helix formed by residues 185 - 201 (chain F) in PDB entry 3PRJ
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 185 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155F GLN* 5.2 0.5 + - - -
183F ASP* 3.1 17.5 + - + +
184F GLU* 1.3 82.1 - - - +
186F PRO* 1.4 76.0 - - - +
187F GLU* 3.7 6.7 + - - +
188F GLY* 3.0 21.1 + - - -
189F GLN* 3.0 27.3 + - - +
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Residues in contact with PRO 186 (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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185F THR* 1.4 86.7 - - + +
187F GLU* 1.3 65.5 + - + +
189F GLN* 3.5 6.7 + - + +
190F ARG* 3.4 28.4 + - - +
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Residues in contact with GLU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F TYR* 4.2 9.8 + - - -
153F ASN* 3.0 29.9 + - - +
155F GLN* 3.6 24.3 - - - +
185F THR* 3.3 5.5 + - - +
186F PRO* 1.3 82.9 - - + +
188F GLY* 1.3 63.6 + - - +
190F ARG* 3.4 33.7 + - - +
191F ALA* 3.4 15.8 + - - +
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Residues in contact with GLY 188 (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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155F GLN* 3.9 7.8 + - - -
157F LEU* 4.6 1.6 - - - +
183F ASP* 3.6 29.6 - - - -
185F THR* 3.0 14.6 + - - -
187F GLU* 1.3 74.4 - - - +
189F GLN* 1.3 65.8 + - - +
191F ALA* 3.0 15.7 + - - +
192F VAL* 3.1 17.3 + - - +
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Residues in contact with GLN 189 (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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183F ASP 3.9 5.9 + - - +
184F GLU* 4.0 31.1 - - - +
185F THR 3.0 20.7 + - - +
186F PRO* 4.0 5.8 - - + +
187F GLU 3.5 0.2 - - - -
188F GLY* 1.3 74.4 - - - +
190F ARG* 1.3 56.6 + - - +
192F VAL* 3.4 14.6 + - - +
193F GLN* 2.9 31.9 + - - +
210F THR* 5.6 2.3 + - - -
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Residues in contact with ARG 190 (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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1F MET* 4.8 18.6 - - - +
2F PHE* 4.3 24.9 - - + +
123F TYR* 4.6 10.8 + - - +
186F PRO* 3.4 18.5 + - - +
187F GLU* 3.4 37.0 + - - +
188F GLY 3.2 1.0 - - - -
189F GLN* 1.3 77.8 - - - +
191F ALA* 1.3 57.0 + - - +
193F GLN* 3.7 10.2 + - + +
194F ALA* 3.1 26.2 + - - +
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Residues in contact with ALA 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F TYR* 3.7 19.0 + - - +
125F ILE* 4.0 15.5 - - + +
155F GLN* 3.9 22.4 - - + -
157F LEU* 3.7 20.7 - - + +
187F GLU 3.4 5.2 + - - +
188F GLY* 3.0 10.1 + - - +
190F ARG* 1.3 77.3 - - - +
192F VAL* 1.3 65.1 + - - +
194F ALA* 3.1 12.1 + - - +
195F LEU* 3.2 9.9 + - - +
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Residues in contact with VAL 192 (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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157F LEU* 3.8 13.4 - - + +
180F ILE* 3.8 13.5 - - + +
182F GLY* 3.6 33.2 - - - +
188F GLY 3.1 15.9 + - - +
189F GLN* 3.6 18.4 - - - +
191F ALA* 1.3 75.4 - - - +
193F GLN* 1.3 63.9 + - - +
195F LEU* 3.0 14.4 + - - +
196F CYS* 3.0 18.5 + - - -
210F THR* 3.8 35.0 - - + -
211F THR 5.0 2.7 - - - +
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Residues in contact with GLN 193 (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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189F GLN 2.9 18.9 + - - +
190F ARG* 3.7 11.0 - - + +
192F VAL* 1.3 76.7 - - - +
194F ALA* 1.3 62.5 + - - +
196F CYS* 3.4 13.0 + - - +
197F ALA* 3.2 21.7 + - + +
200F GLU* 5.2 4.0 - - - +
205F ARG* 5.0 8.8 + - - -
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Residues in contact with ALA 194 (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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2F PHE* 4.1 27.1 - - + +
4F ILE* 3.4 21.7 + - + +
125F ILE* 3.9 19.5 - - + -
190F ARG 3.1 15.0 + - - +
191F ALA 3.1 9.8 + - - +
193F GLN* 1.3 76.9 - - - +
195F LEU* 1.3 60.2 + - - +
197F ALA* 3.3 19.6 - - - +
198F VAL* 3.6 4.0 + - - +
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Residues in contact with LEU 195 (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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4F ILE* 4.2 3.8 - - + +
84F LEU* 4.2 28.7 - - + -
86F PHE* 4.6 7.0 - - + -
125F ILE* 5.9 0.2 - - + -
127F THR* 4.0 21.1 - - + +
157F LEU* 3.6 24.9 - - + -
159F ASN* 4.1 8.7 - - + -
180F ILE* 4.0 23.1 - - + -
191F ALA 3.2 9.8 + - - +
192F VAL 3.0 9.7 + - - +
194F ALA* 1.3 72.9 - - - +
196F CYS* 1.3 66.5 + - - +
197F ALA 3.1 1.1 - - - -
198F VAL* 3.1 23.4 + - + +
199F TYR* 3.3 35.4 + - + -
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Residues in contact with CYS 196 (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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180F ILE* 3.9 19.9 - - - +
192F VAL* 3.0 23.0 + - - -
193F GLN* 3.5 14.4 - - - +
195F LEU* 1.3 74.1 - - - +
197F ALA* 1.3 53.7 + - - +
199F TYR* 2.9 7.2 + - - +
200F GLU* 2.6 51.0 + - + +
205F ARG* 4.4 13.0 - - - +
208F ILE* 4.0 19.7 - - + +
210F THR* 4.0 16.8 - - - -
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Residues in contact with ALA 197 (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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2F PHE 5.8 2.7 - - - +
3F GLU* 6.4 2.5 - - + -
193F GLN* 3.2 11.3 + - - +
194F ALA* 3.3 15.3 - - - +
195F LEU 3.1 0.6 - - - -
196F CYS* 1.3 79.5 - - - +
198F VAL* 1.3 62.4 + - + +
200F GLU* 3.4 19.0 + - - +
201F HIS* 3.0 22.4 + - + -
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Residues in contact with VAL 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ILE* 3.9 30.5 - - + +
7F ILE* 4.5 10.5 - - + -
23F ILE* 4.1 30.3 - - + -
27F CYS* 3.7 7.7 - - - -
30F ILE* 4.5 9.2 - - + -
84F LEU* 5.5 0.2 - - + -
86F PHE* 6.5 0.2 - - + -
194F ALA 3.7 13.9 - - - +
195F LEU* 3.1 19.6 + - + +
197F ALA* 1.3 77.9 - - + +
199F TYR* 1.3 65.0 + - + +
201F HIS* 3.3 26.0 + - - +
202F TRP* 3.4 9.5 - - + -
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Residues in contact with TYR 199 (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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19F THR* 5.2 0.5 + - - -
23F ILE* 5.1 7.4 - - + +
86F PHE* 4.5 5.9 - + - -
129F LYS* 3.4 16.8 + - - -
159F ASN* 2.5 33.7 + - - -
161F GLU* 4.7 1.5 + - - -
172F LEU* 6.3 2.7 - - + -
178F VAL* 3.9 35.7 - - + -
180F ILE* 4.2 7.6 - - + -
195F LEU* 3.3 37.2 + - + -
196F CYS 2.9 7.3 + - - +
198F VAL* 1.3 78.1 - - + +
200F GLU* 1.3 52.2 + - - +
201F HIS 3.0 5.6 - - - -
202F TRP* 2.9 42.9 + + - -
203F VAL* 2.8 35.7 + - + +
208F ILE* 4.0 15.5 - - + -
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Residues in contact with GLU 200 (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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193F GLN* 5.2 3.8 - - - +
196F CYS* 2.6 26.8 + - - +
197F ALA* 3.7 18.0 + - - +
198F VAL 3.4 0.2 - - - -
199F TYR* 1.3 67.7 - - - +
201F HIS* 1.3 63.7 + - - +
202F TRP* 3.1 1.1 + - - -
203F VAL 3.5 16.4 + - - +
205F ARG* 3.1 39.2 + - + +
208F ILE* 4.0 15.0 - - + -
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Residues in contact with HIS 201 (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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26F MET 4.0 16.0 - - - +
27F CYS* 3.6 23.5 - - - -
28F PRO* 5.2 1.8 - - + -
29F GLU* 3.0 34.9 + - - -
30F ILE* 4.9 4.9 - - + -
197F ALA* 3.0 28.8 + - + -
198F VAL* 3.3 16.5 + - - +
199F TYR 3.0 0.6 - - - -
200F GLU* 1.3 77.2 - - - +
202F TRP* 1.3 62.0 + - + +
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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