Contacts of the helix formed by residues 176 - 188 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174T GLN 3.5 1.4 - - - -
175T THR* 1.3 81.0 - - - +
177T LYS* 1.3 58.5 + - - +
178T THR 3.2 2.9 - - - -
179T ALA* 3.6 15.4 - - - +
180T VAL* 2.9 36.7 + - - +
354T LEU* 3.8 3.6 - - - -
359T PHE* 4.2 7.9 - - - -
613T PO4 3.4 9.9 + - - -
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Residues in contact with LYS 177 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169T ILE* 3.6 37.0 - - + +
171T GLY* 3.2 27.1 - - - +
172T ASP 2.9 17.0 + - - -
173T ARG* 4.0 6.1 - - - +
174T GLN 4.0 0.2 - - - +
175T THR* 3.6 13.0 - - - +
176T GLY* 1.3 79.0 - - - +
178T THR* 1.3 59.9 + - - +
180T VAL 3.8 0.2 + - - -
181T ALA* 3.4 21.0 + - - +
272T ASP* 4.6 2.0 - - - -
328T VAL* 3.7 24.9 - - + +
329T ILE 3.6 7.2 - - - +
330T GLU* 4.1 16.9 + - - +
354T LEU* 3.7 15.7 - - + -
613T PO4 2.8 36.5 + - - +
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Residues in contact with THR 178 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177T LYS* 1.3 74.9 - - - +
179T ALA* 1.3 61.2 + - - +
180T VAL 3.3 0.4 - - - -
181T ALA* 3.8 3.9 - - + +
182T LEU* 2.9 33.5 + - + +
205T TYR* 3.9 25.6 - - + +
210T GLN* 4.7 4.7 + - - +
218T LEU* 4.8 10.1 - - + -
271T ASP* 3.2 19.7 + - - +
328T VAL* 5.5 0.2 - - - +
613T PO4 2.9 25.7 + - - -
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Residues in contact with ALA 179 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176T GLY* 3.3 20.2 + - - +
178T THR* 1.3 77.2 - - - +
180T VAL* 1.3 63.3 + - + +
182T LEU* 3.9 3.3 - - - +
183T ASP* 3.1 31.5 + - - +
434T GLN* 3.3 34.5 - - + +
613T PO4 4.1 1.2 + - - +
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Residues in contact with VAL 180 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150T THR* 5.5 4.4 - - + -
152T LEU* 4.7 8.2 - - + +
155T VAL* 4.7 18.4 - - + -
169T ILE* 4.7 17.3 - - + -
176T GLY 2.9 21.0 + - - +
177T LYS 4.0 4.0 - - - +
179T ALA* 1.3 78.9 - - + +
181T ALA* 1.3 60.1 + - - +
183T ASP* 3.7 5.4 + - - +
184T THR* 3.1 22.0 + - - +
352T ILE* 5.6 11.7 - - + -
354T LEU* 4.1 15.5 - - + -
365T PRO* 4.1 28.9 - - + -
367T ILE* 5.4 2.2 - - + -
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Residues in contact with ALA 181 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169T ILE* 3.7 19.3 - - + -
177T LYS 3.4 16.0 + - - +
178T THR* 3.5 8.7 + - + +
179T ALA 3.3 0.4 - - - -
180T VAL* 1.3 80.0 - - - +
182T LEU* 1.3 61.0 + - - +
184T THR* 3.3 14.4 - - - -
185T ILE* 2.9 22.1 - - - +
205T TYR* 5.5 3.8 - - + -
269T VAL* 4.0 26.5 - - + +
271T ASP* 5.5 0.7 - - - +
326T LEU* 5.1 3.8 - - + +
328T VAL* 5.1 2.2 - - + -
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Residues in contact with LEU 182 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178T THR* 2.9 23.9 + - + +
179T ALA* 3.9 3.8 - - - +
180T VAL 3.3 0.2 - - - -
181T ALA* 1.3 73.6 - - - +
183T ASP* 1.3 58.0 + - - +
184T THR 2.9 10.4 + - - -
185T ILE* 3.1 22.1 + - + +
186T LEU* 3.2 21.2 + - + +
205T TYR* 6.2 5.4 - - + -
218T LEU* 4.6 23.1 - - + +
221T THR* 4.7 11.9 - - + -
222T LEU* 4.3 24.2 - - + -
434T GLN* 4.7 4.7 - - - +
435T TYR* 3.6 35.7 - - + +
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Residues in contact with ASP 183 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150T THR* 3.3 9.1 - - - +
152T LEU* 5.2 14.3 - - + +
179T ALA 3.1 17.9 + - - +
180T VAL* 4.1 5.8 - - - +
181T ALA 3.5 0.2 - - - -
182T LEU* 1.3 74.4 - - - +
184T THR* 1.3 56.2 + - - +
186T LEU* 4.0 8.0 - - - +
187T ASN* 3.2 25.8 + - - +
432T GLN* 5.4 3.1 + - - -
433T ASN 4.2 3.3 - - - +
434T GLN* 3.7 15.8 - - - +
435T TYR* 2.9 46.0 + - - -
436T SER 3.9 6.9 + - - -
437T PRO* 5.1 6.4 - - + +
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Residues in contact with THR 184 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148T VAL* 4.7 8.1 - - + -
149T GLN 4.6 0.4 - - - +
150T THR* 3.9 32.6 - - + +
180T VAL* 3.1 16.1 + - - +
181T ALA* 3.3 12.7 + - - -
182T LEU 2.9 0.4 - - - -
183T ASP* 1.3 78.5 - - - +
185T ILE* 1.3 65.0 + - - +
187T ASN* 3.2 5.5 + - - +
188T GLN* 3.0 36.5 + - - +
267T LEU* 3.5 27.6 - - + -
326T LEU* 4.6 11.8 - - + +
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Residues in contact with ILE 185 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181T ALA 2.9 32.1 - - - +
182T LEU* 3.1 15.8 + - + +
184T THR* 1.3 78.2 - - - +
186T LEU* 1.3 57.2 + - - +
188T GLN* 3.3 6.8 + - - +
203T CYS* 3.5 41.3 - - + -
205T TYR* 5.1 15.5 - - + -
222T LEU* 4.3 16.2 - - + -
227T ALA* 4.0 14.4 - - + +
230T TYR* 2.7 39.3 + - + -
231T SER* 4.7 3.6 - - - -
267T LEU* 4.6 4.3 - - + -
269T VAL* 4.5 16.2 - - + -
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Residues in contact with LEU 186 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182T LEU* 3.2 30.9 + - + +
183T ASP* 4.1 11.7 - - - +
185T ILE* 1.3 77.1 - - + +
187T ASN* 1.3 61.2 + - - +
188T GLN 3.4 0.3 + - - -
189T LYS* 3.5 21.8 + - - +
221T THR* 4.8 5.2 - - + +
222T LEU* 4.6 11.0 - - + -
225T HIS* 3.6 42.4 - - + +
227T ALA* 3.8 14.3 - - + +
230T TYR* 4.1 3.1 - - - -
435T TYR* 3.6 35.7 - - + -
437T PRO* 4.7 12.0 - - + +
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Residues in contact with ASN 187 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149T GLN* 2.8 33.5 + - - +
150T THR 3.3 10.3 - - - +
151T GLY* 3.1 17.4 - - - +
183T ASP 3.2 19.0 + - - +
184T THR 3.2 6.7 + - - +
185T ILE 3.2 0.6 - - - -
186T LEU* 1.3 72.2 - - - +
188T GLN* 1.3 58.9 + - - +
189T LYS* 3.0 10.9 + - - +
190T ARG* 2.8 45.9 + - - +
191T TRP* 4.3 6.2 - - - -
437T PRO* 3.2 22.2 - - + +
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Residues in contact with GLN 188 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148T VAL* 4.9 0.4 - - - +
149T GLN* 2.7 34.1 + - - +
163T ARG* 5.1 4.2 + - - -
184T THR* 3.0 31.4 + - + +
185T ILE* 3.6 12.1 - - - +
186T LEU 3.2 1.8 - - - -
187T ASN* 1.3 76.7 - - - +
189T LYS* 1.3 59.2 + - - +
190T ARG* 3.0 6.8 + - - -
191T TRP* 3.8 19.0 + - + +
192T ASN* 2.9 40.0 + - - +
201T LEU* 3.4 39.2 - - + +
203T CYS* 4.4 4.0 - - - -
230T TYR* 3.7 5.2 - - + -
267T LEU* 5.3 0.2 - - + -
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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