Contacts of the helix formed by residues 176 - 187 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174K GLN 3.5 2.2 - - - -
175K THR* 1.3 80.2 - - - +
177K LYS* 1.3 64.8 + - - +
178K THR 3.6 0.4 - - - -
179K ALA* 3.5 16.5 - - - +
180K VAL* 3.1 30.1 + - - +
354K LEU* 3.5 4.0 - - - +
359K PHE* 4.2 8.9 - - - -
607K PO4 2.8 11.0 + - - -
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Residues in contact with LYS 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K ILE* 3.7 22.1 - - + +
171K GLY 3.8 14.4 - - - +
172K ASP 3.2 23.8 + - - -
173K ARG* 3.8 7.1 - - - +
175K THR* 3.8 11.4 - - - +
176K GLY* 1.3 79.8 - - - +
178K THR* 1.3 63.7 - - - +
180K VAL* 3.2 10.6 + - - +
181K ALA* 3.5 10.4 + - - +
271K ASP* 6.0 0.2 - - - -
272K ASP* 3.8 11.4 - - - -
328K VAL* 3.6 30.5 - - + +
329K ILE 3.4 20.6 - - - +
330K GLU* 4.0 16.2 + - - +
354K LEU* 3.8 7.4 - - + -
607K PO4 2.9 30.3 + - - +
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Residues in contact with THR 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177K LYS* 1.3 77.1 - - - +
179K ALA* 1.3 56.9 + - - +
181K ALA* 3.4 4.6 + - + +
182K LEU* 2.9 35.7 + - + +
205K TYR* 3.5 30.2 + - + +
210K GLN* 4.3 3.4 + - - +
218K LEU* 4.3 12.1 - - + -
271K ASP* 2.7 23.8 + - - +
328K VAL* 5.6 0.2 - - - -
607K PO4 3.0 18.1 + - - -
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Residues in contact with ALA 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176K GLY* 3.5 23.0 - - - +
177K LYS 3.1 0.2 - - - -
178K THR* 1.3 79.4 - - - +
180K VAL* 1.3 61.6 + - + +
182K LEU* 3.7 6.0 + - - +
183K ASP* 3.2 30.5 + - - +
434K GLN* 4.2 25.6 + - + +
607K PO4 3.8 3.1 + - - +
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Residues in contact with VAL 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K THR* 5.6 2.9 - - + -
152K LEU* 4.2 17.6 - - + +
155K VAL* 4.6 12.6 - - + -
169K ILE* 5.1 13.2 - - + -
176K GLY 3.1 17.6 + - - +
177K LYS 3.2 4.7 + - - +
179K ALA* 1.3 76.5 - - + +
181K ALA* 1.3 65.5 + - - +
183K ASP* 3.4 9.8 + - - +
184K THR* 3.0 24.0 + - - +
352K ILE* 5.3 11.2 - - + -
354K LEU* 4.3 12.3 - - + -
365K PRO* 4.2 27.4 - - + -
367K ILE* 5.6 1.8 - - + -
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Residues in contact with ALA 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K ILE* 5.2 10.0 - - + +
177K LYS 3.5 8.3 + - - +
178K THR* 3.4 10.6 + - - +
180K VAL* 1.3 75.7 - - - +
182K LEU* 1.3 68.7 + - - +
184K THR* 2.9 20.4 + - - -
185K ILE* 3.0 18.7 - - + +
205K TYR* 5.4 4.0 - - + -
269K VAL* 3.8 33.4 - - + -
326K LEU* 5.1 7.0 - - + -
328K VAL* 5.3 3.1 - - + -
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Residues in contact with LEU 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178K THR* 2.9 22.4 + - + +
179K ALA* 3.8 6.3 - - - +
180K VAL 3.3 0.2 - - - -
181K ALA* 1.3 76.7 - - - +
183K ASP* 1.3 64.7 + - - +
185K ILE* 3.1 12.3 + - + +
186K LEU* 3.1 31.3 + - + +
205K TYR* 6.1 4.6 - - + -
218K LEU* 4.3 27.6 - - + +
221K THR* 5.0 7.0 - - + -
222K LEU* 4.2 24.0 - - + -
434K GLN* 4.9 6.1 - - - +
435K TYR* 3.5 40.2 - - + +
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Residues in contact with ASP 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K THR* 3.5 7.2 - - - +
151K GLY 6.2 0.4 - - - +
152K LEU* 4.7 17.2 - - + +
179K ALA 3.2 17.6 - - - +
180K VAL* 3.4 8.6 + - - +
181K ALA 3.2 0.4 - - - -
182K LEU* 1.3 79.3 - - - +
184K THR* 1.3 56.8 + - - +
186K LEU* 3.8 7.4 - - - +
187K ASN* 2.9 32.7 + - - +
432K GLN* 5.4 5.2 + - - +
433K ASN 4.6 3.5 - - - +
434K GLN* 4.3 13.2 - - - +
435K TYR* 3.9 33.2 + - - -
436K SER 5.3 1.3 + - - -
437K PRO* 4.7 8.9 - - + +
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Residues in contact with THR 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K VAL* 4.3 10.3 - - + -
149K GLN 4.5 0.2 - - - +
150K THR* 3.6 43.9 - - + +
180K VAL* 3.0 17.7 + - - +
181K ALA* 2.9 15.8 + - - -
183K ASP* 1.3 79.4 - - - +
185K ILE* 1.3 58.5 + - - +
187K ASN* 3.5 5.0 + - - +
188K GLN* 3.3 22.2 + - - +
267K LEU* 3.7 24.0 - - + -
326K LEU* 4.3 12.9 - - + +
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Residues in contact with ILE 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181K ALA* 3.0 31.9 - - + +
182K LEU* 3.1 10.2 + - + +
184K THR* 1.3 79.1 - - - +
186K LEU* 1.3 59.5 + - + +
188K GLN* 3.0 14.0 + - - +
203K CYS* 3.7 32.8 - - + -
204K VAL 6.3 0.9 - - - -
205K TYR* 5.4 11.9 - - + -
222K LEU* 4.5 20.0 - - + -
227K ALA* 4.6 1.6 - - + -
230K TYR* 2.8 43.3 + - + +
231K SER* 4.8 6.7 - - - -
267K LEU* 4.6 3.1 - - + -
269K VAL* 3.9 24.7 - - + -
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Residues in contact with LEU 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K LEU* 3.1 29.9 + - + +
183K ASP* 3.3 8.7 + - - +
185K ILE* 1.3 75.8 - - - +
187K ASN* 1.3 61.3 + - - +
188K GLN 3.1 1.1 + - - -
189K LYS* 3.2 23.2 + - - +
221K THR* 4.6 2.7 - - + +
222K LEU* 3.7 27.1 - - + -
225K HIS* 3.9 29.4 - - + +
227K ALA* 3.7 15.4 - - + +
230K TYR* 3.8 3.1 - - - -
435K TYR* 3.7 37.7 - - + -
437K PRO* 4.9 10.2 - - + +
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Residues in contact with ASN 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K GLN* 2.9 24.7 + - - +
150K THR 3.3 18.2 - - - +
151K GLY* 3.3 18.1 - - - +
183K ASP 2.9 9.9 + - - +
184K THR 3.9 3.8 - - - +
185K ILE 3.2 0.4 - - - -
186K LEU* 1.3 72.6 - - - +
188K GLN* 1.3 56.9 + - - +
189K LYS* 3.0 9.5 + - - -
190K ARG* 2.8 35.3 + - - +
191K TRP* 3.3 25.1 - - - -
437K PRO* 3.1 23.7 - - + +
438K LEU 3.4 3.2 + - - +
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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