Contacts of the helix formed by residues 221 - 234 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C GLY 5.1 3.3 + - - -
116C PRO* 6.4 0.7 - - - -
218C PRO* 3.8 23.1 - - - -
219C ALA 4.1 0.6 - - - -
220C VAL* 1.3 74.1 - - - +
222C GLU* 1.3 66.8 + - - +
223C LYS* 3.8 8.8 + - - +
224C ASP* 2.9 33.0 + - - -
225C ILE* 2.9 33.6 + - - +
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Residues in contact with GLU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C PRO* 5.0 5.2 - - - +
221C SER* 1.3 80.8 - - - +
223C LYS* 1.3 64.2 + - + +
225C ILE* 3.8 13.5 + - - +
226C GLN* 3.4 26.0 + - - +
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Residues in contact with LYS 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PHE* 3.6 16.4 + - - -
76C SER 5.6 1.6 - - - -
78C GLY 5.1 7.3 + - - -
114C LYS* 3.6 37.9 - - + +
221C SER* 3.2 7.5 + - - +
222C GLU* 1.3 83.4 - - + +
224C ASP* 1.3 63.8 + - - +
226C GLN* 3.2 9.6 + - - +
227C ASP* 2.9 52.2 + - - +
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Residues in contact with ASP 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C THR* 4.1 9.7 - - + +
114C LYS* 3.3 19.4 + - - +
115C GLY* 3.2 40.2 + - - -
218C PRO 5.3 0.2 - - - +
219C ALA 4.1 4.4 - - - +
220C VAL* 3.9 9.9 - - + -
221C SER* 2.9 34.0 + - - +
223C LYS* 1.3 75.4 - - - +
225C ILE* 1.3 56.5 + - - +
227C ASP* 3.2 10.5 + - - +
228C LEU* 2.8 41.0 + - + +
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Residues in contact with ILE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C VAL* 3.8 20.2 - - + +
221C SER 2.9 24.9 + - - +
222C GLU* 3.9 11.2 - - - +
223C LYS 3.3 0.2 - - - -
224C ASP* 1.3 72.5 - - - +
226C GLN* 1.3 63.2 + - + +
228C LEU* 3.3 1.2 + - - +
229C LYS* 2.9 45.8 + - + +
252C GLU* 6.1 0.7 - - - +
256C VAL* 3.9 31.9 - - + -
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Residues in contact with GLN 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C HIS* 3.4 26.4 + - - +
222C GLU 3.4 15.4 + - - +
223C LYS* 3.2 13.3 + - - +
225C ILE* 1.3 80.9 - - + +
227C ASP* 1.3 60.9 + - - +
229C LYS* 4.1 12.4 - - - +
230C PHE* 3.2 17.3 + - - +
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Residues in contact with ASP 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PHE* 3.5 35.0 - - + +
80C HIS* 3.3 23.7 + - - -
111C LEU* 3.4 20.2 - - + +
113C THR* 5.6 2.9 - - + -
114C LYS* 4.8 1.0 + - - +
223C LYS* 2.9 47.6 + - - +
224C ASP* 3.2 18.4 + - - +
226C GLN* 1.3 78.0 - - - +
228C LEU* 1.3 57.6 + - + +
230C PHE* 3.5 4.0 - - - +
231C GLY 3.2 18.9 + - - -
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Residues in contact with LEU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU* 4.3 4.9 - - + -
113C THR* 3.8 27.4 - - + -
220C VAL* 4.4 14.6 - - + -
224C ASP* 2.8 22.4 + - + +
225C ILE 3.9 3.1 - - - +
227C ASP* 1.3 70.4 - - - +
229C LYS* 1.3 60.6 + - - +
230C PHE 3.1 1.6 - - - -
231C GLY* 2.9 17.1 + - - -
232C VAL* 3.1 17.8 + - - +
239C VAL* 3.8 22.7 - - + -
253C VAL* 4.0 21.3 - - + +
256C VAL* 3.9 31.4 - - + -
257C LEU* 3.8 21.3 - - + +
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Residues in contact with LYS 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C ILE* 2.9 35.4 + - + +
226C GLN* 4.2 13.7 - - - +
228C LEU* 1.3 76.9 - - - +
230C PHE* 1.3 61.6 + - - +
232C VAL* 3.5 10.5 + - + +
233C GLU* 3.5 25.8 + - - +
256C VAL* 4.5 17.0 + - + +
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Residues in contact with PHE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PHE* 4.0 24.0 - + - -
80C HIS* 3.2 58.8 - + + +
84C ALA* 3.7 18.6 - - + -
87C ILE* 4.4 7.0 - - + -
111C LEU* 5.2 0.2 - - + -
226C GLN 3.2 19.6 + - - +
227C ASP 3.5 4.3 - - - +
228C LEU 3.1 0.4 - - - -
229C LYS* 1.3 77.6 - - - +
231C GLY* 1.3 59.4 + - - +
233C GLU* 3.4 18.1 - - - +
234C GLN* 2.9 65.5 + - + +
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Residues in contact with GLY 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU* 3.6 24.2 - - - -
227C ASP 3.2 6.9 + - - -
228C LEU* 2.9 8.9 + - - -
230C PHE* 1.3 76.3 - - - +
232C VAL* 1.3 59.2 + - - +
234C GLN* 4.6 1.8 - - - -
235C ASP 2.9 7.1 + - - -
236C VAL* 2.9 44.3 + - - +
257C LEU* 6.0 0.7 - - - -
264C ILE* 4.5 0.6 - - - +
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Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C LEU 3.4 15.5 - - - +
229C LYS* 3.8 9.6 - - - +
230C PHE 3.3 0.2 - - - -
231C GLY* 1.3 77.2 - - - +
233C GLU* 1.3 63.6 + - - +
235C ASP* 3.1 15.2 + - - +
256C VAL 5.0 1.8 - - - +
257C LEU* 4.0 33.7 - - + +
260C LYS* 4.0 20.4 - - + +
261C GLY* 3.9 21.8 - - - +
264C ILE* 4.3 12.8 - - + +
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Residues in contact with GLU 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C LYS* 3.5 14.2 + - - +
230C PHE* 3.4 26.5 - - - +
232C VAL* 1.3 76.2 - - - +
234C GLN* 1.3 71.0 + - + +
235C ASP* 3.1 8.5 + - - +
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Residues in contact with GLN 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ALA* 3.7 19.4 - - - +
87C ILE* 3.7 29.7 - - + +
91C ARG* 2.8 38.3 + - - -
230C PHE* 2.9 56.5 + - + +
231C GLY* 4.4 3.6 - - - +
233C GLU* 1.3 77.8 + - + +
235C ASP* 1.3 57.5 + - - +
236C VAL* 5.2 1.5 - - + +
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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