Contacts of the helix formed by residues 297 - 307 (chain K) in PDB entry 3STJ
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 297 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163K GLY 4.7 0.3 + - - -
165K SER* 4.2 5.4 + - - -
248K GLU* 3.3 21.8 - - - -
264K GLY 3.7 12.4 - - - +
295K LEU* 3.4 12.2 - - - +
296K ASN* 1.4 88.5 + - - +
298K PHE* 1.4 61.6 + - - +
299K ALA* 3.5 6.5 + - - +
300K GLU* 2.9 27.6 + - - +
301K LEU* 3.4 14.7 + - - +
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Residues in contact with PHE 298 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244K ILE* 4.5 17.7 - - + -
245K LYS* 5.5 0.2 - - - -
246K GLY* 3.7 37.5 - - - -
247K THR* 3.8 16.2 - - - +
248K GLU* 2.9 22.6 + - + +
264K GLY 3.2 13.1 + - - +
265K ALA* 3.4 24.5 - - + -
297K SER* 1.4 68.6 - - - +
299K ALA* 1.3 56.7 + - + +
301K LEU* 3.1 17.2 + - + +
302K ARG* 2.9 59.8 + - + +
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Residues in contact with ALA 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K SER* 3.6 27.6 - - - -
166K GLY* 5.1 2.7 - - - +
173K GLU 4.2 1.9 + - - +
248K GLU* 3.1 12.9 + - - +
297K SER* 3.7 5.6 - - - +
298K PHE* 1.3 80.2 - - - +
300K GLU* 1.4 58.0 + - - +
302K ARG* 3.4 15.3 + - - +
303K SER* 3.0 27.3 + - - -
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Residues in contact with GLU 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163K GLY* 4.8 1.1 - - - -
165K SER* 4.0 7.5 + - - +
174K ASN* 3.3 24.0 - - - +
293K LYS* 4.7 4.5 - - - +
294K PRO 4.3 8.3 - - - +
295K LEU* 3.7 10.9 - - + +
296K ASN* 2.8 49.3 + - - +
297K SER* 2.9 22.1 + - - +
298K PHE 3.3 0.2 - - - -
299K ALA* 1.4 72.4 - - - +
301K LEU* 1.3 59.4 + - - +
303K SER* 3.0 8.3 + - - -
304K ARG* 2.8 65.0 + - - +
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Residues in contact with LEU 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242K LEU* 3.8 24.2 - - + -
244K ILE* 5.2 2.0 - - + -
265K ALA* 4.4 11.2 - - + -
287K ILE* 4.3 20.9 - - + -
290K LEU* 4.0 16.8 - - + -
295K LEU* 3.8 30.9 - - + +
297K SER 3.4 9.0 + - - +
298K PHE* 3.1 21.9 + - + +
300K GLU* 1.3 78.8 - - - +
302K ARG* 1.3 56.4 + - - +
304K ARG* 3.9 2.1 - - - -
305K ILE* 2.9 56.9 + - + +
316K LEU* 4.9 0.9 - - + -
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Residues in contact with ARG 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K GLN* 5.6 2.8 + - - -
171K GLY 3.4 24.9 + - - -
172K LEU* 4.1 16.4 - - + +
298K PHE* 2.9 43.3 + - + +
299K ALA* 3.4 18.4 + - - +
301K LEU* 1.3 75.5 - - - +
303K SER* 1.4 56.8 + - - +
305K ILE* 3.3 3.7 + - - +
306K ALA* 2.9 33.4 + - + +
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Residues in contact with SER 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K LEU* 4.0 20.0 - - - +
173K GLU 3.2 38.1 + - - -
174K ASN* 3.6 10.2 - - - +
223K MET* 3.8 6.8 - - - +
299K ALA 3.0 10.0 + - - -
300K GLU* 3.0 17.8 + - - -
302K ARG* 1.4 76.0 - - - +
304K ARG* 1.3 58.8 + - - +
306K ALA* 4.4 0.2 - - - +
307K THR* 2.9 30.8 + - - +
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Residues in contact with ARG 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K ASP* 3.1 36.0 + - - -
163K GLY* 6.2 0.2 - - - -
174K ASN* 3.5 24.2 + - - +
222K ASN* 6.1 1.4 - - - +
223K MET* 4.7 4.0 - - + -
290K LEU* 3.6 30.7 - - + -
293K LYS* 3.7 19.4 - - - +
295K LEU* 4.5 5.6 - - - +
300K GLU* 2.8 52.8 + - - +
301K LEU 3.9 0.9 - - - +
303K SER* 1.3 75.7 - - - +
305K ILE* 1.4 58.0 + - - +
307K THR* 3.4 9.9 - - + +
308K THR* 2.5 35.0 + - - +
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Residues in contact with ILE 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240K GLY* 3.6 18.2 - - - +
241K LEU* 3.8 15.3 - - - -
242K LEU* 3.8 32.8 - - + +
290K LEU* 3.8 34.8 - - + -
301K LEU* 2.9 34.4 + - + +
302K ARG* 3.8 4.0 - - - +
304K ARG* 1.4 73.5 - - - +
306K ALA* 1.3 60.8 + - - +
308K THR* 2.9 32.0 + - - +
314K VAL* 4.4 12.1 - - + -
331K LEU* 3.9 11.6 - - + +
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Residues in contact with ALA 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K LEU* 3.7 30.5 - - + -
238K LYS 4.1 1.2 - - - +
239K ARG* 3.0 37.1 + - + +
240K GLY 3.4 23.8 + - - +
302K ARG* 2.9 20.5 + - + +
303K SER 4.4 0.2 - - - +
305K ILE* 1.3 73.3 - - - +
307K THR* 1.3 58.6 + - - +
308K THR 3.8 0.3 - - - +
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Residues in contact with THR 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K SER* 4.9 3.3 - - - -
172K LEU* 4.9 3.1 - - - +
223K MET* 3.5 43.2 - - + +
226K THR* 3.5 15.5 - - + +
227K LEU* 3.6 19.8 - - + +
230K GLN* 3.2 19.7 - - - +
238K LYS 5.2 0.4 - - - -
239K ARG* 4.4 7.8 + - - +
303K SER 2.9 17.2 + - - +
304K ARG* 3.4 16.4 - - + +
305K ILE 3.1 0.8 - - - -
306K ALA* 1.3 75.7 - - - +
308K THR* 1.3 60.2 + - - +
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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