Contacts of the helix formed by residues 297 - 308 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E GLY 4.7 0.5 + - - -
165E SER* 4.0 6.7 + - - -
248E GLU* 3.3 22.2 - - - -
264E GLY* 4.0 11.6 - - - +
295E LEU* 3.3 7.7 + - - +
296E ASN* 1.4 89.4 + - - +
298E PHE* 1.3 63.3 + - - +
299E ALA* 3.8 7.0 + - - +
300E GLU* 3.1 26.9 + - - +
301E LEU* 3.2 19.2 + - - +
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Residues in contact with PHE 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E ILE* 4.5 19.5 - - + -
245E LYS* 5.4 0.2 - - - -
246E GLY* 3.7 36.3 - - - -
247E THR* 3.8 19.7 - - - +
248E GLU* 2.9 23.7 + - + +
264E GLY 3.5 8.2 + - - +
265E ALA* 3.3 24.9 - - + -
297E SER* 1.3 69.7 - - - +
299E ALA* 1.3 56.0 + - - +
301E LEU* 3.2 15.7 + - + +
302E ARG* 2.8 54.8 + - + +
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Residues in contact with ALA 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E SER* 3.6 28.5 - - - -
166E GLY* 5.2 1.8 - - - +
173E GLU 4.2 1.6 - - - +
248E GLU* 3.1 14.6 + - - +
297E SER* 3.8 3.1 - - - +
298E PHE* 1.3 78.3 - - + +
300E GLU* 1.4 60.0 + - - +
302E ARG* 3.5 14.9 + - - +
303E SER* 3.0 27.3 + - - -
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Residues in contact with GLU 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E GLY* 4.8 1.2 - - - -
165E SER* 4.0 6.0 + - - +
174E ASN* 3.3 24.0 + - - +
293E LYS* 4.7 3.8 - - - +
294E PRO 4.3 8.2 - - - +
295E LEU* 3.7 9.8 - - + +
296E ASN* 2.8 48.5 + - - +
297E SER* 3.1 23.0 + - - +
299E ALA* 1.4 71.3 - - - +
301E LEU* 1.4 56.2 + - - +
303E SER* 2.9 7.7 + - - -
304E ARG* 2.9 71.5 + - - +
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Residues in contact with LEU 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E LEU* 3.8 25.4 - - + -
244E ILE* 5.2 1.8 - - + -
265E ALA* 4.4 10.8 - - + -
287E ILE* 4.3 20.2 - - + -
290E LEU* 4.0 19.7 - - + -
295E LEU* 3.7 30.9 - - + +
297E SER 3.2 9.2 + - - +
298E PHE* 3.2 22.4 + - + +
300E GLU* 1.4 76.5 - - - +
302E ARG* 1.4 63.4 + - - +
304E ARG* 3.2 3.5 + - - -
305E ILE* 3.0 53.7 + - + +
316E LEU* 5.2 0.7 - - + -
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Residues in contact with ARG 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E GLN* 4.8 6.1 + - - -
171E GLY* 3.1 29.5 + - - -
172E LEU* 3.9 19.8 - - + +
173E GLU 5.7 0.2 - - - +
298E PHE* 2.8 42.6 + - + +
299E ALA* 3.6 13.6 + - - +
301E LEU* 1.4 73.1 - - - +
303E SER* 1.3 57.6 + - - +
305E ILE* 3.5 11.5 + - + +
306E ALA* 3.1 32.2 + - + +
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Residues in contact with SER 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E LEU* 3.9 20.7 - - - +
173E GLU 3.0 38.8 + - - -
174E ASN* 3.8 5.4 - - - +
223E MET* 3.9 8.5 - - - +
299E ALA 3.0 14.4 + - - -
300E GLU* 2.9 16.6 + - - -
302E ARG* 1.3 73.2 - - - +
304E ARG* 1.3 60.7 + - - +
306E ALA* 4.4 0.5 - - - +
307E THR* 3.0 30.8 + - - +
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Residues in contact with ARG 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ASP* 2.7 39.4 + - - -
174E ASN* 3.8 23.1 + - - +
222E ASN* 6.0 1.8 - - - +
223E MET* 4.7 4.0 - - + +
290E LEU* 3.7 30.0 - - + +
293E LYS* 3.5 21.1 - - - +
295E LEU* 4.5 6.3 - - - +
300E GLU* 2.9 51.2 + - - +
301E LEU 3.8 1.8 - - - +
303E SER* 1.3 78.9 - - - +
305E ILE* 1.4 55.2 + - - +
307E THR* 3.6 10.1 + - + +
308E THR* 2.6 32.9 + - - -
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Residues in contact with ILE 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E GLY* 3.2 16.6 - - - +
241E LEU* 4.8 0.7 - - - -
242E LEU* 3.7 46.0 - - + +
290E LEU* 4.1 18.6 - - + -
301E LEU* 3.0 54.6 + - + +
302E ARG* 3.8 9.2 - - + +
304E ARG* 1.4 72.3 - - - +
306E ALA* 1.4 59.5 + - + +
307E THR 3.2 4.9 - - - -
308E THR* 3.2 28.6 + - - +
314E VAL* 4.9 3.1 - - + -
331E LEU* 3.9 15.7 - - + +
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Residues in contact with ALA 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E LEU* 3.8 23.6 - - + -
238E LYS 4.1 0.9 - - - +
239E ARG* 2.7 54.9 + - + +
240E GLY 3.4 13.8 + - - +
302E ARG* 3.1 20.5 + - + +
303E SER 4.5 0.4 - - - +
305E ILE* 1.4 76.3 - - + +
307E THR* 1.3 57.5 + - - +
308E THR 3.5 0.2 - - - -
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Residues in contact with THR 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E SER* 4.9 1.0 - - - -
172E LEU* 4.6 10.0 - - - +
223E MET* 3.8 46.6 - - + +
226E THR* 3.4 13.6 - - + +
227E LEU* 4.1 21.0 - - + +
230E GLN* 3.2 20.8 - - - +
238E LYS 5.1 0.9 - - - -
239E ARG* 4.6 0.4 - - - +
303E SER 3.0 19.8 + - - +
304E ARG* 3.6 10.3 - - + +
306E ALA* 1.3 76.7 - - - +
308E THR* 1.4 59.3 + - - +
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Residues in contact with THR 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E THR* 4.8 5.6 - - + -
238E LYS 3.7 2.6 - - - +
240E GLY* 3.2 26.2 + - - -
290E LEU* 5.8 1.4 - - - +
304E ARG 2.6 23.0 + - - -
305E ILE* 3.2 15.1 + - - +
307E THR* 1.4 79.0 - - - +
309E GLU* 1.3 64.2 + - - +
312E THR* 3.7 32.5 - - + -
314E VAL* 4.6 9.7 - - + +
331E LEU* 3.7 11.7 - - + -
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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