Contacts of the helix formed by residues 221 - 235 (chain F) in PDB entry 3SRF
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 SER 221 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115F GLY 5.5 1.5 + - - -
116F PRO* 6.5 0.4 - - - -
218F PRO* 3.8 23.8 - - - -
219F ALA 4.0 0.2 - - - -
220F VAL* 1.3 72.8 - - - +
222F GLU* 1.3 84.8 + - - +
223F LYS* 3.5 4.5 + - - +
224F ASP* 2.8 36.8 + - - +
225F ILE* 3.0 28.1 + - - +
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Residues in contact with GLU 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F PRO* 5.0 5.0 - - - +
221F SER* 1.3 95.2 + - - +
223F LYS* 1.3 66.5 + - + +
225F ILE* 3.6 14.8 + - - +
226F GLN* 3.4 28.4 + - - +
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Residues in contact with LYS 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F PHE* 3.9 15.9 + - - -
76F SER 5.9 0.2 - - - -
78F GLY 5.2 7.3 + - - -
80F HIS* 5.2 3.2 + - - -
114F LYS* 3.5 39.3 - - + +
221F SER* 3.2 8.2 - - - +
222F GLU* 1.3 84.1 + - + +
224F ASP* 1.3 69.0 + - - +
226F GLN* 3.0 10.7 + - + +
227F ASP* 2.9 53.3 + - - +
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Residues in contact with ASP 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F THR* 4.2 9.1 - - + +
114F LYS* 3.9 12.3 + - - +
115F GLY* 3.1 34.7 + - - -
218F PRO 4.6 0.3 - - - +
219F ALA 3.5 12.9 - - - +
220F VAL* 4.0 9.9 - - + -
221F SER* 2.8 40.2 + - - +
223F LYS* 1.3 78.0 - - - +
225F ILE* 1.3 57.8 + - - +
227F ASP* 3.3 7.7 + - - +
228F LEU* 2.9 39.5 + - + +
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Residues in contact with ILE 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F VAL* 3.8 18.6 - - + +
221F SER 3.0 25.5 + - - +
222F GLU* 3.7 12.6 - - - +
223F LYS 3.2 0.2 - - - -
224F ASP* 1.3 75.7 - - - +
226F GLN* 1.3 62.0 + - - +
228F LEU* 3.2 1.6 + - - +
229F LYS* 2.7 61.4 + - + +
252F GLU* 5.8 2.2 - - - +
256F VAL* 4.1 24.6 - - + +
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Residues in contact with GLN 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F HIS* 3.3 11.6 - - + +
222F GLU* 3.4 20.4 + - - +
223F LYS* 3.0 12.0 + - - +
225F ILE* 1.3 86.8 - - - +
227F ASP* 1.3 61.5 + - - +
229F LYS* 3.7 13.0 + - - +
230F PHE* 3.1 27.7 + - - +
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Residues in contact with ASP 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F PHE* 3.3 35.8 - - + +
80F HIS* 2.9 26.0 + - - -
111F LEU* 3.4 19.3 - - + +
113F THR* 5.5 4.0 - - + -
114F LYS* 4.9 4.7 + - - +
223F LYS* 2.9 46.1 + - - +
224F ASP* 3.6 9.9 - - - +
226F GLN* 1.3 77.1 - - - +
228F LEU* 1.3 59.8 + - + +
230F PHE* 3.4 2.8 - - - +
231F GLY 3.1 21.0 + - - -
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Residues in contact with LEU 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F LEU* 4.6 4.5 - - + -
113F THR* 4.2 16.6 - - + -
220F VAL* 4.3 14.1 - - + -
224F ASP* 2.9 24.2 + - + +
225F ILE 3.2 0.2 + - - -
227F ASP* 1.3 75.1 - - - +
229F LYS* 1.3 63.1 - - - +
230F PHE 3.2 0.2 - - - -
231F GLY* 3.3 3.3 + - - +
232F VAL* 3.2 27.0 + - - +
239F VAL* 3.6 34.3 - - + -
253F VAL* 3.8 26.2 - - + -
256F VAL* 3.7 29.6 - - + -
257F LEU* 3.9 19.8 - - + +
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Residues in contact with LYS 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F ILE* 2.7 43.4 + - + +
226F GLN* 4.0 15.3 - - - +
228F LEU* 1.3 70.3 - - - +
230F PHE* 1.3 61.6 + - - +
232F VAL* 3.6 10.2 + - - +
233F GLU* 3.5 22.3 + - - +
256F VAL* 4.6 18.3 + - + +
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Residues in contact with PHE 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F PHE* 3.8 26.5 - + - -
80F HIS* 3.1 54.3 - + + +
83F HIS* 4.4 2.0 - - + -
84F ALA* 3.7 14.1 - - + -
87F ILE* 4.6 5.2 - - + -
111F LEU* 5.0 0.7 - - + -
226F GLN 3.1 19.8 + - - +
227F ASP 3.4 4.3 - - - +
228F LEU 3.2 0.2 - - - -
229F LYS* 1.3 75.2 - - - +
231F GLY* 1.3 60.0 + - - +
233F GLU* 3.4 21.0 - - - +
234F GLN* 2.9 72.1 + - + +
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Residues in contact with GLY 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F LEU* 3.7 22.9 - - - -
227F ASP 3.1 11.1 + - - -
228F LEU 3.3 4.1 + - - -
230F PHE* 1.3 77.5 - - - +
232F VAL* 1.3 52.9 + - - +
234F GLN* 3.6 2.4 - - - -
235F ASP 2.8 26.9 + - - -
236F VAL* 2.9 31.5 + - - +
257F LEU* 6.2 0.2 - - - -
264F ILE* 4.7 0.2 - - - -
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Residues in contact with VAL 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228F LEU 3.2 17.9 + - - +
229F LYS* 3.7 11.4 - - + +
230F PHE 3.2 0.8 - - - -
231F GLY* 1.3 76.4 - - - +
233F GLU* 1.3 62.6 + - - +
235F ASP* 3.2 15.8 + - - +
256F VAL 5.4 0.4 - - - +
257F LEU* 3.9 34.1 - - + +
260F LYS* 3.6 43.7 - - + +
261F GLY* 4.2 1.1 - - - -
264F ILE* 4.1 12.6 - - + +
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Residues in contact with GLU 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229F LYS 3.5 10.6 + - - +
230F PHE* 3.4 34.0 - - + +
232F VAL* 1.3 76.1 - - + +
234F GLN* 1.3 65.7 + - + +
235F ASP* 3.1 8.3 + - - +
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Residues in contact with GLN 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F ALA* 4.0 13.1 - - - +
87F ILE* 3.7 38.2 - - + +
91F ARG* 2.7 40.8 + - - -
230F PHE* 2.9 63.7 + - + +
231F GLY* 3.9 7.2 - - - +
233F GLU* 1.3 80.0 - - + +
235F ASP* 1.3 57.5 + - - +
236F VAL* 4.6 1.8 - - + -
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Residues in contact with ASP 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ARG* 3.2 15.6 + - - +
231F GLY 2.8 9.1 + - - -
232F VAL* 3.2 10.3 + - - +
233F GLU 3.1 6.4 - - - +
234F GLN* 1.3 82.0 - - - +
236F VAL* 1.3 68.5 + - - +
237F ASP* 4.1 8.5 - - - +
264F ILE* 5.6 3.3 - - - +
457F GLN* 4.5 12.5 + - - +
460F ARG* 4.7 14.3 + - - -
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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