Contacts of the helix formed by residues 228 - 238 (chain P) 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 ALA 228 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87P ILE* 3.9 6.1 - - + -
167P ASN* 3.9 25.1 - - + +
169P PRO* 4.1 12.3 - - + -
175P PHE* 4.6 13.1 - - + +
224P GLN 2.9 22.2 + - - +
225P GLY 2.9 3.7 + - - +
227P ALA* 1.3 78.1 - - - +
229P GLU* 1.3 60.3 + - - +
230P ILE 3.1 0.9 - - - -
231P SER* 3.3 5.4 + - - -
232P ALA* 3.1 24.8 + - - +
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Residues in contact with GLU 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78P THR* 4.1 5.7 - - - -
79P SER* 2.8 45.8 + - - -
84P CYS* 4.0 5.3 - - + +
87P ILE* 3.3 29.7 - - + +
88P HIS* 4.0 9.6 - - - -
134P GLY* 4.6 6.1 - - - -
225P GLY 3.2 19.9 - - - +
226P TYR* 4.6 6.9 - - - -
228P ALA* 1.3 76.6 - - - +
230P ILE* 1.3 64.3 + - + +
231P SER 3.2 0.2 - - - -
232P ALA* 3.6 6.1 - - - +
233P ARG* 2.8 48.8 + - - +
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Residues in contact with ILE 230 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P ALA* 3.9 16.1 - - - +
30P ARG* 3.4 65.3 - - + +
31P LEU* 4.8 6.1 - - - +
34P ALA* 5.0 0.7 - - + -
135P LYS 5.4 2.5 - - - +
136P ASP 5.7 2.2 - - - +
226P TYR 4.2 14.4 - - - +
227P ALA* 3.4 22.2 - - + +
228P ALA 3.1 1.2 - - - +
229P GLU* 1.3 84.8 - - + +
231P SER* 1.3 66.0 + - - +
233P ARG* 3.7 23.6 - - - +
234P ARG* 3.2 23.9 + - - +
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Residues in contact with SER 231 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P LEU* 5.3 8.3 + - - +
35P GLU* 5.7 1.0 + - - -
171P SER 5.9 0.4 - - - -
172P SER* 4.3 22.1 + - - -
173P LEU* 5.7 1.9 - - - +
227P ALA 3.8 10.6 + - - -
228P ALA* 3.3 7.7 + - - -
230P ILE* 1.3 82.6 - - - +
232P ALA* 1.3 65.2 + - - +
233P ARG 3.1 1.6 - - - -
234P ARG* 3.8 21.6 + - - +
235P ASN* 3.2 24.9 + - - +
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Residues in contact with ALA 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P CYS* 2.9 28.0 - - + +
86P SER 6.2 0.2 - - - +
87P ILE* 4.6 12.3 - - + +
173P LEU 6.0 2.0 - - - -
175P PHE* 5.1 10.1 - - + -
228P ALA 3.1 17.3 + - - +
229P GLU* 3.7 10.8 - - - +
231P SER* 1.3 76.9 - - - +
233P ARG* 1.3 57.8 + - - +
235P ASN* 3.8 4.3 + - - +
236P ALA* 3.0 20.6 + - - +
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Residues in contact with ARG 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P MET* 4.2 27.5 - - - +
27P ALA* 4.7 10.5 - - + +
30P ARG* 4.4 10.2 - - - +
79P SER* 5.8 0.2 - - - -
81P LYS* 3.3 46.5 + - - +
82P GLY 3.4 18.4 + - - -
83P LEU* 3.6 14.1 + - - +
84P CYS* 3.9 13.9 + - + +
229P GLU* 2.8 34.4 + - - +
230P ILE* 3.7 29.7 - - - +
232P ALA* 1.3 74.3 - - - +
234P ARG* 1.3 56.4 + - - +
235P ASN 2.9 4.7 + - - -
236P ALA 4.2 0.2 - - - +
237P MET* 2.7 47.4 + - + +
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Residues in contact with ARG 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P MET 4.6 2.9 - - - -
24P LYS* 3.8 18.8 - - + +
27P ALA* 3.8 16.1 - - + +
28P SER* 3.1 30.1 - - - +
31P LEU* 4.4 18.0 - - - +
172P SER* 3.2 33.6 + - - -
173P LEU* 3.2 24.0 - - - +
230P ILE 3.2 17.0 + - - +
231P SER* 3.8 21.4 + - - +
233P ARG* 1.3 78.4 - - - +
235P ASN* 1.3 70.5 + - - +
238P ASP* 3.5 23.3 + - - +
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Residues in contact with ASN 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407K GLN* 3.3 44.7 + - - +
173P LEU* 3.8 32.9 + - - +
231P SER 3.2 16.6 + - - +
232P ALA* 4.2 3.8 - - - +
233P ARG 2.9 0.6 - - - -
234P ARG* 1.3 87.9 - - - +
236P ALA* 1.3 56.3 + - - +
237P MET 3.1 5.4 - - - -
238P ASP* 3.6 6.6 + - - +
239P ASN* 3.1 23.0 + - - +
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Residues in contact with ALA 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391O LEU 4.8 7.2 - - - +
83P LEU 4.2 7.4 - - - +
84P CYS 3.7 19.7 - - - +
85P GLY* 4.5 4.0 - - - +
232P ALA 3.0 20.7 + - - +
233P ARG 3.0 3.6 + - - +
235P ASN* 1.3 76.9 + - - +
237P MET* 1.3 64.8 + - - +
239P ASN* 3.4 23.8 + - - +
240P ALA* 3.5 8.7 + - - +
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Residues in contact with MET 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391M LEU* 5.4 2.0 - - + -
19P ILE* 6.2 0.2 - - + -
20P THR* 3.9 24.1 - - + +
23P MET* 3.5 57.7 - - + +
24P LYS 4.4 0.9 - - - +
83P LEU* 3.5 61.5 - - + +
233P ARG* 2.7 19.8 + - + +
234P ARG 4.3 2.5 - - - +
236P ALA* 1.3 81.5 - - - +
238P ASP* 1.3 57.3 + - - +
239P ASN 2.8 4.3 - - - -
240P ALA* 2.8 23.5 + - - +
241P SER* 2.8 16.9 + - - -
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Residues in contact with ASP 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407K GLN* 5.7 6.3 + - - +
24P LYS* 3.2 40.8 + - + +
234P ARG 3.5 13.7 + - - +
235P ASN* 3.9 7.2 - - - +
237P MET* 1.3 78.4 - - - +
239P ASN* 1.3 57.6 + - - +
241P SER* 3.4 13.4 + - - -
242P LYS* 3.3 35.4 + - - +
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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