Contacts of the helix formed by residues 221 - 234 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114D LYS* 6.1 0.7 - - - +
115D GLY 5.1 5.1 + - - -
116D PRO* 6.2 0.7 - - - -
218D PRO* 4.3 20.4 - - - -
219D ALA 3.8 0.4 + - - -
220D VAL* 1.3 75.0 - - - +
222D GLU* 1.3 79.3 + - - +
223D LYS* 3.2 9.2 + - - +
224D ASP* 2.7 34.6 + - - -
225D ILE* 3.1 26.7 + - - +
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Residues in contact with GLU 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D PRO* 5.2 4.3 - - - +
221D SER* 1.3 83.1 - - - +
223D LYS* 1.3 65.8 + - + +
225D ILE* 3.7 9.6 + - - +
226D GLN* 3.3 27.9 + - - +
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Residues in contact with LYS 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D PHE* 3.2 26.0 + - - +
76D SER* 5.1 2.0 - - - +
77D HIS 5.8 0.4 - - - -
78D GLY 4.7 10.5 + - - -
80D HIS* 5.4 3.2 + - - -
114D LYS* 3.7 37.2 - - + +
221D SER* 3.2 8.2 + - - +
222D GLU* 1.3 83.1 - - + +
224D ASP* 1.3 62.0 + - - +
226D GLN* 3.0 9.3 + - + +
227D ASP* 2.8 62.3 + - - +
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Residues in contact with ASP 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D THR* 4.1 11.7 - - - +
114D LYS* 3.6 15.9 + - - +
115D GLY* 3.2 28.6 + - - +
219D ALA 3.0 16.3 - - - +
220D VAL* 3.9 11.0 - - + -
221D SER* 2.7 39.3 + - - +
223D LYS* 1.3 77.8 - - - +
225D ILE* 1.3 50.9 - - - +
227D ASP* 3.3 7.9 + - - +
228D LEU* 2.8 43.6 + - + +
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Residues in contact with ILE 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D VAL* 3.7 20.9 - - + +
221D SER 3.1 21.0 + - - +
222D GLU* 4.0 8.1 - - - +
223D LYS 3.3 0.2 - - - -
224D ASP* 1.3 73.1 - - - +
226D GLN* 1.3 72.5 + - - +
228D LEU* 3.3 0.8 + - - +
229D LYS* 3.1 37.6 + - + +
252D GLU* 6.2 0.2 - - - +
256D VAL* 4.0 32.8 - - + -
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Residues in contact with GLN 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D HIS* 3.6 13.0 - - + +
222D GLU 3.3 16.6 + - - +
223D LYS* 3.0 11.3 + - - +
225D ILE* 1.3 84.7 - - - +
227D ASP* 1.3 67.4 + - - +
229D LYS* 3.6 4.6 + - - +
230D PHE* 3.2 22.2 + - - +
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Residues in contact with ASP 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D PHE* 3.2 33.3 - - + +
80D HIS* 3.0 26.7 + - - -
111D LEU* 3.3 17.9 - - + +
113D THR* 5.5 3.4 - - + -
114D LYS* 5.0 3.3 + - - +
223D LYS* 2.8 54.9 + - - +
224D ASP* 3.6 7.7 - - - +
226D GLN* 1.3 75.8 - - - +
228D LEU* 1.3 62.8 + - - +
230D PHE* 3.3 4.5 - - - +
231D GLY 3.2 15.9 + - - -
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Residues in contact with LEU 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LEU* 4.4 3.6 - - + -
113D THR* 4.0 18.6 - - + -
220D VAL* 4.1 20.4 - - + -
224D ASP* 2.8 27.1 + - + +
225D ILE 3.8 0.4 - - - +
227D ASP* 1.3 71.5 - - - +
229D LYS* 1.3 59.5 + - - +
231D GLY* 3.0 16.6 + - - -
232D VAL* 3.4 15.6 + - - +
239D VAL* 3.8 39.7 - - + -
253D VAL* 3.9 26.0 - - + -
256D VAL* 3.8 29.2 - - + -
257D LEU* 4.0 12.7 - - + +
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Residues in contact with LYS 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D ILE* 3.1 30.9 + - + +
226D GLN* 4.1 5.4 - - - +
228D LEU* 1.3 76.5 - - - +
230D PHE* 1.3 59.7 - - - +
232D VAL* 3.5 16.4 + - + +
233D GLU* 3.3 23.4 + - - +
256D VAL* 3.7 29.1 + - + +
257D LEU* 5.7 0.6 + - - +
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Residues in contact with PHE 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D PHE* 3.7 33.7 - + - -
80D HIS* 3.2 56.5 - + + +
83D HIS* 4.2 5.8 - - + -
84D ALA* 4.0 8.1 - - + -
87D ILE* 4.5 5.4 - - + -
111D LEU* 4.7 1.3 - - + -
226D GLN 3.2 14.9 + - - +
227D ASP 3.3 8.7 - - - +
228D LEU 3.1 0.2 - - - -
229D LYS* 1.3 76.7 - - - +
231D GLY* 1.3 62.9 + - - +
233D GLU* 3.4 19.3 + - - +
234D GLN* 3.2 57.3 + - + +
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Residues in contact with GLY 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LEU* 3.8 20.8 - - - +
227D ASP 3.2 5.9 + - - -
228D LEU 3.0 9.7 + - - -
230D PHE* 1.3 76.5 - - - +
232D VAL* 1.3 57.5 + - - +
234D GLN* 3.5 0.8 + - - -
235D ASP 3.0 8.5 + - - -
236D VAL* 2.9 47.2 + - - +
257D LEU* 5.8 0.4 - - - -
264D ILE* 4.8 0.2 - - - -
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D LEU 3.4 15.9 + - - +
229D LYS* 3.8 13.9 - - + +
230D PHE 3.4 0.4 - - - -
231D GLY* 1.3 76.5 - - - +
233D GLU* 1.3 57.4 + - + +
235D ASP* 3.0 21.0 + - - +
256D VAL 5.6 0.2 - - - +
257D LEU* 3.7 32.5 - - + +
260D LYS* 3.6 44.2 - - + +
261D GLY* 3.8 4.3 - - - +
264D ILE* 4.1 10.5 - - + +
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Residues in contact with GLU 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D LYS* 3.3 21.8 - - - +
230D PHE* 3.4 29.3 - - + +
232D VAL* 1.3 72.4 - - - +
234D GLN* 1.3 62.8 + - + +
235D ASP* 3.2 7.3 + - - +
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Residues in contact with GLN 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ALA* 3.9 25.7 - - - +
87D ILE* 4.0 28.9 - - + +
88D LYS 5.5 0.3 + - - -
91D ARG* 2.7 43.8 + - - -
230D PHE* 3.2 48.5 + - + +
231D GLY* 4.0 4.3 - - - +
233D GLU* 1.3 79.1 + - + +
235D ASP* 1.3 57.6 + - - +
236D VAL* 4.7 1.3 - - + -
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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