Contacts of the helix formed by residues 162 - 174 (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 GLY 162 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375K ARG* 3.3 18.6 - - - -
160O GLY 3.2 4.4 - - - -
161O VAL* 1.3 80.6 - - - +
163O LYS* 1.3 66.2 + - - +
164O THR 3.4 0.7 - - - -
165O VAL* 3.4 11.8 + - - +
166O PHE* 3.1 22.7 + - - +
335O LEU* 4.5 3.4 - - - +
345O TYR* 6.3 1.8 - - - -
611O PO4 3.2 3.9 + - - -
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Residues in contact with LYS 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155O LEU* 4.1 12.5 - - + +
156O PHE 4.6 1.6 - - - -
157O GLY 3.5 17.2 + - - +
158O GLY 3.0 24.0 + - - -
161O VAL* 3.8 15.4 - - + +
162O GLY* 1.3 74.5 - - - +
164O THR* 1.3 63.5 + - - +
166O PHE* 2.9 14.9 + - - +
167O ILE* 3.0 23.0 + - + +
189O GLU* 5.3 5.1 + - - -
256O ASP* 5.4 1.1 - - - +
257O ASN* 3.2 28.0 - - - +
309O ALA* 4.8 1.8 - - + -
310O VAL 3.8 12.6 - - - +
311O TYR* 3.5 22.3 - - - +
335O LEU* 3.9 15.3 - - + -
611O PO4 2.6 27.4 + - - +
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Residues in contact with THR 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375K ARG* 3.4 13.5 - - - -
163O LYS* 1.3 76.2 - - - +
165O VAL* 1.3 63.2 + - - +
167O ILE* 3.1 21.4 + - + +
168O GLN* 3.1 31.6 + - + +
189O GLU* 4.2 8.8 + - - -
190O ARG* 3.3 19.4 + - - -
193O GLU* 3.1 30.5 + - + +
256O ASP* 4.7 11.6 + - - +
611O PO4 3.1 7.1 + - - -
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Residues in contact with VAL 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375K ARG* 3.7 30.3 - - - +
162O GLY* 3.7 10.3 - - - +
163O LYS 3.2 0.4 - - - -
164O THR* 1.3 76.6 - - - +
166O PHE* 1.3 60.9 + - - +
167O ILE 3.5 0.2 + - - -
168O GLN* 3.7 12.3 + - - +
169O GLU* 3.5 21.1 + - - +
193O GLU* 5.5 0.9 - - - +
418O PHE* 4.8 13.7 - - + -
420O VAL* 4.7 6.9 - - + +
421O ALA* 3.9 33.2 - - + +
424O PHE* 4.3 20.4 - - + -
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Residues in contact with PHE 166 (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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138O ILE* 4.4 13.0 - - + -
141O VAL* 3.8 25.1 - - + -
147O TYR* 3.4 21.1 - + - -
155O LEU* 3.4 26.0 - - + -
162O GLY 3.1 13.2 + - - +
163O LYS 2.9 11.5 + - - +
165O VAL* 1.3 76.7 - - - +
167O ILE* 1.3 57.6 + - - +
169O GLU* 4.1 5.1 + - - +
170O LEU* 3.3 35.6 + - + +
333O THR* 4.2 8.1 - - - -
335O LEU* 5.0 7.2 - - + -
346O PRO* 4.0 34.8 - - + -
348O VAL* 4.4 10.5 - - + -
418O PHE* 4.3 16.8 - + - -
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Residues in contact with ILE 167 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155O LEU* 4.3 15.5 - - + -
163O LYS* 3.0 17.4 + - + +
164O THR* 3.1 10.7 + - + +
166O PHE* 1.3 78.0 - - - +
168O GLN* 1.3 65.6 + - + +
170O LEU* 3.0 18.4 + - + +
171O ILE* 3.1 32.4 + - + +
184O PHE* 4.4 11.0 - - + -
254O PHE* 4.3 18.8 - - + -
255O ILE 5.2 0.7 - - - +
256O ASP* 3.7 25.6 - - + +
307O VAL* 5.8 2.2 - - + +
309O ALA* 3.5 30.3 - - + +
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Residues in contact with GLN 168 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164O THR* 3.1 33.3 + - + +
165O VAL* 4.1 5.6 - - - +
167O ILE* 1.3 76.4 - - + +
169O GLU* 1.3 62.2 + - - +
171O ILE* 3.0 15.0 + - + +
172O ASN* 3.0 26.0 + - - +
193O GLU* 4.2 15.9 - - - +
196O ASP* 5.8 5.8 - - - +
197O LEU* 5.4 19.5 - - + +
200O GLU* 5.7 7.7 - - - +
420O VAL* 3.2 38.7 - - + +
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Residues in contact with GLU 169 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138O ILE* 4.8 6.3 - - + -
165O VAL 3.5 14.0 + - - +
166O PHE 4.2 4.9 - - - +
167O ILE 3.2 0.2 - - - -
168O GLN* 1.3 77.9 - - - +
170O LEU* 1.3 58.0 + - - +
172O ASN* 3.1 3.1 + - - +
173O ASN* 2.9 65.2 + - - +
416O GLN* 5.4 3.6 + - - -
417O PRO 5.1 0.7 - - - +
418O PHE* 3.2 39.8 - - + +
419O ALA* 3.0 34.2 + - - +
420O VAL* 3.6 11.4 + - + +
430O LYS 5.6 2.6 - - - +
431O LEU* 5.5 4.3 - - - +
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Residues in contact with LEU 170 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136O THR* 4.5 0.9 - - - -
138O ILE* 4.2 20.6 - - + -
147O TYR* 3.8 30.5 - - + +
155O LEU* 5.3 2.7 - - + -
166O PHE* 3.3 39.9 + - + +
167O ILE* 3.0 13.3 + - - +
169O GLU* 1.3 79.0 - - + +
171O ILE* 1.3 58.3 + - - +
173O ASN* 4.1 1.6 - - - +
174O ILE* 3.5 48.3 + - + +
175O ALA 3.8 1.2 + - - -
254O PHE* 4.0 15.4 - - + -
307O VAL* 4.2 23.1 - - + -
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Residues in contact with ILE 171 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167O ILE* 3.1 21.5 - - + +
168O GLN* 3.0 10.0 + - + +
170O LEU* 1.3 79.2 - - - +
172O ASN* 1.3 63.7 + - - +
173O ASN 3.2 2.0 - - - -
175O ALA* 3.1 29.7 - - + +
176O LYS* 3.4 11.4 + - - +
184O PHE* 3.7 35.7 - - + -
197O LEU* 4.2 17.3 - - + -
201O MET* 3.6 32.5 - - + -
254O PHE* 4.0 18.2 - - + -
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Residues in contact with ASN 172 (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* 3.0 14.7 + - - +
169O GLU* 3.1 11.0 + - - +
171O ILE* 1.3 79.0 - - - +
173O ASN* 1.3 67.3 + - - +
176O LYS* 3.1 51.2 + - - +
200O GLU* 4.0 20.3 + - - +
201O MET* 4.3 10.7 - - - +
419O ALA* 4.9 12.5 - - + +
420O VAL* 4.6 14.8 - - + +
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Residues in contact with ASN 173 (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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136O THR 3.0 22.7 + - - +
137O GLY* 4.6 1.0 - - - -
138O ILE* 4.5 5.9 - - - +
169O GLU* 2.9 49.3 + - - +
172O ASN* 1.3 86.3 - - - +
174O ILE* 1.3 79.8 + - + +
176O LYS* 4.5 0.9 - - - +
177O ALA* 4.0 15.4 + - - +
416O GLN* 6.1 1.0 - - - +
419O ALA* 5.9 0.2 - - - +
431O LEU* 3.9 24.6 - - + +
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Residues in contact with ILE 174 (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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134O LEU* 4.4 31.9 - - + -
135O GLU 4.0 13.7 - - - +
136O THR* 4.1 17.5 - - + +
147O TYR* 5.9 0.4 - - + -
170O LEU* 3.5 36.2 + - + +
173O ASN* 1.3 92.8 - - + +
175O ALA* 1.3 68.1 + - - +
176O LYS 3.1 3.1 + - - -
177O ALA 3.1 14.7 + - - +
178O HIS* 3.2 21.3 + - + +
252O LEU* 3.8 20.9 - - + -
254O PHE* 5.7 0.4 - - + -
305O THR* 6.2 1.1 - - + -
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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