Contacts of the helix formed by residues 590 - 598 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 5.4 3.1 - - + -
215A PHE* 3.9 26.5 - + - -
249A LEU* 4.8 0.2 - - + -
252A SER* 4.0 19.3 - - - +
253A ILE* 3.9 23.6 - - + -
256A ASN* 3.6 28.7 - - - +
259A PHE* 4.4 13.7 - + - -
258C TRP* 4.4 11.9 - + - +
589E ASP* 1.3 78.5 - - - +
591E PHE* 1.3 81.2 + + + +
593E ILE* 3.3 12.0 + - - +
594E LEU* 2.9 53.0 + - + +
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Residues in contact with PHE 591 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A TRP* 3.8 29.2 - + + -
212A ILE* 4.9 8.7 - - + -
215A PHE* 3.8 28.5 - + - -
257C LYS* 3.6 34.3 - - + -
258C TRP* 3.5 52.3 - + - -
589E ASP 3.3 3.9 - - - +
590E PHE* 1.3 88.0 - + + +
592E ASP* 1.3 58.5 + - - +
594E LEU* 3.1 7.6 - - + +
595E VAL* 3.0 33.3 + - + +
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Residues in contact with ASP 592 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589E ASP* 2.9 46.5 + - - +
591E PHE* 1.3 77.8 - - - +
593E ILE* 1.3 68.7 + - - +
595E VAL* 3.3 11.6 - - + +
596E LYS* 2.9 32.3 + - - +
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Residues in contact with ILE 593 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LYS* 4.7 25.4 - - + +
249A LEU* 4.4 13.2 - - - -
252A SER* 4.0 33.2 - - - +
589E ASP* 3.2 35.6 + - - +
590E PHE* 3.3 8.5 - - - +
591E PHE 3.2 0.2 - - - -
592E ASP* 1.3 86.1 + - - +
594E LEU* 1.3 67.2 + - - +
596E LYS* 3.0 10.3 + - + +
597E CYS* 3.0 34.9 + - - +
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Residues in contact with LEU 594 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 4.8 15.3 - - + -
201A VAL* 5.7 1.6 - - + -
202A GLY 5.1 4.3 - - - +
211A TRP* 5.0 15.0 - - + -
215A PHE* 4.7 17.3 - - + -
249A LEU* 3.9 22.2 - - + +
590E PHE* 2.9 43.3 + - + +
591E PHE* 3.1 15.3 - - + +
593E ILE* 1.3 76.0 - - - +
595E VAL* 1.3 65.7 + - + +
597E CYS* 3.7 1.4 + - - +
598E GLN* 3.1 56.4 + - + +
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Residues in contact with VAL 595 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLY* 5.0 13.7 - - - +
211A TRP* 5.4 10.8 - - + -
591E PHE* 3.0 19.6 + - + +
592E ASP* 3.3 18.4 - - + +
594E LEU* 1.3 79.6 - - + +
596E LYS* 1.3 67.2 + - - +
597E CYS 3.1 3.1 + - - -
598E GLN* 3.6 11.2 + - + +
599E GLY* 4.3 6.8 + - - +
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Residues in contact with LYS 596 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLU* 4.0 20.4 - - - +
245A GLU* 4.5 4.0 - - - +
248A LYS* 5.5 9.6 - - + +
592E ASP* 2.9 23.7 + - - +
593E ILE* 3.0 12.8 + - + +
595E VAL* 1.3 77.3 - - - +
597E CYS* 1.3 68.2 + - - +
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Residues in contact with CYS 597 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 4.1 15.4 - - + +
240A MET* 6.2 0.2 - - - -
242A ARG* 5.7 0.2 + - - -
245A GLU* 3.8 55.1 - - + +
248A LYS* 5.1 8.7 - - - -
249A LEU* 4.7 16.2 - - + -
593E ILE* 3.0 28.4 + - - +
594E LEU 4.5 1.1 - - - +
596E LYS* 1.3 92.0 - - - +
598E GLN* 1.3 65.6 + - - +
600E SER* 3.6 8.1 + - - -
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Residues in contact with GLN 598 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU 5.6 0.2 + - - -
39A LEU* 4.9 9.4 - - - +
40A GLY 3.4 30.9 + - - +
41A ALA* 4.6 5.4 - - - +
42A GLY* 4.1 15.1 + - - +
46A LYS* 4.2 12.9 - - - +
201A VAL* 5.5 0.4 - - - +
202A GLY* 3.7 31.4 + - - +
203A GLY* 5.3 2.7 - - - -
249A LEU* 4.1 13.2 - - - +
594E LEU* 3.1 41.4 + - + +
595E VAL* 3.6 7.1 + - + +
597E CYS* 1.3 76.2 - - - +
599E GLY* 1.3 56.1 - - - +
600E SER* 2.2 35.4 + - - -
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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