Contacts of the helix formed by residues 292 - 305 (chain A) in PDB entry 3PWH
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 ILE 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU* 5.2 0.9 - - + -
230A HIS* 4.9 7.0 - - + -
231A ALA* 5.2 8.5 - - + -
234A SER* 4.0 20.9 - - - +
288A TYR* 2.8 38.0 + - + +
290A TYR 4.8 0.4 - - - -
291A ARG* 1.3 87.9 - - + +
293A ARG* 1.3 63.8 + - + +
294A GLU* 3.7 11.0 - - + +
295A PHE* 3.4 42.2 - - + +
296A ARG* 3.2 19.9 + - - +
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Residues in contact with ARG 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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227A LYS* 3.3 49.0 - - - +
230A HIS* 5.1 9.7 + - - -
291A ARG 4.0 3.6 + - - -
292A ILE* 1.3 70.9 - - + +
294A GLU* 1.3 70.5 + - + +
296A ARG* 3.1 28.6 - - + +
297A GLN* 3.1 30.5 - - - +
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Residues in contact with GLU 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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34A ASN* 2.8 37.6 + - - +
36A ASN* 3.5 22.2 + - - +
37A LEU* 3.4 22.4 - - + -
292A ILE* 3.2 10.2 - - + +
293A ARG* 1.3 88.5 - - + +
295A PHE* 1.3 58.0 + - - +
297A GLN* 3.8 11.6 + - - +
298A THR* 2.9 25.3 + - - -
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Residues in contact with PHE 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.1 20.4 - - + -
30A ALA* 4.9 1.3 - - + -
31A VAL* 4.1 14.6 - - + -
37A LEU* 3.5 31.9 - - + -
42A ASN* 3.6 25.4 - - - -
45A VAL* 5.1 6.1 - - + -
288A TYR* 3.7 23.6 - + + +
292A ILE* 3.3 39.9 + - + +
293A ARG 3.3 0.6 - - - -
294A GLU* 1.3 78.9 - - - +
296A ARG* 1.3 67.7 + - - +
298A THR* 2.9 16.1 + - - -
299A PHE* 3.0 52.1 + + + -
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ALA* 3.1 32.0 + - + +
290A TYR* 3.2 38.2 + - - +
292A ILE 3.2 9.3 + - - +
293A ARG* 3.1 29.3 - - - +
295A PHE* 1.3 78.1 - - - +
297A GLN* 1.3 62.2 + - + +
299A PHE* 3.3 13.0 + - - +
300A ARG* 3.0 50.7 + - - +
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Residues in contact with GLN 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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293A ARG* 3.1 32.9 + - - +
294A GLU* 4.1 12.9 - - - +
295A PHE 3.2 0.6 - - - -
296A ARG* 1.3 83.9 - - + +
298A THR* 1.3 61.0 + - - +
300A ARG* 3.6 20.4 + - - +
301A LYS* 3.3 20.3 + - - +
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Residues in contact with THR 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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30A ALA* 3.6 41.5 - - + +
33A LEU* 5.2 2.0 - - + -
34A ASN* 3.0 32.3 + - + +
37A LEU* 3.8 6.6 - - + +
294A GLU 2.9 15.8 + - - -
295A PHE 2.9 9.5 + - - -
297A GLN* 1.3 75.5 - - - +
299A PHE* 1.3 63.8 + - - +
301A LYS* 3.1 26.8 + - - +
302A ILE* 3.2 16.6 + - + +
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Residues in contact with PHE 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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23A GLY 5.2 0.2 - - - -
26A LEU* 3.4 52.0 - - + -
27A VAL* 3.7 21.3 - - + -
30A ALA* 3.6 13.7 - - + -
285A PRO* 4.5 2.7 - - + -
288A TYR* 4.4 1.8 - - + -
289A ALA* 3.8 24.7 - - + -
295A PHE* 3.0 61.0 + + + -
296A ARG* 3.7 9.0 - - - +
298A THR* 1.3 75.3 - - - +
300A ARG* 1.3 63.6 + - - +
302A ILE* 3.1 17.3 + - - +
303A ILE* 3.1 23.3 + - + +
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Residues in contact with ARG 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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296A ARG* 3.0 42.0 + - - +
297A GLN* 3.6 18.7 - - - +
298A THR 3.2 0.2 - - - -
299A PHE* 1.3 78.1 - - - +
301A LYS* 1.3 61.0 + - - +
303A ILE* 3.6 7.3 + - - +
304A ARG* 3.2 76.5 + - + +
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Residues in contact with LYS 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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33A LEU* 4.6 31.0 + - + +
34A ASN* 4.8 12.6 - - - +
297A GLN 3.3 8.2 + - - +
298A THR* 3.1 23.9 + - + +
300A ARG* 1.3 79.4 - - - +
302A ILE* 1.3 65.7 + - + +
304A ARG* 3.9 4.0 - - - +
305A SER* 2.9 31.0 + - - -
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Residues in contact with ILE 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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26A LEU* 3.8 28.7 - - + -
29A TRP* 3.4 39.0 - - + -
30A ALA* 3.9 36.6 - - + +
33A LEU* 4.0 22.0 - - + -
298A THR* 3.5 13.0 - - + +
299A PHE* 3.1 8.0 + - - +
301A LYS* 1.3 78.6 - - + +
303A ILE* 1.3 65.5 + - + +
305A SER* 3.0 23.0 - - - +
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Residues in contact with ILE 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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26A LEU* 5.0 17.5 - - + -
299A PHE* 3.1 20.0 + - + +
300A ARG* 4.0 5.6 - - - +
302A ILE* 1.3 83.3 - - + +
304A ARG* 1.3 68.5 + - + +
305A SER 3.8 4.7 - - - +
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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
----------------------------------------------------------
300A ARG* 3.2 58.0 + - + +
301A LYS* 4.0 3.8 - - - +
303A ILE* 1.3 83.5 - - + +
305A SER* 1.3 59.9 + - - +
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Residues in contact with SER 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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29A TRP* 6.6 0.4 - - - -
301A LYS* 2.9 23.9 + - - -
302A ILE* 3.0 18.1 - - - +
303A ILE 3.8 3.8 - - - +
304A ARG* 1.3 80.5 - - - +
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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