Contacts of the helix formed by residues 176 - 188 (chain U) in PDB entry 3FKS
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 GLY 176 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174U GLN* 3.5 2.4 - - - +
175U THR* 1.3 81.8 - - - +
177U LYS* 1.3 62.9 + - - -
178U THR 3.4 0.9 - - - -
179U ALA* 3.4 16.4 + - - +
180U VAL* 3.2 28.2 + - - +
354U LEU* 3.9 2.4 - - - +
359U PHE* 5.7 3.6 - - - -
614U PO4 2.8 14.4 + - - -
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Residues in contact with LYS 177 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169U ILE* 3.7 27.7 - - + +
170U ILE 4.0 2.0 - - - -
171U GLY 3.4 32.8 + - - +
172U ASP 2.8 27.5 + - - -
173U ARG* 4.0 5.1 - - - +
175U THR* 3.5 13.0 - - - +
176U GLY* 1.3 74.2 - - - +
178U THR* 1.3 65.3 + - - +
179U ALA 3.3 0.7 + - - -
180U VAL* 3.4 9.4 + - - +
181U ALA* 3.6 8.5 + - - +
272U ASP* 4.5 2.7 - - - -
328U VAL* 4.0 19.5 - - + +
329U ILE 3.8 13.7 - - - +
330U GLU* 4.0 15.7 - - - +
354U LEU* 3.5 17.9 - - + -
614U PO4 2.8 25.2 + - - +
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Residues in contact with THR 178 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177U LYS* 1.3 76.9 - - - +
179U ALA* 1.3 57.7 + - - +
181U ALA* 3.5 5.4 + - - +
182U LEU* 3.0 34.0 + - + +
205U TYR* 3.5 28.6 + - + +
218U LEU* 5.1 9.2 - - + -
271U ASP* 3.3 19.8 + - - +
328U VAL* 5.8 1.6 - - - -
614U PO4 3.0 18.7 + - - -
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Residues in contact with ALA 179 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176U GLY* 3.4 21.2 + - - +
177U LYS 3.1 0.4 - - - -
178U THR* 1.3 80.9 - - - +
180U VAL* 1.3 62.7 + - + +
182U LEU* 4.4 6.5 - - - -
183U ASP* 3.1 33.1 + - - +
434U GLN* 3.4 33.2 - - + +
614U PO4 4.3 0.6 + - - -
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Residues in contact with VAL 180 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152U LEU* 3.6 27.1 - - + +
155U VAL* 4.5 11.9 - - + -
169U ILE* 4.7 12.1 - - + -
176U GLY 3.2 17.4 + - - +
177U LYS 3.9 4.9 - - - +
178U THR 3.3 0.8 - - - -
179U ALA* 1.3 78.4 - - + +
181U ALA* 1.3 59.8 + - - +
183U ASP* 3.9 0.4 + - - -
184U THR* 3.1 24.2 + - - +
352U ILE* 5.0 11.9 - - + -
354U LEU* 4.2 24.7 - - + -
365U PRO* 4.4 16.4 - - + -
367U ILE* 5.5 1.3 - - + -
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Residues in contact with ALA 181 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169U ILE* 3.9 21.9 - - + +
177U LYS 3.6 5.2 + - - +
178U THR* 3.5 7.7 + - - +
179U ALA 3.3 0.4 - - - -
180U VAL* 1.3 78.3 - - - +
182U LEU* 1.3 65.6 + - - +
184U THR* 3.0 17.8 + - - -
185U ILE* 3.0 18.5 + - + +
205U TYR* 5.5 5.2 - - + -
269U VAL* 4.1 30.9 - - + +
326U LEU* 4.8 4.5 - - + -
328U VAL* 5.3 1.3 - - + -
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Residues in contact with LEU 182 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178U THR* 3.0 22.4 + - + +
179U ALA* 3.8 7.4 - - - +
181U ALA* 1.3 76.0 - - - +
183U ASP* 1.3 64.4 + - - +
185U ILE* 3.0 13.9 + - + +
186U LEU* 3.0 29.8 + - + +
205U TYR* 5.6 8.0 - - + -
218U LEU* 3.6 33.2 - - + -
221U THR* 5.0 6.7 - - + -
222U LEU* 3.7 26.2 - - + -
435U TYR* 3.6 38.6 - - + +
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Residues in contact with ASP 183 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150U THR 4.1 1.8 - - - -
152U LEU* 4.3 25.1 - - + +
179U ALA* 3.1 19.5 + - - +
180U VAL* 4.2 4.3 - - - +
182U LEU* 1.3 79.6 - - - +
184U THR* 1.3 56.4 + - - +
186U LEU* 3.4 6.8 + - - +
187U ASN* 3.0 29.8 + - - +
432U GLN* 4.8 1.6 + - - -
433U ASN 4.5 1.9 - - - +
434U GLN* 3.8 13.5 + - - +
435U TYR* 3.3 41.1 + - - -
436U SER 4.4 2.4 + - - -
437U PRO* 3.7 14.1 - - + +
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Residues in contact with THR 184 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148U VAL* 4.4 12.3 - - + -
150U THR* 3.2 51.7 - - + +
152U LEU* 4.5 2.6 - - - +
180U VAL* 3.1 14.9 + - - +
181U ALA* 3.0 13.5 + - - -
183U ASP* 1.3 76.0 - - - +
185U ILE* 1.3 68.4 + - + +
187U ASN* 3.3 10.2 + - - +
188U GLN* 3.3 17.3 + - + +
267U LEU* 4.4 14.1 - - + -
326U LEU* 4.9 8.9 - - + +
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Residues in contact with ILE 185 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181U ALA* 3.0 17.2 + - + +
182U LEU* 3.3 14.1 - - + +
184U THR* 1.3 78.4 - - + +
186U LEU* 1.3 63.6 + - + +
188U GLN* 3.3 18.3 + - - +
203U CYS* 3.4 42.2 - - + -
204U VAL 5.5 1.6 - - - +
205U TYR* 5.5 12.1 - - + -
222U LEU* 4.6 14.8 - - + -
227U ALA* 4.9 1.6 - - + -
230U TYR* 3.7 11.5 + - + -
231U SER* 3.9 13.7 - - - +
267U LEU* 4.1 22.0 - - + +
269U VAL* 4.6 10.3 - - + +
326U LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 186 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182U LEU* 3.0 22.6 + - + +
183U ASP* 3.7 11.2 - - - +
185U ILE* 1.3 76.4 - - - +
187U ASN* 1.3 61.9 + - - +
188U GLN 3.1 1.2 + - - -
189U LYS* 3.1 23.0 + - - +
221U THR* 5.5 1.3 - - + -
222U LEU* 3.7 28.7 - - + -
225U HIS* 3.9 37.0 - - + +
227U ALA* 3.9 14.6 - - + -
230U TYR* 3.7 4.0 + - - -
435U TYR* 3.6 36.3 - - + -
437U PRO* 5.1 6.3 - - + -
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Residues in contact with ASN 187 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149U GLN* 2.7 28.0 + - - +
150U THR 3.4 17.0 - - - +
151U GLY* 3.5 11.6 - - - -
183U ASP 3.0 11.0 + - - +
184U THR 3.3 2.9 + - - +
186U LEU* 1.3 72.9 - - - +
188U GLN* 1.3 56.2 + - - +
189U LYS* 3.0 10.2 + - - -
190U ARG* 3.3 30.1 + - - +
191U TRP* 3.1 24.1 - - - -
437U PRO* 3.2 27.6 - - + +
438U LEU 3.7 6.8 + - - +
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Residues in contact with GLN 188 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148U VAL* 3.7 13.1 - - - +
149U GLN 3.3 27.7 + - - +
163U ARG* 3.9 5.7 + - - +
184U THR* 3.3 19.9 + - + +
185U ILE* 3.4 13.7 - - - +
186U LEU 3.1 1.4 - - - -
187U ASN* 1.3 74.4 - - - +
189U LYS* 1.3 55.9 + - - +
190U ARG 3.2 2.4 + - - -
191U TRP* 3.5 21.5 + - - +
192U ASN* 2.8 48.7 + - - +
199U LYS 4.7 0.3 - - - +
201U LEU* 3.2 49.2 + - + +
203U CYS* 4.6 3.4 - - - -
230U TYR* 4.0 1.1 - - + -
267U LEU* 5.8 0.7 - - + -
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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