Contacts of the helix formed by residues 590 - 598 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A TRP* 4.4 12.8 - + - +
39C LEU* 5.3 0.9 - - + -
215C PHE* 4.6 10.8 - + - -
252C SER* 3.8 38.1 - - - +
253C ILE* 3.9 20.6 - - + -
256C ASN* 3.7 23.8 - - - +
259C PHE* 4.5 13.5 - + - -
589G ASP* 1.3 78.7 - - - +
591G PHE* 1.3 90.4 + + + +
593G ILE* 3.2 12.3 + - - +
594G LEU* 2.9 49.5 + - + +
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Residues in contact with PHE 591 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A LYS* 4.2 27.6 - - + -
258A TRP* 3.7 53.4 - + - -
211C TRP* 3.7 36.6 - + + -
212C ILE* 4.2 13.5 - - + -
215C PHE* 4.4 10.8 - + - -
589G ASP 3.4 2.8 - - - +
590G PHE* 1.3 98.5 - + + +
592G ASP* 1.3 58.7 + - - +
594G LEU* 3.0 11.0 - - + +
595G VAL* 2.9 32.9 + - + +
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Residues in contact with ASP 592 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589G ASP* 2.8 45.3 + - - +
591G PHE* 1.3 75.4 - - - +
593G ILE* 1.3 71.9 + - - +
595G VAL* 3.3 12.2 - - + +
596G LYS* 2.9 28.9 + - - +
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Residues in contact with ILE 593 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C LYS* 4.7 24.2 - - + -
249C LEU* 4.5 9.9 - - + -
252C SER* 4.1 28.7 - - - +
589G ASP* 3.2 32.3 - - - +
590G PHE* 3.2 14.8 + - - +
592G ASP* 1.3 80.2 + - - +
594G LEU* 1.3 67.6 + - - +
596G LYS* 3.0 17.5 + - + +
597G CYS* 3.0 29.4 + - - +
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Residues in contact with LEU 594 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU* 4.7 20.9 - - + -
201C VAL* 5.5 1.6 - - + -
202C GLY 5.5 1.8 - - - +
211C TRP* 5.2 12.1 - - + -
215C PHE* 4.9 7.9 - - + -
249C LEU* 3.9 25.7 - - + +
253C ILE* 5.0 0.7 - - + -
590G PHE* 2.9 39.4 + - + +
591G PHE* 3.0 26.5 - - + +
593G ILE* 1.3 75.4 - - - +
595G VAL* 1.3 62.1 + - + +
597G CYS* 4.2 1.7 - - - +
598G GLN* 3.2 57.0 + - + +
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Residues in contact with VAL 595 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C TRP* 5.6 10.1 - - + -
591G PHE* 2.9 19.6 + - + +
592G ASP* 3.3 19.3 - - + +
594G LEU* 1.3 79.9 - - + +
596G LYS* 1.3 68.5 + - - +
597G CYS 3.1 2.9 + - - -
598G GLN* 3.6 16.4 + - + +
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Residues in contact with LYS 596 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C GLU* 4.5 5.0 - - - +
592G ASP 2.9 21.8 + - - +
593G ILE* 3.0 9.8 + - - +
595G VAL* 1.3 77.5 - - - +
597G CYS* 1.3 63.9 + - - +
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Residues in contact with CYS 597 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ALA* 4.1 14.6 - - + +
245C GLU* 3.9 50.2 - - + +
246C SER* 5.5 0.4 - - - +
248C LYS* 5.0 8.7 - - - -
249C LEU* 4.3 20.0 - - + -
593G ILE* 3.0 30.3 + - - +
596G LYS* 1.3 85.7 - - - +
598G GLN* 1.3 65.6 + - - +
600G SER* 4.1 5.1 + - - -
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Residues in contact with GLN 598 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU 5.9 0.2 + - - -
39C LEU* 5.0 6.9 - - - +
40C GLY 3.0 35.8 + - - +
41C ALA* 4.1 5.7 + - - +
42C GLY* 4.1 13.1 + - - +
46C LYS* 4.8 4.9 - - - +
201C VAL* 4.8 2.2 - - - +
202C GLY* 3.6 42.5 + - - +
249C LEU* 4.1 9.2 - - - +
594G LEU* 3.2 37.8 + - + +
595G VAL* 3.6 13.2 + - - +
597G CYS* 1.3 79.6 - - - +
600G SER* 2.6 45.8 + - - -
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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