Contacts of the helix formed by residues 185 - 197 (chain F) in PDB entry 5K58
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 ASP 185 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157E LEU* 3.7 36.2 - - + +
183F THR 3.8 0.6 + - - -
184F ASP* 1.3 83.2 - - - +
186F PHE* 1.3 60.9 + - - +
187F ASP 3.6 1.6 - - - +
188F ALA* 3.9 10.6 - - + +
189F ARG* 3.0 29.4 + - + +
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Residues in contact with PHE 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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89F ARG* 3.7 36.2 + - - -
92F VAL* 3.7 21.8 - - + -
93F LEU* 3.4 61.5 - - + -
96F LEU* 4.5 17.5 - - + -
165F PHE* 5.8 2.0 - + - -
182F PRO 5.4 0.7 - - - +
183F THR* 4.0 20.1 + - - +
184F ASP 4.4 0.2 - - - -
185F ASP* 1.3 74.9 - - - +
187F ASP* 1.3 66.4 + - - +
188F ALA 3.0 1.5 + - - -
189F ARG* 4.1 8.7 - - + +
190F TRP* 3.3 30.4 + + + +
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Residues in contact with ASP 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ARG* 3.0 29.4 + - - +
185F ASP 3.6 0.2 - - - -
186F PHE* 1.3 78.0 - - - +
188F ALA* 1.3 59.7 + - - +
190F TRP* 4.2 1.7 - - - +
191F PRO* 3.5 16.6 - - - +
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Residues in contact with ALA 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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153E THR* 5.7 0.3 - - - +
157E LEU* 3.7 29.4 - - + -
185F ASP* 3.9 15.1 - - + +
186F PHE 3.0 0.6 - - - -
187F ASP* 1.3 77.1 - - - +
189F ARG* 1.3 64.1 + - - +
190F TRP 3.0 5.3 + - - -
191F PRO* 3.1 13.9 - - - +
192F LEU* 3.7 11.0 - - - +
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Residues in contact with ARG 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E LEU* 3.4 28.7 + - + +
160E SER* 3.3 32.1 + - - -
161E GLN* 3.4 28.9 + - - +
96F LEU* 5.3 2.7 - - - -
165F PHE* 3.9 9.4 - - + -
169F MET* 3.3 34.8 - - - +
172F ARG* 6.2 0.4 - - - +
180F TYR* 5.8 7.5 - - - -
181F ARG 5.0 5.9 + - - -
182F PRO 4.6 2.2 + - - -
184F ASP* 3.4 23.1 + - - +
185F ASP* 3.0 23.1 + - - +
186F PHE* 3.9 9.6 + - + +
188F ALA* 1.3 77.7 - - - +
190F TRP* 1.3 64.8 + - - +
192F LEU* 3.3 22.5 + - - +
193F ILE* 3.8 4.0 + - - +
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Residues in contact with TRP 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F THR* 3.6 21.9 - - + +
88F LEU 3.3 28.3 - - - -
89F ARG* 3.3 54.1 - - + +
92F VAL* 4.2 10.5 - - + -
186F PHE* 3.3 31.2 + + + +
187F ASP 4.2 1.8 - - - +
188F ALA 3.0 4.0 + - - -
189F ARG* 1.3 79.0 - - - +
191F PRO* 1.4 68.6 - - + +
192F LEU 2.8 7.1 + - - -
193F ILE* 3.2 37.0 + - + +
194F ALA* 2.8 35.5 + - + +
197F LEU* 4.5 11.9 - - + -
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Residues in contact with PRO 191 (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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198E GLN* 4.2 2.0 + - - -
187F ASP 3.5 11.4 - - - +
188F ALA* 3.1 14.6 - - - +
190F TRP* 1.4 97.8 - - + +
192F LEU* 1.3 56.8 + - + +
194F ALA* 3.6 11.8 - - + +
195F ALA* 2.7 32.4 + - - +
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Residues in contact with LEU 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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153E THR* 3.6 28.0 - - + -
157E LEU* 4.4 9.0 - - + +
158E LEU* 3.6 26.2 - - + -
161E GLN* 3.9 30.5 - - + +
196E GLN* 3.2 29.1 - - + +
198E GLN* 3.7 19.7 - - - +
188F ALA 3.7 20.2 - - - +
189F ARG* 3.4 10.1 - - - +
190F TRP 2.8 1.4 + - - -
191F PRO* 1.3 80.0 - - + +
193F ILE* 1.3 63.2 + - - +
195F ALA* 3.2 4.0 + - - +
196F GLN 3.1 18.9 + - - -
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Residues in contact with ILE 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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161E GLN* 4.5 10.3 - - - +
196E GLN* 3.8 0.2 + - - -
92F VAL* 5.4 1.6 - - + -
161F GLN 5.8 0.2 - - - +
162F ILE* 3.3 52.0 - - + -
165F PHE* 5.0 14.8 - - + -
189F ARG 3.8 1.9 + - - +
190F TRP* 3.2 41.0 + - + +
192F LEU* 1.3 77.0 - - - +
194F ALA* 1.3 68.2 + - - +
196F GLN* 3.0 38.4 + - + +
197F LEU* 3.2 16.1 + - + +
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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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85F THR* 5.6 4.3 - - + -
190F TRP* 2.8 38.0 + - + +
191F PRO* 3.6 12.6 - - + +
193F ILE* 1.3 80.3 - - - +
195F ALA* 1.3 55.8 + - - +
197F LEU* 3.0 38.7 + - + +
198F GLN* 5.1 0.2 - - - -
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Residues in contact with ALA 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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195E ALA* 4.1 15.2 - - + +
198E GLN* 3.2 27.1 - - + +
191F PRO 2.7 22.9 + - - +
192F LEU 3.4 2.0 - - - +
193F ILE 3.2 0.4 - - - -
194F ALA* 1.3 69.7 - - - +
196F GLN* 1.3 64.3 + - - +
197F LEU 3.3 0.2 - - - -
198F GLN* 3.5 19.9 - - - +
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Residues in contact with GLN 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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161E GLN* 5.2 1.2 - - - +
192E LEU* 3.0 54.3 - - + +
193E ILE* 4.9 0.8 - - - +
195E ALA* 5.0 0.4 - - - -
196E GLN* 2.4 29.6 + - - +
153F THR* 4.8 1.7 + - - -
158F LEU* 4.8 0.3 - - - +
161F GLN* 2.8 42.5 + - - +
162F ILE* 5.4 1.8 - - + -
165F PHE* 5.8 2.8 - - - +
192F LEU 3.1 13.2 + - - +
193F ILE* 3.0 40.5 + - + +
195F ALA* 1.3 74.0 - - - +
197F LEU* 1.3 51.0 + - + +
198F GLN* 2.5 26.5 + - - +
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Residues in contact with LEU 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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85F THR* 5.1 11.7 - - + +
88F LEU* 3.7 39.0 - - + -
140F MET* 5.1 0.2 - - + -
151F TYR* 3.5 29.6 - - + +
153F THR* 5.6 0.4 - - - -
158F LEU* 5.0 14.8 - - + -
162F ILE* 4.3 12.1 - - + -
190F TRP* 4.5 13.5 - - + -
193F ILE* 3.2 30.3 + - + +
194F ALA* 3.0 23.8 + - + +
196F GLN* 1.3 73.4 - - - +
198F GLN* 1.3 63.8 + - - +
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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