Contacts of the helix formed by residues 288 - 298 (chain A) in PDB entry 6A08
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 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.2 1.2 - - - +
286A ILE* 3.8 1.5 - - - +
287A ARG* 1.3 80.3 - - - +
289A GLY* 1.3 65.5 + - - +
290A GLY* 3.3 6.8 + - - -
291A ASP* 3.0 37.2 + - - +
292A VAL* 3.1 15.2 + - - +
328A LEU* 3.9 10.2 - - - +
331A GLU* 3.2 16.8 - - - -
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Residues in contact with GLY 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A SER* 1.3 73.1 - - - +
290A GLY* 1.3 57.1 + - - +
292A VAL* 3.2 4.7 + - - +
293A LEU* 2.9 26.9 + - - +
328A LEU* 4.0 2.1 - - - +
331A GLU* 2.8 33.7 + - - +
332A VAL* 3.8 23.7 - - - +
335A ALA* 3.9 9.5 - - - +
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Residues in contact with GLY 290 (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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47A VAL* 5.4 0.3 - - - +
288A SER* 3.2 7.3 + - - -
289A GLY* 1.3 77.7 - - - +
291A ASP* 1.3 57.3 + - - +
293A LEU* 3.2 6.6 + - - +
294A LYS* 3.0 35.2 + - - +
331A GLU* 4.6 1.6 + - - +
335A ALA* 4.2 15.0 - - - +
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Residues in contact with ASP 291 (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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39A ARG* 2.8 34.7 + - - -
42A LEU* 4.1 11.6 - - + +
286A ILE* 4.0 17.1 - - + +
287A ARG* 2.9 22.6 + - - +
288A SER* 3.0 25.2 + - - +
290A GLY* 1.3 73.3 - - - +
292A VAL* 1.3 66.8 + - - +
294A LYS* 3.2 25.4 + - - +
295A ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO* 3.8 36.3 - - + +
73A MET* 4.1 11.9 - - + -
286A ILE* 3.8 17.7 - - + -
288A SER 3.1 15.3 + - - +
289A GLY* 3.2 7.2 + - - +
291A ASP* 1.3 75.5 - - - +
293A LEU* 1.3 62.1 + - - +
295A ALA* 3.3 2.8 + - - +
296A THR* 2.8 32.5 + - - +
303A VAL* 4.1 20.1 - - + +
328A LEU* 5.4 0.2 - - + -
332A VAL* 4.0 25.8 - - + -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 4.2 20.6 - - + -
289A GLY 2.9 13.3 + - - +
290A GLY* 3.4 9.4 - - - +
291A ASP 3.2 0.4 - - - -
292A VAL* 1.3 77.8 - - - +
294A LYS* 1.3 56.7 + - - +
296A THR* 3.2 5.4 + - - -
297A ALA* 2.8 28.3 + - - +
332A VAL* 6.1 0.4 - - - +
335A ALA* 3.7 28.7 - - + +
336A MET* 4.0 26.0 - - + -
339A ALA* 3.8 14.6 - - + -
341A CYS* 5.1 0.2 - - - -
347A ALA* 3.8 28.3 - - + -
350A LEU* 3.9 11.4 - - + -
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Residues in contact with LYS 294 (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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42A LEU* 3.0 36.2 + - + +
43A GLU* 4.2 8.1 + - - +
45A VAL* 3.0 40.9 + - + +
46A PHE* 5.0 5.1 - - - +
47A VAL* 3.9 22.0 - - + +
290A GLY 3.0 20.4 + - - +
291A ASP* 3.2 24.8 + - - +
293A LEU* 1.3 76.2 - - - +
295A ALA* 1.3 63.5 + - - +
297A ALA* 3.2 3.9 + - - +
298A LEU* 3.0 30.2 + - + +
352A THR* 4.9 0.3 - - - +
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Residues in contact with ALA 295 (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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264A ILE* 4.1 18.0 - - + +
267A LEU* 3.6 4.1 - - - +
282A VAL* 3.7 16.8 - - + -
286A ILE* 4.4 2.7 - - + -
291A ASP 3.0 12.0 + - - +
292A VAL 3.6 3.6 - - - +
294A LYS* 1.3 77.1 - - - +
296A THR* 1.3 62.9 + - - +
298A LEU 3.3 1.7 + - - -
299A GLY 3.2 5.7 + - - -
300A ALA* 3.0 22.9 + - + +
303A VAL* 3.5 31.9 - - + -
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Residues in contact with THR 296 (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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72A PRO* 4.7 8.1 - - - +
292A VAL* 2.8 27.3 + - - +
293A LEU* 3.6 5.8 - - - -
295A ALA* 1.3 76.4 - - - +
297A ALA* 1.3 60.1 + - - +
299A GLY* 2.8 18.2 + - - -
300A ALA* 3.8 12.9 + - - +
301A SER 5.9 0.5 - - - -
302A ALA* 5.9 1.0 - - - -
303A VAL* 5.6 1.0 - - - +
344A VAL* 3.7 16.9 - - + +
347A ALA* 3.5 26.5 - - + -
348A ARG* 3.2 41.9 - - + +
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Residues in contact with ALA 297 (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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47A VAL* 4.7 4.3 - - + -
293A LEU 2.8 17.1 + - - +
294A LYS* 3.6 6.7 - - - +
296A THR* 1.3 75.8 - - - +
298A LEU* 1.3 60.1 + - - +
299A GLY* 3.2 0.7 + - - -
347A ALA 3.4 18.3 + - - +
348A ARG 3.8 6.2 - - - +
350A LEU* 3.3 32.9 - - + +
352A THR* 3.7 24.2 + - + +
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Residues in contact with LEU 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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45A VAL* 4.3 18.6 - - + -
264A ILE* 3.5 45.3 - - + +
267A LEU* 3.7 14.2 - - + +
268A GLY* 3.7 28.3 - - - +
271A VAL* 4.2 3.6 - - - +
294A LYS* 3.0 19.7 + - + +
295A ALA 3.7 4.9 - - - +
296A THR 3.1 0.2 - - - -
297A ALA* 1.3 77.3 - - - +
299A GLY* 1.3 56.1 + - - +
300A ALA 3.8 0.7 - - - -
352A THR* 3.7 28.3 - - + +
354A LEU* 6.2 2.9 - - + -
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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