Contacts of the helix formed by residues 299 - 307 (chain A) in PDB entry 5PMW
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 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU* 3.0 41.4 + - - +
44A HIS* 3.6 37.8 - - - +
199A TYR* 3.7 6.5 + - - +
275A PHE* 4.5 0.6 - - - +
276A PRO* 3.8 19.9 + - - +
297A THR* 3.2 9.8 + - - +
298A PRO* 1.4 79.1 - - - +
300A TRP* 1.3 62.3 + - - +
301A ILE 3.4 0.3 + - - -
302A ASP* 3.9 7.6 + - - +
303A TYR* 3.4 51.1 + - + -
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Residues in contact with TRP 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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160A ILE* 4.4 5.2 - - + -
163A LEU* 4.2 2.2 - - + -
164A LEU* 4.0 21.5 - - + -
196A MET* 2.8 40.3 + - + -
197A ASP 3.2 22.5 + - - -
198A LEU* 3.4 30.1 - - + +
199A TYR* 4.0 11.1 - + + -
276A PRO* 4.1 12.1 - - + -
296A ALA* 3.6 20.2 - - + -
297A THR* 3.0 21.4 + - - +
299A ARG* 1.3 78.2 - - - +
301A ILE* 1.4 97.0 + - + +
303A TYR* 2.8 15.9 + - + -
304A GLY* 2.9 24.7 + - - +
324A PHE* 4.9 3.8 - + - -
328A LEU* 3.7 17.0 - - + -
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Residues in contact with ILE 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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163A LEU* 3.9 13.0 - - + -
164A LEU* 3.5 31.0 - - + -
167A GLU* 4.2 18.8 - - + +
168A CYS* 4.1 17.9 - - - -
298A PRO 3.3 16.3 + - - +
300A TRP* 1.4 94.7 - - + +
302A ASP* 1.3 65.8 + - - +
304A GLY* 3.1 2.8 + - - -
305A LYS* 3.0 49.5 + - + +
328A LEU* 4.4 5.7 - - + +
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Residues in contact with ASP 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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298A PRO 4.8 0.6 + - - -
299A ARG 3.9 8.3 + - - +
300A TRP 3.2 0.8 - - - -
301A ILE* 1.3 80.1 - - - +
303A TYR* 1.3 65.4 + - + +
305A LYS* 3.5 30.0 + - - +
306A MET* 3.4 37.2 + - + +
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Residues in contact with TYR 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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44A HIS* 5.7 0.7 - - - -
196A MET 4.4 2.0 - - - -
197A ASP* 4.3 9.7 - - + +
217A PRO* 5.0 10.5 - - + +
276A PRO* 3.6 39.9 - - + -
277A TYR* 3.9 21.3 - + + -
299A ARG* 3.4 50.0 + - + -
300A TRP* 2.8 15.7 + - + +
302A ASP* 1.3 73.4 - - + +
304A GLY* 1.3 64.2 + - - +
306A MET* 3.1 21.0 + - + +
307A ALA* 3.0 24.6 + - - +
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Residues in contact with GLY 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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196A MET* 3.3 40.9 - - - +
300A TRP* 2.9 29.1 + - - +
301A ILE 3.1 3.5 + - - -
303A TYR* 1.3 76.7 - - - +
305A LYS* 1.3 61.3 + - - +
306A MET 3.3 0.5 + - - -
307A ALA* 3.5 2.9 + - - +
328A LEU* 4.0 8.7 - - - -
329A GLN* 3.4 5.0 + - - -
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Residues in contact with LYS 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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168A CYS* 5.8 2.8 - - - -
301A ILE* 3.0 32.5 + - - +
302A ASP* 3.5 32.6 + - - +
303A TYR 3.2 0.2 - - - -
304A GLY* 1.3 76.2 - - - +
306A MET* 1.3 61.3 + - + +
307A ALA 3.6 0.4 - - - -
328A LEU* 4.1 36.7 - - + +
329A GLN* 3.3 15.6 + - - +
332A ARG* 5.2 1.2 + - - -
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Residues in contact with MET 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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197A ASP* 5.1 0.2 - - - -
302A ASP* 3.4 28.9 - - + +
303A TYR* 3.1 23.1 + - + +
305A LYS* 1.3 80.8 - - + +
307A ALA* 1.3 65.6 + - - +
308A SER* 3.4 6.4 + - - -
329A GLN* 4.0 0.7 - - - -
332A ARG* 4.1 7.8 + - - +
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Residues in contact with ALA 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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196A MET* 3.8 26.7 - - - -
197A ASP* 3.6 24.9 - - - +
243A ARG* 3.9 5.8 - - - +
303A TYR 3.0 10.3 + - - +
304A GLY 3.5 7.6 + - - +
306A MET* 1.3 75.5 - - - +
308A SER* 1.3 62.8 + - - +
309A GLN* 3.8 10.6 + - - +
329A GLN* 2.8 25.0 + - - +
332A ARG* 3.0 7.6 + - - -
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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