Contacts of the helix formed by residues 176 - 188 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175S THR* 1.3 80.4 - - - +
177S LYS* 1.3 66.0 + - - +
178S THR 3.1 3.1 - - - -
179S ALA* 3.6 16.8 - - - -
180S VAL* 3.0 32.3 + - - +
354S LEU* 3.6 7.4 - - - -
359S PHE* 4.7 4.4 - - - -
365S PRO* 6.2 1.1 - - - -
612S PO4 3.0 9.6 + - - -
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Residues in contact with LYS 177 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169S ILE* 3.8 28.5 - - + +
170S ILE 4.3 1.1 - - - -
171S GLY* 3.2 29.2 - - - +
172S ASP 3.1 22.9 - - - -
173S ARG* 4.3 1.0 - - - +
175S THR* 3.6 9.8 - - - +
176S GLY* 1.3 78.2 - - - +
178S THR* 1.3 58.1 + - - +
180S VAL* 4.5 0.2 - - - +
181S ALA* 3.9 15.6 + - - +
271S ASP* 5.0 1.6 + - - -
272S ASP* 5.5 3.6 + - - -
328S VAL* 3.6 31.2 - - + +
329S ILE 3.5 15.9 - - - +
330S GLU* 4.0 18.5 + - - +
354S LEU* 3.7 5.1 - - + +
612S PO4 2.8 26.9 + - - +
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Residues in contact with THR 178 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177S LYS* 1.3 74.7 + - - +
179S ALA* 1.3 61.7 + - - +
180S VAL 3.1 2.2 - - - -
181S ALA* 3.8 4.5 - - + +
182S LEU* 3.0 30.6 + - + +
205S TYR* 3.8 25.1 - - + +
210S GLN* 5.4 0.2 + - - -
214S THR* 6.6 0.4 - - + -
218S LEU* 5.0 12.6 - - + -
271S ASP* 2.9 27.8 + - - +
612S PO4 2.9 18.0 + - - -
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Residues in contact with ALA 179 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152S LEU* 5.5 0.2 - - - +
176S GLY* 3.1 20.4 + - - +
178S THR* 1.3 77.8 - - - +
180S VAL* 1.3 61.1 + - + +
182S LEU* 4.1 2.7 - - - -
183S ASP* 3.1 32.7 + - - +
434S GLN* 3.7 33.0 - - + +
612S PO4 4.8 2.3 + - - +
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Residues in contact with VAL 180 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150S THR* 5.7 1.1 - - + -
152S LEU* 3.6 26.5 - - + +
155S VAL* 4.8 11.4 - - + -
169S ILE* 4.6 16.6 - - + -
176S GLY* 3.0 21.2 + - - +
177S LYS* 4.5 3.8 - - - +
179S ALA* 1.3 76.8 - - + +
181S ALA* 1.3 65.1 + - - +
182S LEU 3.2 1.6 - - - -
183S ASP* 3.4 2.8 + - - +
184S THR* 2.9 32.3 + - - +
352S ILE* 6.1 6.3 - - + -
354S LEU* 4.7 9.2 - - + -
365S PRO* 4.1 26.0 - - + -
367S ILE* 6.0 1.3 - - + -
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Residues in contact with ALA 181 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169S ILE* 4.4 11.8 - - + +
177S LYS 3.9 12.0 + - - +
178S THR* 3.4 12.8 + - + +
180S VAL* 1.3 80.7 - - - +
182S LEU* 1.3 61.8 + - - +
184S THR* 3.3 10.5 - - - -
185S ILE* 3.3 27.0 + - - +
205S TYR* 5.5 2.9 - - + -
269S VAL* 3.8 34.6 - - + +
271S ASP* 5.7 0.2 - - - +
326S LEU* 5.3 3.1 - - + -
328S VAL* 5.5 1.1 - - + -
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Residues in contact with LEU 182 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178S THR* 3.0 19.3 + - + +
179S ALA* 4.2 2.0 - - - +
181S ALA* 1.3 73.9 - - - +
183S ASP* 1.3 64.4 + - - +
184S THR 3.0 4.0 - - - -
185S ILE* 2.9 30.3 + - + +
186S LEU* 2.9 21.0 + - + +
205S TYR* 6.0 3.5 - - + -
218S LEU* 4.0 36.3 - - + +
221S THR* 4.9 5.6 - - + -
222S LEU* 3.5 31.6 - - + -
434S GLN* 4.6 6.7 - - - +
435S TYR* 3.6 34.8 - - + +
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Residues in contact with ASP 183 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150S THR 3.4 9.5 - - - +
152S LEU* 4.6 22.5 - - + +
179S ALA 3.1 20.3 + - - +
180S VAL 3.4 4.8 + - - +
182S LEU* 1.3 80.1 - - - +
184S THR* 1.3 60.0 + - - +
186S LEU* 3.6 17.6 - - + +
187S ASN 3.3 14.6 + - - -
433S ASN 4.4 1.6 - - - +
434S GLN* 3.4 17.1 - - - +
435S TYR* 2.9 34.9 + - - -
436S SER 4.2 2.0 + - - -
437S PRO* 3.6 15.5 - - + +
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Residues in contact with THR 184 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148S VAL* 4.8 4.0 - - + -
149S GLN 4.6 0.2 - - - +
150S THR* 3.4 46.0 - - + +
152S LEU* 5.0 0.3 - - - +
180S VAL* 2.9 21.6 + - - +
181S ALA* 3.3 13.2 - - - -
182S LEU 3.0 0.6 - - - -
183S ASP* 1.3 74.9 - - - +
185S ILE* 1.3 64.2 + - - +
187S ASN* 3.2 7.8 + - - +
188S GLN* 2.9 29.9 + - - +
267S LEU* 3.9 24.7 - - + -
326S LEU* 4.6 10.2 - - + +
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Residues in contact with ILE 185 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181S ALA 3.4 14.6 - - - +
182S LEU* 2.9 15.7 + - + +
184S THR* 1.3 75.0 - - - +
186S LEU* 1.3 63.8 - - - +
188S GLN* 3.1 12.4 + - - +
203S CYS* 3.5 44.0 - - + -
205S TYR* 4.5 30.1 - - + -
222S LEU* 4.6 21.1 - - + -
227S ALA* 4.8 1.1 - - + +
230S TYR* 2.9 28.2 + - + +
231S SER* 4.6 8.3 - - - -
267S LEU* 4.9 7.0 - - + -
269S VAL* 4.8 10.3 - - + -
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Residues in contact with LEU 186 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182S LEU* 2.9 21.2 + - + +
183S ASP* 3.6 33.2 - - + +
184S THR 3.3 0.2 - - - -
185S ILE* 1.3 75.3 - - - +
187S ASN* 1.3 60.4 + - - +
189S LYS* 3.0 36.3 - - - +
221S THR* 4.7 1.6 - - + +
222S LEU* 4.0 23.6 - - + -
225S HIS* 3.8 37.0 - - + +
227S ALA* 4.1 3.8 - - + -
230S TYR* 4.2 3.6 - - - -
435S TYR* 3.7 32.3 - - + -
437S PRO* 4.1 9.4 - - + +
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Residues in contact with ASN 187 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149S GLN* 3.2 25.3 + - - +
150S THR 3.5 11.7 - - - +
151S GLY* 3.2 24.5 - - - +
183S ASP 3.3 4.8 + - - +
184S THR 3.2 12.0 + - - +
185S ILE 3.1 1.0 - - - -
186S LEU* 1.3 75.8 - - - +
188S GLN* 1.3 57.5 + - - +
189S LYS* 2.9 11.3 + - - -
190S ARG* 3.0 34.8 + - - +
191S TRP* 3.5 23.8 - - - -
437S PRO* 3.4 17.6 - - + +
438S LEU 4.3 2.1 + - - +
439S ALA* 5.7 0.4 - - - +
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Residues in contact with GLN 188 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148S VAL* 4.9 1.5 - - - +
149S GLN 3.1 25.7 + - - +
163S ARG* 5.0 2.9 + - - -
184S THR* 2.9 26.3 + - - +
185S ILE* 3.1 16.4 + - - +
187S ASN* 1.3 77.1 - - - +
189S LYS* 1.3 62.2 + - - +
190S ARG 3.2 0.9 - - - -
191S TRP* 3.3 18.2 + - + +
192S ASN* 2.9 46.3 + - - +
199S LYS 5.4 0.3 - - - +
201S LEU* 3.2 47.6 + - + +
203S CYS* 3.9 12.1 - - - -
230S TYR* 4.0 1.6 - - + +
267S LEU* 5.2 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