Contacts of the helix formed by residues 590 - 598 (chain F) in PDB entry 4G5S
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 PHE 590 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 5.1 1.8 - - + -
215B PHE* 4.3 15.5 - + - -
252B SER* 3.8 22.4 - - - +
253B ILE* 3.7 29.6 - - + -
256B ASN* 3.7 26.9 - - - +
258B TRP* 4.9 4.5 - + - -
259B PHE* 4.1 20.4 - + - -
589F ASP* 1.3 79.4 - - - +
591F PHE* 1.3 91.7 + + + +
593F ILE* 3.4 11.2 + - - +
594F LEU* 2.9 46.6 + - + +
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Residues in contact with PHE 591 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B TRP* 3.3 31.6 - + + -
212B ILE* 4.1 21.8 - - + -
215B PHE* 3.4 36.1 - + - -
258B TRP* 3.9 34.5 - + - -
589F ASP 3.3 6.2 - - - +
590F PHE* 1.3 92.4 - + + +
592F ASP* 1.3 60.6 + - - +
594F LEU* 3.1 7.7 + - + +
595F VAL* 2.9 32.7 + - + +
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Residues in contact with ASP 592 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589F ASP* 3.1 38.9 + - - +
591F PHE* 1.3 75.8 - - - +
593F ILE* 1.3 67.4 + - - +
595F VAL* 3.3 11.8 - - + +
596F LYS* 2.9 46.9 + - - +
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Residues in contact with ILE 593 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B LYS* 4.5 28.5 - - + -
249B LEU* 4.2 22.7 - - + +
252B SER* 4.1 21.5 - - - +
589F ASP* 3.2 29.8 + - - +
590F PHE* 3.5 6.7 - - - +
591F PHE 3.2 0.2 - - - -
592F ASP* 1.3 85.9 + - - +
594F LEU* 1.3 65.6 + - - +
596F LYS* 3.1 13.1 + - - +
597F CYS* 2.9 41.3 + - - +
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Residues in contact with LEU 594 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.3 21.3 - - + -
201B VAL* 4.7 7.4 - - + -
202B GLY 4.7 1.3 - - - +
211B TRP* 4.4 18.8 - - + -
215B PHE* 4.4 11.9 - - + -
249B LEU* 3.7 28.1 - - + +
590F PHE* 2.9 36.4 + - + +
591F PHE* 3.1 14.8 - - - +
593F ILE* 1.3 77.2 - - - +
595F VAL* 1.3 59.9 + - + +
597F CYS* 3.6 1.6 + - - +
598F GLN* 3.1 58.1 + - + +
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Residues in contact with VAL 595 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B GLY* 5.6 8.1 - - - +
206B SER 4.8 16.8 - - - +
207B GLU* 5.2 7.2 - - + -
211B TRP* 4.3 23.1 - - + -
591F PHE* 2.9 18.2 + - + +
592F ASP* 3.3 18.2 - - + +
594F LEU* 1.3 74.0 - - + +
596F LYS* 1.3 68.0 + - - +
597F CYS 3.1 2.5 + - - -
598F GLN* 3.5 11.9 + - + +
599F GLY* 4.1 8.7 + - - +
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Residues in contact with LYS 596 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B GLU* 3.1 27.8 - - + +
245B GLU* 4.0 9.8 - - + +
248B LYS* 5.0 13.5 - - - +
592F ASP* 2.9 43.8 + - - +
593F ILE* 3.1 17.0 + - - +
595F VAL* 1.3 78.6 - - + +
597F CYS* 1.3 64.2 + - - +
598F GLN 5.5 0.2 - - - -
600F SER* 5.4 1.2 + - - -
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Residues in contact with CYS 597 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA* 3.5 19.9 - - + +
242B ARG* 5.5 0.2 + - - -
245B GLU* 3.6 51.2 - - + +
246B SER* 5.8 0.2 - - - -
248B LYS* 5.2 5.4 - - - -
249B LEU* 4.2 20.4 - - + -
593F ILE* 2.9 34.3 + - - +
596F LYS* 1.3 89.3 - - - +
598F GLN* 1.3 64.9 + - - +
600F SER* 3.8 5.5 + - - -
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Residues in contact with GLN 598 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU 5.1 0.2 + - - -
39B LEU* 4.6 5.7 - - - +
40B GLY 3.2 37.7 + - - +
41B ALA* 4.3 4.5 - - - +
42B GLY* 3.6 13.3 + - - +
46B LYS* 3.9 11.7 - - - +
201B VAL* 4.5 2.8 - - - +
202B GLY* 3.5 44.0 + - - +
203B GLY* 5.4 1.1 - - - -
249B LEU* 4.1 6.4 - - - +
594F LEU* 3.1 40.8 + - + +
595F VAL* 3.5 6.5 + - - +
597F CYS* 1.3 76.0 - - - +
599F GLY* 1.3 54.3 - - - +
600F SER* 2.3 35.2 + - - -
601F ARG* 6.3 0.4 - - - +
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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