Contacts of the helix formed by residues 297 - 307 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLY 4.8 0.2 + - - -
165A SER* 4.2 6.0 + - - -
248A GLU* 3.3 22.7 - - - -
264A GLY* 3.9 12.0 - - - +
295A LEU* 3.3 11.7 + - - +
296A ASN* 1.4 87.3 + - - +
298A PHE* 1.3 62.3 + - - +
299A ALA* 3.5 6.5 + - - +
300A GLU* 2.9 28.1 + - - +
301A LEU* 3.4 15.2 + - - +
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Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ILE* 4.4 18.8 - - + -
245A LYS* 5.4 0.2 - - - -
246A GLY* 3.7 37.9 - - - -
247A THR* 3.8 20.0 - - - +
248A GLU* 2.9 23.1 + - + +
264A GLY 3.5 8.7 + - - +
265A ALA* 3.3 24.9 - - + -
297A SER* 1.3 69.9 - - - +
299A ALA* 1.3 58.7 + - - +
301A LEU* 3.2 16.4 + - + +
302A ARG* 2.8 53.8 + - + +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER* 3.5 28.9 - - - -
166A GLY* 5.1 2.5 - - - +
173A GLU 4.1 1.7 + - - +
248A GLU* 3.1 12.2 + - - +
297A SER* 3.6 4.9 - - - +
298A PHE* 1.3 77.3 - - - +
300A GLU* 1.4 57.9 + - - +
302A ARG* 3.5 13.8 + - - +
303A SER* 3.0 29.6 + - - -
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLY* 4.8 1.1 - - - +
165A SER* 3.9 6.2 + - - +
174A ASN* 3.3 23.8 + - - +
293A LYS* 4.7 4.9 - - - +
294A PRO 4.2 8.7 - - - +
295A LEU* 3.7 10.4 - - + +
296A ASN* 2.8 48.4 + - - +
297A SER* 2.9 22.8 + - - +
298A PHE 3.3 0.2 - - - -
299A ALA* 1.4 73.1 - - - +
301A LEU* 1.4 55.4 + - - +
303A SER* 2.7 21.4 + - - -
304A ARG* 2.9 59.0 + - - +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A LEU* 3.8 24.0 - - + -
244A ILE* 5.2 2.2 - - + -
265A ALA* 4.4 11.4 - - + -
287A ILE* 4.3 21.3 - - + -
290A LEU* 4.0 20.2 - - + -
295A LEU* 3.7 30.2 - - + +
297A SER 3.4 9.2 + - - +
298A PHE* 3.2 22.0 + - + +
300A GLU* 1.4 77.1 - - - +
302A ARG* 1.3 56.8 + - - +
304A ARG* 3.2 2.2 + - - -
305A ILE* 2.9 54.3 + - + +
316A LEU* 5.2 0.9 - - + -
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLN* 4.6 7.5 + - - -
171A GLY* 3.0 29.1 + - - -
172A LEU* 3.9 19.3 - - + +
173A GLU 5.7 0.4 - - - +
298A PHE* 2.8 41.3 + - + +
299A ALA* 3.6 14.4 + - - +
301A LEU* 1.3 75.3 - - - +
303A SER* 1.3 56.6 + - - +
305A ILE* 4.1 4.4 - - - +
306A ALA* 3.1 32.1 + - + +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 4.0 18.1 - - - +
173A GLU 3.3 38.3 + - - -
174A ASN* 3.5 11.3 - - - +
223A MET* 4.0 6.4 - - - +
299A ALA 3.0 11.8 + - - -
300A GLU* 2.7 22.3 + - - -
302A ARG* 1.3 76.3 - - - +
304A ARG* 1.3 59.9 + - - +
306A ALA* 3.8 0.9 + - - +
307A THR* 3.1 29.6 + - - -
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ASP* 2.7 38.5 + - - -
174A ASN* 3.8 24.1 + - - +
222A ASN* 6.0 1.8 - - - +
223A MET* 4.7 7.2 - - + -
290A LEU* 3.7 30.2 - - + +
293A LYS* 3.5 25.2 - - - +
295A LEU* 4.5 5.6 - - - -
300A GLU* 2.9 48.4 + - - +
301A LEU 3.8 1.3 - - - +
303A SER* 1.3 71.8 + - - +
305A ILE* 1.3 59.2 + - - +
307A THR* 3.6 3.8 + - - -
308A THR* 2.6 33.1 + - - -
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Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A GLY 3.7 15.2 - - - +
241A LEU* 3.9 3.1 - - - -
242A LEU* 3.8 48.9 - - + +
290A LEU* 3.8 29.8 - - + -
301A LEU* 2.9 36.3 + - + +
302A ARG* 4.1 4.0 - - - +
304A ARG* 1.3 76.4 - - - +
306A ALA* 1.4 57.0 + - - +
308A THR* 3.1 29.1 + - - +
314A VAL* 4.1 13.5 - - + -
331A LEU* 3.9 11.1 - - + +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 3.8 24.9 - - + -
238A LYS 4.0 1.4 - - - +
239A ARG* 2.9 51.8 + - + +
240A GLY 3.6 13.7 + - - +
302A ARG* 3.1 19.2 + - + +
303A SER 3.8 0.6 + - - +
304A ARG 3.4 0.2 - - - -
305A ILE* 1.4 75.2 - - - +
307A THR* 1.3 58.3 + - - +
308A THR 3.2 1.7 - - - +
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Residues in contact with THR 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 5.0 0.3 - - - -
172A LEU* 4.3 7.8 - - - +
223A MET* 3.5 45.5 - - + +
226A THR* 3.2 23.2 - - + +
227A LEU* 3.8 20.0 - - + +
230A GLN* 3.3 10.0 - - - +
238A LYS 5.2 0.2 - - - -
239A ARG* 4.1 13.5 + - - +
303A SER 3.1 18.3 + - - -
304A ARG* 4.0 5.2 - - - +
305A ILE 3.3 0.6 - - - -
306A ALA* 1.3 76.0 - - - +
308A THR* 1.3 60.6 + - - +
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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