Contacts of the helix formed by residues 387 - 393 (chain A) in PDB entry 5WIU
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 GLY 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLU* 3.3 29.8 - - - +
384A LYS 3.1 9.9 + - - -
385A ILE 3.3 1.2 + - - -
386A THR* 1.3 79.3 - - - +
388A ARG* 1.3 63.7 + - - +
389A GLU 3.4 2.0 - - - -
390A ARG* 3.6 5.4 + - - +
391A LYS* 3.2 22.1 + - - +
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Residues in contact with ARG 388 (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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383A ALA* 3.0 17.1 + - + +
386A THR* 3.2 15.0 - - - +
387A GLY* 1.3 76.9 - - - +
389A GLU* 1.3 60.7 + - - +
391A LYS* 3.2 8.2 + - - +
392A ALA* 2.9 29.6 + - - +
1004A GLU* 2.9 39.1 + - - +
1007A TRP* 4.0 22.6 - - - -
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Residues in contact with GLU 389 (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 ARG* 4.5 14.6 + - - +
136A ALA* 5.3 2.4 - - - +
137A VAL* 4.1 11.8 - - - +
219A LEU* 3.7 27.1 - - + +
383A ALA* 2.8 20.3 + - + +
384A LYS* 3.7 29.1 + - - +
387A GLY* 4.5 0.2 - - - -
388A ARG* 1.3 76.9 - - - +
390A ARG* 1.3 62.8 + - - +
392A ALA* 3.3 15.4 + - + +
393A MET* 3.4 20.8 + - + +
1104A LYS 4.3 6.1 - - - +
1223A GOL 5.2 1.9 + - - -
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Residues in contact with ARG 390 (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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216A PHE* 3.7 24.5 - - + +
219A LEU* 3.9 29.0 - - + +
220A GLN* 3.0 41.6 - - - +
223A GLU* 2.5 50.2 + - - +
384A LYS 5.6 0.6 + - - -
387A GLY 3.6 3.4 + - - +
388A ARG 3.3 0.4 - - - -
389A GLU* 1.3 80.2 - - - +
391A LYS* 1.3 62.3 + - - +
393A MET* 3.2 17.7 + - - +
394A ARG* 3.7 3.6 + - - +
1203A PO4 3.2 30.7 + - - -
1210A OLA 3.0 29.9 + - - -
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Residues in contact with LYS 391 (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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387A GLY 3.2 11.8 + - - +
388A ARG* 3.2 12.5 + - - +
390A ARG* 1.3 79.6 - - - +
392A ALA* 1.3 60.2 + - - +
393A MET 3.1 0.2 - - - -
394A ARG* 3.2 24.2 + - - +
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Residues in contact with ALA 392 (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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388A ARG 2.9 15.3 + - - +
389A GLU* 3.7 9.4 - - + +
390A ARG 3.2 0.4 - - - -
391A LYS* 1.3 76.7 - - - +
393A MET* 1.3 58.5 + - + +
394A ARG 3.2 2.0 + - - -
395A VAL* 4.4 6.2 + - - +
452A ASN* 3.8 22.2 + - - +
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Residues in contact with MET 393 (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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69A THR* 5.6 1.8 - - + +
133A ARG* 4.5 21.1 - - + -
137A VAL* 5.3 0.9 - - - -
212A TYR* 5.2 3.6 - - + -
215A THR* 3.6 26.0 - - + -
216A PHE* 3.4 36.9 - - + -
219A LEU* 3.7 24.7 - - + -
389A GLU* 3.4 13.4 + - + +
390A ARG 3.2 11.6 + - - +
391A LYS 3.1 1.2 - - - -
392A ALA* 1.3 77.6 - - - +
394A ARG* 1.3 64.2 + - - +
395A VAL 3.1 3.6 - - - -
396A LEU* 3.0 42.5 + - + +
397A PRO* 3.1 10.0 - - - +
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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