Contacts of the helix formed by residues 191 - 204 (chain O) 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 THR 191 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136K PRO 4.1 3.4 - - - +
137K GLY* 3.9 30.1 - - - +
138K ILE* 4.1 17.0 - - + -
141K ARG* 4.0 15.4 - - - +
309K GLU* 2.7 35.9 + - - -
190O ARG* 1.3 71.9 - - - +
192O ARG* 1.3 61.5 + - - +
193O GLU 3.3 0.7 - - - -
194O GLY* 3.0 14.9 + - - +
195O ASN* 3.2 13.0 + - - +
221O GLN* 3.2 26.0 - - + +
223O ASN* 3.5 4.6 + - - +
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Residues in contact with ARG 192 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141K ARG* 3.8 24.2 - - - +
142K ARG 6.0 1.6 - - - +
143K SER* 5.3 9.0 + - - +
144K VAL* 5.6 9.2 - - + +
164K GLY 4.9 12.1 - - - +
165K GLN* 6.3 0.7 - - - -
166K ARG* 3.4 22.8 - - - +
309K GLU* 4.5 0.2 + - - -
312K ALA* 5.5 2.2 - - + -
313K LYS 6.1 0.7 - - - +
349K ASP* 3.8 32.7 + - - +
375K ARG* 4.5 6.1 + - - +
376K VAL* 3.5 29.9 - - - +
190O ARG 3.4 0.4 - - - -
191O THR* 1.3 80.6 - - - +
193O GLU* 1.3 88.3 + - - +
194O GLY 3.3 1.0 + - - -
195O ASN* 3.5 5.6 + - - +
196O ASP* 2.8 50.4 + - - +
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Residues in contact with GLU 193 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375K ARG* 3.3 24.0 + - - +
164O THR* 3.1 31.7 + - + +
165O VAL* 5.5 1.0 - - - +
168O GLN* 4.2 14.7 - - - +
190O ARG* 3.3 38.8 + - + +
191O THR 3.3 0.2 - - - -
192O ARG* 1.3 108.9 + - - +
194O GLY* 1.3 60.8 + - - +
196O ASP* 3.7 11.0 - - + +
197O LEU* 3.4 21.0 + - - +
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Residues in contact with GLY 194 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138K ILE* 4.2 7.7 - - - +
190O ARG 3.9 4.8 + - - -
191O THR 3.0 12.2 + - - -
193O GLU* 1.3 78.1 - - - +
195O ASN* 1.3 65.0 + - - +
197O LEU* 3.3 6.5 + - - +
198O TYR* 3.1 20.8 + - - +
219O PHE* 3.8 29.0 - - - -
221O GLN* 4.8 0.4 - - - -
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Residues in contact with ASN 195 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138K ILE* 3.0 35.4 + - - +
139K LEU* 4.6 4.6 + - - +
141K ARG* 3.3 37.2 + - + +
142K ARG* 3.6 12.0 + - - -
143K SER 4.1 2.8 + - - -
191O THR 3.2 9.9 + - - +
192O ARG 3.5 8.9 + - - +
194O GLY* 1.3 74.5 - - - +
196O ASP* 1.3 59.9 + - - +
198O TYR* 3.2 14.2 + - - +
199O ARG* 2.9 36.5 + - - +
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Residues in contact with ASP 196 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143K SER* 3.6 29.8 + - - -
168O GLN* 5.8 5.8 - - - +
192O ARG* 2.8 49.6 + - - +
193O GLU* 3.7 10.6 - - + +
194O GLY 3.2 0.2 - - - -
195O ASN* 1.3 79.5 - - - +
197O LEU* 1.3 51.2 + - - +
199O ARG* 3.1 9.3 + - - +
200O GLU* 2.8 36.2 + - - +
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Residues in contact with LEU 197 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O GLN* 5.4 19.0 - - + +
171O ILE* 4.2 17.5 - - + -
184O PHE* 3.7 48.0 - - + -
193O GLU 3.4 13.3 + - - +
194O GLY* 3.3 9.5 + - - +
196O ASP* 1.3 77.8 - - - +
198O TYR* 1.3 57.8 + - - +
200O GLU* 4.2 7.4 - - + -
201O MET* 2.8 61.9 + - + +
217O LEU* 5.4 7.0 - - + -
219O PHE* 5.1 7.2 - - + -
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Residues in contact with TYR 198 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138K ILE* 4.7 10.1 - - + -
139K LEU* 4.6 19.2 - - + +
93O GLY 5.1 5.3 + - - -
95O ILE* 3.4 28.7 - - + +
104O ASP* 4.6 8.0 + - + +
106O ARG* 5.2 11.8 + - - -
194O GLY 3.1 12.8 + - - +
195O ASN* 3.2 22.2 + - - +
197O LEU* 1.3 77.5 - - - +
199O ARG* 1.3 60.8 + - + +
201O MET* 4.3 3.4 - - - +
202O LYS* 3.2 58.3 + - + +
207O ILE* 4.6 18.6 - - + +
217O LEU* 3.7 27.1 - - + +
219O PHE* 6.2 1.1 - - + -
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Residues in contact with ARG 199 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K ARG 4.4 3.4 + - - -
142K ARG* 3.8 36.8 - - - +
143K SER* 3.7 33.6 - - - +
315K SER* 6.2 0.2 - - - -
195O ASN* 2.9 23.7 + - - +
196O ASP* 3.1 11.4 + - - +
198O TYR* 1.3 79.6 - - + +
200O GLU* 1.3 60.6 + - - +
202O LYS* 3.6 6.8 + - - +
203O GLU* 3.1 55.8 + - + +
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Residues in contact with GLU 200 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O GLN* 5.7 7.4 - - - +
172O ASN* 4.0 20.5 + - - +
176O LYS* 4.7 0.2 + - - -
196O ASP 2.8 16.8 + - - +
197O LEU* 3.7 10.8 - - + +
199O ARG* 1.3 73.1 - - - +
201O MET* 1.3 73.7 + - + +
202O LYS 3.1 1.6 - - - -
203O GLU* 3.2 6.1 + - - +
204O THR* 2.8 55.5 + - + +
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Residues in contact with MET 201 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171O ILE* 3.6 34.1 - - + +
172O ASN* 4.3 15.0 - - - +
175O ALA* 5.9 1.1 - - - -
176O LYS* 4.6 5.4 - - - -
197O LEU* 2.8 41.0 + - + +
198O TYR* 4.4 2.9 - - - +
200O GLU* 1.3 80.4 - - + +
202O LYS* 1.3 53.7 + - - +
204O THR* 3.4 12.5 + - - +
206O VAL* 3.1 35.1 + - + +
207O ILE* 2.7 46.8 + - + -
215O VAL* 5.2 8.5 - - + -
217O LEU* 5.6 7.9 - - + -
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Residues in contact with LYS 202 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198O TYR* 3.2 51.3 + - + +
199O ARG* 4.0 7.6 - - - +
200O GLU 3.1 0.6 - - - -
201O MET* 1.3 81.6 - - - +
203O GLU* 1.3 67.0 + - + +
204O THR 3.7 0.3 + - - -
205O GLY* 3.9 6.2 + - - -
207O ILE* 3.5 36.0 - - + +
209O LEU* 4.3 33.3 - - + +
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Residues in contact with GLU 203 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199O ARG* 3.1 46.1 + - + +
200O GLU* 4.2 6.2 - - - +
202O LYS* 1.3 82.6 - - + +
204O THR* 1.3 62.8 + - + +
205O GLY 3.4 0.4 - - - -
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Residues in contact with THR 204 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176O LYS* 3.8 26.2 - - - +
200O GLU* 2.8 48.3 + - + +
201O MET* 3.4 13.0 + - - +
203O GLU* 1.3 81.8 - - + +
205O GLY* 1.3 59.6 + - - +
206O VAL* 3.5 14.0 - - - +
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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