Contacts of the helix formed by residues 289 - 299 (chain A) in PDB entry 2A7P
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 ARG 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A PHE 5.0 2.0 + - - -
7A ASN* 3.6 43.1 - - - +
9A GLU* 6.2 0.4 - - - +
41A ARG* 4.8 10.8 - - - +
288A ARG* 1.3 79.4 - - + +
290A GLY* 1.3 64.9 + - - +
291A SER* 3.6 17.9 - - - +
292A ASP* 2.6 36.0 + - - +
293A ILE* 3.3 9.5 + - - +
329A LEU* 4.4 3.4 - - - -
332A ASP* 4.0 15.8 + - - +
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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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289A ARG* 1.3 72.5 - - - +
291A SER* 1.3 56.7 + - - +
293A ILE* 3.1 10.5 + - - +
294A VAL* 2.9 34.8 + - - +
329A LEU* 4.2 2.9 - - - +
332A ASP* 3.0 35.8 + - - -
333A ILE* 4.2 16.4 - - - -
336A THR* 4.5 1.8 - - - -
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Residues in contact with SER 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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49A PHE* 3.8 27.1 - - - -
289A ARG* 3.6 16.0 - - - +
290A GLY* 1.3 75.1 - - - +
292A ASP* 1.3 69.2 + - - +
294A VAL* 4.4 2.7 - - - +
295A LYS* 3.0 39.1 + - - +
332A ASP* 4.2 4.6 + - - -
336A THR* 4.3 8.0 + - - -
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Residues in contact with ASP 292 (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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41A ARG* 3.4 12.8 + - - -
44A PHE* 3.1 53.2 - - + +
45A GLN* 5.6 0.7 - - - +
287A PHE* 3.5 21.9 - - + -
288A ARG 3.1 7.4 + - - -
289A ARG* 2.6 40.2 + - - +
291A SER* 1.3 81.8 + - - +
293A ILE* 1.3 62.8 + - - +
295A LYS* 3.3 6.0 + - - +
296A ALA 3.2 17.0 + - - -
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Residues in contact with ILE 293 (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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74A PRO 5.0 0.4 - - - +
75A LEU* 3.6 34.3 - - + -
287A PHE* 3.9 23.1 - - + -
288A ARG 5.9 0.9 - - - +
289A ARG 3.7 12.3 - - - +
290A GLY* 3.2 13.0 - - - +
292A ASP* 1.3 77.7 - - - +
294A VAL* 1.3 57.8 + - + +
296A ALA* 3.4 3.6 + - - +
297A LEU* 3.0 47.0 + - + +
304A VAL* 4.2 11.7 - - + +
306A LEU* 4.5 11.4 - - + -
329A LEU* 4.5 12.3 - - + -
333A ILE* 3.9 28.5 - - + -
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Residues in contact with VAL 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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49A PHE* 4.0 19.1 - - + -
290A GLY 2.9 22.9 + - - +
291A SER 3.9 3.8 - - - +
293A ILE* 1.3 71.3 - - + +
295A LYS* 1.3 57.2 + - - +
297A LEU* 3.2 7.8 + - + +
298A ALA* 2.6 35.4 + - + +
333A ILE* 4.3 21.3 - - + -
336A THR* 3.8 25.8 - - + -
337A LEU* 4.5 8.1 - - + -
340A ILE* 4.0 18.2 - - + -
348A LEU* 4.0 17.7 - - + -
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Residues in contact with LYS 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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44A PHE* 2.7 43.2 + - + +
45A GLN* 4.5 9.5 + - - +
47A TRP* 3.0 32.1 + - + +
48A ARG* 4.8 0.8 - - - +
49A PHE* 3.7 32.3 - - + -
267A MET* 4.3 11.2 - - + -
291A SER* 3.0 33.9 + - - +
292A ASP* 3.5 6.0 + - - +
294A VAL* 1.3 78.0 - - - +
296A ALA* 1.3 62.6 + - - +
298A ALA* 3.3 6.7 + - - +
299A LEU* 3.0 27.5 + - - +
353A LEU* 3.8 13.5 - - + +
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Residues in contact with ALA 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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267A MET* 3.7 18.3 - - - +
270A LEU* 3.3 17.4 - - + +
283A ILE* 4.1 8.7 - - + -
287A PHE* 3.6 32.5 - - + -
292A ASP 3.2 3.2 + - - -
293A ILE 3.8 4.0 - - - +
294A VAL 3.3 0.2 - - - -
295A LYS* 1.3 79.3 - - - +
297A LEU* 1.3 62.7 + - - +
299A LEU 3.1 7.4 + - - -
300A GLY 3.2 0.7 + - - -
301A ALA* 3.0 22.8 + - + +
304A VAL* 4.3 2.9 - - + -
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Residues in contact with LEU 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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74A PRO* 3.9 24.2 - - + +
293A ILE* 3.0 41.7 + - + +
294A VAL* 3.5 7.6 - - + +
296A ALA* 1.3 77.6 - - - +
298A ALA* 1.3 57.8 + - - +
300A GLY* 2.9 21.0 + - - -
301A ALA* 3.5 25.2 + - + +
302A GLU 4.2 4.7 - - - +
303A ALA* 4.2 8.1 - - - -
304A VAL* 4.7 4.3 - - + -
333A ILE* 5.4 0.2 - - + -
345A ILE* 3.5 36.1 - - + +
348A LEU* 3.6 20.9 - - + +
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Residues in contact with ALA 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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294A VAL* 2.6 22.8 + - + +
295A LYS 3.6 5.8 - - - +
297A LEU* 1.3 72.9 - - - +
299A LEU* 1.3 60.8 + - - +
300A GLY* 3.2 1.1 + - - -
348A LEU* 3.9 20.9 - - + +
349A SER* 3.1 43.1 - - - +
350A PRO* 3.1 7.6 - - - +
352A TYR* 5.4 2.7 - - + -
353A LEU* 3.8 20.9 - - + -
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Residues in contact with LEU 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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47A TRP* 3.8 39.0 - - + +
267A MET* 4.0 21.3 - - + +
270A LEU* 3.6 15.6 - - + +
271A ALA* 4.0 34.3 - - + +
274A VAL* 4.1 7.3 - - - +
295A LYS 3.0 16.9 + - - +
296A ALA 3.5 9.6 - - - +
297A LEU 3.0 0.8 - - - -
298A ALA* 1.3 78.1 - - - +
300A GLY* 1.3 55.7 + - - +
301A ALA 3.7 0.7 - - - -
350A PRO* 4.7 18.9 - - + +
353A LEU* 3.8 18.2 - - + -
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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