Contacts of the helix formed by residues 297 - 308 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D GLY 4.8 0.2 + - - -
165D SER* 4.2 5.8 + - - -
248D GLU* 3.3 22.9 - - - -
264D GLY* 3.9 11.1 - - - +
295D LEU* 3.3 9.2 - - - +
296D ASN* 1.4 87.4 + - - +
298D PHE* 1.3 62.1 + - - +
299D ALA* 3.5 6.9 + - - +
300D GLU* 2.9 27.8 + - - +
301D LEU* 3.4 17.7 + - - +
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Residues in contact with PHE 298 (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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244D ILE* 4.5 19.1 - - + -
245D LYS* 5.2 0.4 - - - -
246D GLY* 3.7 37.2 - - - -
247D THR* 3.8 20.6 - - - +
248D GLU* 2.9 22.3 + - + +
264D GLY 3.4 8.9 + - - +
265D ALA* 3.3 24.0 - - + -
297D SER* 1.3 70.5 - - - +
299D ALA* 1.3 56.2 + - - +
301D LEU* 3.2 15.1 + - + +
302D ARG* 2.7 62.7 + - + +
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Residues in contact with ALA 299 (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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165D SER* 3.6 28.3 - - - -
166D GLY* 4.9 4.9 - - - +
173D GLU 4.2 1.6 + - - +
248D GLU* 3.1 12.6 + - - +
297D SER* 3.7 5.2 - - - +
298D PHE* 1.3 80.8 - - + +
300D GLU* 1.4 55.1 + - - +
302D ARG* 3.6 13.3 + - - +
303D SER* 2.9 30.3 + - - -
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Residues in contact with GLU 300 (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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163D GLY* 4.8 0.8 - - - -
165D SER* 4.1 7.5 + - - +
174D ASN* 3.3 26.1 + - - +
293D LYS* 4.8 3.1 - - - +
294D PRO 4.2 8.2 - - - +
295D LEU* 3.7 11.7 - - + +
296D ASN* 2.8 48.7 + - - +
297D SER* 2.9 22.6 + - - +
299D ALA* 1.4 72.2 - - - +
301D LEU* 1.3 58.1 + - - +
303D SER* 3.2 7.7 + - - -
304D ARG* 2.9 67.7 + - - +
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Residues in contact with LEU 301 (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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242D LEU* 3.8 24.9 - - + -
244D ILE* 5.2 2.0 - - + -
265D ALA* 4.4 11.9 - - + -
287D ILE* 4.3 20.4 - - + -
290D LEU* 4.0 20.0 - - + -
295D LEU* 3.7 30.6 - - + +
297D SER 3.4 9.6 + - - +
298D PHE* 3.2 21.5 + - + +
300D GLU* 1.3 74.6 - - - +
302D ARG* 1.3 65.9 + - - +
304D ARG* 3.9 2.3 - - - +
305D ILE* 3.0 46.8 + - + +
316D LEU* 5.1 1.1 - - + -
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Residues in contact with ARG 302 (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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110D GLN* 5.3 4.9 + - - -
171D GLY* 3.2 26.9 + - - -
172D LEU* 4.0 16.3 - - + +
298D PHE* 2.7 48.2 + - + +
299D ALA* 3.6 12.1 + - - +
301D LEU* 1.3 74.5 - - - +
303D SER* 1.3 60.1 - - - +
305D ILE* 4.1 4.4 - - - +
306D ALA* 3.3 23.6 + - - +
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Residues in contact with SER 303 (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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172D LEU* 4.0 18.5 - - - +
173D GLU 3.5 27.1 + - - -
174D ASN* 3.4 23.6 - - - +
223D MET* 3.5 5.2 - - - +
299D ALA 2.9 17.9 + - - -
300D GLU 3.2 5.7 + - - -
302D ARG* 1.3 75.0 - - - +
304D ARG* 1.4 65.7 + - - +
305D ILE 3.3 0.2 + - - -
306D ALA* 3.3 4.3 + - - +
307D THR* 2.9 28.4 + - - -
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Residues in contact with ARG 304 (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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133D ASP* 2.8 37.2 + - - -
174D ASN* 3.9 23.0 + - - +
222D ASN* 5.8 3.2 - - - +
223D MET* 4.6 5.7 - - + +
290D LEU* 3.8 30.0 - - + +
293D LYS* 3.4 24.8 - - - +
295D LEU* 4.6 5.7 - - - +
300D GLU* 2.9 48.2 + - - +
301D LEU 4.0 0.4 - - - +
303D SER* 1.4 77.0 + - - +
305D ILE* 1.4 54.3 + - - +
307D THR* 3.4 10.0 - - - +
308D THR* 2.6 33.9 + - - -
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Residues in contact with ILE 305 (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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240D GLY* 3.6 20.3 - - - +
241D LEU* 3.8 16.2 - - - -
242D LEU* 3.9 32.8 - - + +
290D LEU* 3.9 31.6 - - + -
301D LEU* 3.0 39.7 + - + +
302D ARG* 4.1 4.7 - - - +
304D ARG* 1.4 73.9 - - - +
306D ALA* 1.3 64.2 + - - +
307D THR 3.2 0.2 - - - -
308D THR* 3.1 26.0 + - - +
314D VAL* 4.4 7.0 - - + -
331D LEU* 4.1 13.9 - - + +
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Residues in contact with ALA 306 (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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172D LEU* 3.8 22.9 - - + -
238D LYS 4.0 0.5 - - - +
239D ARG* 2.8 56.1 + - + +
240D GLY 3.5 12.8 - - - +
302D ARG* 3.3 15.7 + - + +
303D SER 3.3 0.4 + - - +
305D ILE* 1.3 77.1 - - + +
307D THR* 1.3 58.9 + - - +
308D THR 3.8 1.0 - - - +
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Residues in contact with THR 307 (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 SER* 5.6 0.7 - - - -
172D LEU* 5.1 5.2 - - - +
222D ASN 5.3 0.2 - - - +
223D MET* 3.6 46.9 - - + +
226D THR* 3.9 18.5 - - + +
227D LEU* 4.3 16.9 - - + +
230D GLN* 2.9 30.1 + - - +
239D ARG* 4.4 0.7 - - - +
303D SER 2.9 16.0 + - - -
304D ARG* 3.4 14.6 - - - +
306D ALA* 1.3 77.4 - - - +
308D THR* 1.3 58.5 + - - +
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Residues in contact with THR 308 (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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226D THR* 4.8 6.5 - - - -
238D LYS 3.6 1.6 - - - +
240D GLY* 3.3 18.4 + - - -
290D LEU* 5.8 1.2 - - - +
304D ARG* 2.6 22.2 + - - +
305D ILE* 3.1 21.5 + - - +
307D THR* 1.3 80.6 - - - +
309D GLU* 1.3 62.1 + - - +
312D THR* 3.7 32.3 - - + +
314D VAL* 4.6 8.8 - - + +
331D LEU* 3.8 14.6 - - + -
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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