Contacts of the helix formed by residues 297 - 308 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G GLY 4.8 0.2 + - - -
165G SER* 4.1 6.8 + - - -
248G GLU* 3.3 22.4 - - - -
264G GLY* 4.1 11.8 - - - +
295G LEU* 3.3 9.6 + - - +
296G ASN* 1.4 86.6 + - - +
298G PHE* 1.3 62.2 + - - +
299G ALA* 3.5 6.6 + - - +
300G GLU* 3.0 27.4 + - - +
301G LEU* 3.4 17.2 + - - +
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Residues in contact with PHE 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G ILE* 4.4 14.6 - - + -
245G LYS* 5.4 0.2 - - - -
246G GLY* 3.7 37.7 - - - -
247G THR* 3.8 19.5 - - - +
248G GLU* 2.9 23.5 + - + +
264G GLY 3.6 7.6 + - - +
265G ALA* 3.3 24.0 - - + -
297G SER* 1.3 69.0 - - - +
299G ALA* 1.3 57.3 + - - +
301G LEU* 3.1 23.7 + - + +
302G ARG* 2.8 55.7 + - + +
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Residues in contact with ALA 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G SER* 3.5 28.9 - - - -
166G GLY* 5.1 2.7 - - - +
173G GLU 4.1 1.7 + - - +
248G GLU* 3.1 12.9 + - - +
297G SER* 3.7 4.9 - - - +
298G PHE* 1.3 79.1 - - - +
300G GLU* 1.4 55.2 + - - +
302G ARG* 3.5 16.1 + - - +
303G SER* 3.1 28.9 + - - -
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Residues in contact with GLU 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163G GLY* 4.8 1.5 - - - +
165G SER* 4.0 6.2 + - - +
174G ASN* 3.3 24.7 + - - +
293G LYS* 4.7 4.5 - - - +
294G PRO 4.3 8.0 - - - +
295G LEU* 4.1 9.8 - - + +
296G ASN* 2.8 49.5 + - - +
297G SER* 3.0 22.2 + - - +
299G ALA* 1.4 71.2 - - - +
301G LEU* 1.3 59.8 + - - +
303G SER* 2.9 8.1 + - - -
304G ARG* 2.9 68.0 + - - +
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Residues in contact with LEU 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G LEU* 3.8 25.4 - - + -
244G ILE* 5.0 2.2 - - + -
265G ALA* 4.4 9.2 - - + -
287G ILE* 4.5 13.7 - - + -
290G LEU* 4.2 18.8 - - + -
295G LEU* 3.9 30.5 - - + +
297G SER 3.4 10.2 + - - +
298G PHE* 3.1 34.5 + - + +
300G GLU* 1.3 79.2 - - - +
302G ARG* 1.4 58.2 + - - +
304G ARG* 3.2 2.9 + - - +
305G ILE* 2.9 49.4 + - + +
316G LEU* 5.1 0.9 - - + -
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Residues in contact with ARG 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G GLN* 5.0 4.9 + - - -
171G GLY* 3.0 28.7 + - - -
172G LEU* 3.7 20.3 - - + +
173G GLU 5.5 0.4 - - - +
298G PHE* 2.8 42.4 + - + +
299G ALA* 3.5 15.4 + - - +
301G LEU* 1.4 74.9 - - - +
303G SER* 1.3 56.4 + - - +
305G ILE* 3.5 4.3 + - - +
306G ALA* 3.1 30.9 + - + +
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Residues in contact with SER 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G LEU* 4.2 19.5 - - - +
173G GLU 3.4 36.2 + - - -
174G ASN* 3.4 14.0 - - - +
223G MET* 3.9 7.4 - - - +
299G ALA 3.1 13.0 + - - -
300G GLU 2.9 11.1 + - - -
302G ARG* 1.3 74.7 - - - +
304G ARG* 1.3 67.7 + - - +
306G ALA* 3.7 1.4 + - - +
307G THR* 3.1 29.1 + - - -
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Residues in contact with ARG 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G ASP* 2.7 38.9 + - - -
174G ASN* 3.8 22.4 + - - +
222G ASN* 6.0 2.0 - - - +
223G MET* 4.8 4.7 - - + -
290G LEU* 3.6 30.8 - - + +
293G LYS* 3.6 21.2 - - - +
295G LEU* 4.5 6.0 - - - +
300G GLU* 2.9 51.9 + - - +
301G LEU 3.6 1.3 - - - +
303G SER* 1.3 78.3 + - - +
305G ILE* 1.4 56.9 + - - +
307G THR* 3.6 7.5 + - - +
308G THR* 2.6 32.6 + - - -
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Residues in contact with ILE 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240G GLY* 3.4 20.0 - - - +
241G LEU* 3.7 17.0 - - - +
242G LEU* 3.8 36.8 - - + +
290G LEU* 3.9 32.8 - - + -
301G LEU* 2.9 25.2 + - + +
302G ARG* 4.0 4.3 - - - +
304G ARG* 1.4 71.8 - - - +
306G ALA* 1.3 56.5 + - - +
307G THR 3.1 4.3 - - - -
308G THR* 2.8 31.4 + - - +
314G VAL* 4.2 16.6 - - + -
331G LEU* 4.1 11.1 - - + +
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Residues in contact with ALA 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G LEU* 3.7 24.2 - - + -
230G GLN* 5.4 0.2 + - - -
238G LYS 4.1 1.0 - - - +
239G ARG* 2.8 54.7 + - + +
240G GLY 3.5 14.5 + - - +
302G ARG* 3.1 18.0 + - + +
303G SER 4.2 0.7 - - - +
304G ARG 3.5 0.2 - - - -
305G ILE* 1.3 75.7 - - - +
307G THR* 1.3 58.6 + - - +
308G THR 4.0 0.3 - - - +
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Residues in contact with THR 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G SER* 5.1 0.7 - - - -
172G LEU* 4.8 5.2 - - - +
223G MET* 3.7 49.3 - - + +
226G THR* 3.4 15.0 - - + +
227G LEU* 4.0 16.1 - - + +
230G GLN* 3.0 23.0 - - - +
238G LYS 5.1 0.4 - - - -
239G ARG* 4.4 8.2 + - - +
303G SER 3.1 20.0 + - - -
304G ARG* 3.8 6.5 - - - +
305G ILE 3.1 0.4 - - - -
306G ALA* 1.3 76.1 - - - +
308G THR* 1.3 60.7 + - - +
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Residues in contact with THR 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G THR* 4.8 4.7 - - - -
238G LYS 3.7 2.0 - - - +
240G GLY* 3.2 20.4 + - - -
290G LEU* 5.8 1.2 - - - +
304G ARG 2.6 22.6 + - - -
305G ILE* 2.8 20.2 + - - +
307G THR* 1.3 80.0 - - - +
309G GLU* 1.3 64.2 + - - +
312G THR* 3.7 32.5 - - + +
314G VAL* 4.6 7.8 - - + +
331G LEU* 3.7 13.0 - - + -
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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
------------------------------------------------------------
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