Contacts of the helix formed by residues 176 - 188 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174L GLN 3.5 1.4 - - - -
175L THR* 1.3 81.2 - - - +
177L LYS* 1.3 65.6 + - - +
178L THR 3.4 1.8 - - - -
179L ALA* 3.3 16.4 + - - +
180L VAL* 3.2 24.3 + - - +
354L LEU* 3.8 3.1 - - - -
359L PHE* 5.4 6.0 - - - -
434L GLN* 5.5 2.7 - - - -
608L PO4 2.9 11.7 + - - -
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Residues in contact with LYS 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L ILE* 3.8 20.4 - - + +
171L GLY* 3.3 28.7 - - - +
172L ASP 3.3 10.7 + - - -
173L ARG* 3.9 7.9 - - - +
175L THR* 3.4 11.9 - - - +
176L GLY* 1.3 77.5 - - - +
178L THR* 1.3 63.7 + - - +
180L VAL* 3.1 14.7 + - - +
181L ALA* 3.3 10.3 + - - +
272L ASP* 4.1 9.2 + - - -
328L VAL* 3.7 26.4 - - + +
329L ILE 3.8 12.8 - - - +
330L GLU* 4.2 9.6 + - - -
354L LEU* 3.6 16.2 - - + -
608L PO4 2.8 43.1 + - - +
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Residues in contact with THR 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177L LYS* 1.3 72.6 - - - +
179L ALA* 1.3 57.0 - - - +
181L ALA* 3.1 6.5 + - - +
182L LEU* 2.8 30.1 + - + +
205L TYR* 3.7 27.8 - - + +
210L GLN* 5.2 1.5 + - - +
214L THR* 6.5 0.9 - - + -
218L LEU* 4.5 17.5 - - + -
271L ASP* 3.3 17.6 + - - +
328L VAL* 5.7 1.1 - - - -
608L PO4 2.7 23.2 + - - -
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Residues in contact with ALA 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176L GLY* 3.3 17.8 + - - +
177L LYS 3.2 0.6 - - - -
178L THR* 1.3 78.9 - - - +
180L VAL* 1.3 57.6 + - + +
182L LEU* 3.7 8.4 - - - +
183L ASP* 2.8 39.6 + - - +
434L GLN* 3.3 37.2 - - + +
608L PO4 5.3 0.4 + - - -
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Residues in contact with VAL 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152L LEU* 3.7 26.7 - - + +
155L VAL* 4.6 12.6 - - + -
169L ILE* 5.1 11.9 - - + -
176L GLY 3.4 13.9 - - - +
177L LYS* 3.1 7.9 + - - +
179L ALA* 1.3 78.2 - - + +
181L ALA* 1.3 61.0 + - - +
183L ASP* 3.7 2.5 + - - +
184L THR* 2.8 30.6 + - - +
352L ILE* 4.9 15.3 - - + -
354L LEU* 4.4 17.9 - - + -
365L PRO* 4.7 15.7 - - + -
367L ILE* 6.2 0.4 - - + -
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Residues in contact with ALA 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L ILE* 5.2 7.1 - - + +
177L LYS 3.3 7.6 + - - +
178L THR* 3.1 11.5 + - - +
180L VAL* 1.3 78.0 - - - +
182L LEU* 1.3 64.3 + - - +
184L THR* 3.5 7.6 + - - -
185L ILE* 3.3 26.7 + - - +
205L TYR* 5.3 3.6 - - + -
269L VAL* 3.9 35.3 - - + +
271L ASP* 6.1 0.2 - - - +
326L LEU* 4.9 7.8 - - + +
328L VAL* 4.8 7.6 - - + -
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Residues in contact with LEU 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178L THR* 2.8 19.3 + - + +
179L ALA* 3.7 8.1 - - - +
181L ALA* 1.3 74.4 - - - +
183L ASP* 1.3 62.9 + - - +
184L THR 3.1 2.0 - - - -
185L ILE* 2.8 27.7 + - + +
186L LEU* 2.9 23.7 + - + +
205L TYR* 5.9 2.9 - - + -
218L LEU* 4.3 26.2 - - + +
221L THR* 5.0 8.5 - - + -
222L LEU* 3.9 33.2 - - + +
435L TYR* 3.8 32.5 - - + +
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Residues in contact with ASP 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L THR 3.8 3.6 - - - +
152L LEU* 3.7 32.5 - - + +
179L ALA* 2.8 26.4 + - - +
180L VAL* 4.0 4.9 - - - +
182L LEU* 1.3 81.5 - - - +
184L THR* 1.3 61.3 - - - +
186L LEU* 4.0 8.1 - - - +
187L ASN* 3.1 25.1 + - - +
433L ASN 4.3 0.9 - - - +
434L GLN* 3.7 15.6 - - - +
435L TYR* 3.6 31.9 + - - +
436L SER 5.0 0.9 + - - -
437L PRO* 4.8 8.0 - - + +
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Residues in contact with THR 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L VAL* 4.4 3.8 - - + -
150L THR* 3.5 46.4 + - + +
152L LEU* 5.0 0.3 - - - +
161L ILE* 6.0 0.2 - - + -
180L VAL* 2.8 21.2 + - - +
181L ALA* 3.6 12.3 - - - -
182L LEU 3.1 0.4 - - - -
183L ASP* 1.3 79.0 - - - +
185L ILE* 1.3 61.2 + - - +
187L ASN* 3.6 3.3 + - - +
188L GLN* 2.8 34.8 + - - +
267L LEU* 4.0 26.0 - - + -
326L LEU* 4.4 10.3 - - + +
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Residues in contact with ILE 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181L ALA 3.3 16.6 - - - +
182L LEU* 2.8 14.6 + - + +
184L THR* 1.3 76.3 - - - +
186L LEU* 1.3 64.1 - - - +
188L GLN* 3.2 12.1 + - - +
203L CYS* 3.6 36.6 - - + -
204L VAL 5.8 0.2 - - - -
205L TYR* 4.2 32.3 - - + -
222L LEU* 4.0 19.3 - - + -
230L TYR* 2.9 21.5 + - + +
231L SER* 3.8 18.8 - - - +
267L LEU* 4.4 9.4 - - + -
269L VAL* 4.3 9.6 - - + -
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Residues in contact with LEU 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182L LEU* 2.9 27.6 + - + +
183L ASP* 4.0 8.5 - - - +
185L ILE* 1.3 76.3 - - - +
187L ASN* 1.3 63.9 + - - +
188L GLN 3.0 1.4 + - - -
189L LYS* 3.1 21.7 + - - +
221L THR* 5.3 0.7 - - + -
222L LEU* 4.0 15.5 - - + +
225L HIS* 3.6 43.1 - - + +
227L ALA* 3.6 15.7 - - + +
230L TYR* 3.8 3.6 + - - -
435L TYR* 3.6 42.6 - - + +
437L PRO* 5.5 6.5 - - + -
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Residues in contact with ASN 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149L GLN* 2.8 32.3 + - - +
150L THR 3.8 4.7 - - - +
151L GLY* 3.0 26.0 - - - +
183L ASP 3.1 19.3 + - - +
184L THR 3.7 6.7 - - - +
186L LEU* 1.3 76.7 - - - +
188L GLN* 1.3 58.5 + - - +
189L LYS* 3.0 5.9 + - - +
190L ARG* 2.7 58.9 + - - +
191L TRP* 3.5 5.7 - - - -
437L PRO* 3.4 11.5 - - + +
438L LEU 5.2 0.2 + - - -
439L ALA* 6.1 0.2 - - - +
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Residues in contact with GLN 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L VAL* 4.3 3.2 - - - +
149L GLN 3.0 28.1 + - - +
163L ARG* 5.7 1.4 + - - -
184L THR* 2.8 31.9 + - + +
185L ILE 3.4 11.4 - - - +
186L LEU 3.0 1.2 + - - -
187L ASN* 1.3 75.0 - - - +
189L LYS* 1.3 64.6 + - - +
190L ARG 3.1 1.7 + - - -
191L TRP* 3.3 19.2 + - - +
192L ASN* 3.1 39.3 + - - +
199L LYS 5.7 0.3 - - - +
201L LEU* 3.2 37.4 - - + +
203L CYS* 4.1 15.5 - - - -
230L TYR* 4.3 1.8 - - + +
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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