Contacts of the helix formed by residues 391 - 397 (chain C) in PDB entry 5W5G
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 TYR 391 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388C PHE 4.8 0.4 - - - -
389C GLY* 3.1 2.7 - - - -
390C LYS* 1.3 97.5 - - + +
392C TRP* 1.3 61.6 + - - +
393C LEU* 3.2 3.8 - - - -
394C SER* 3.2 30.4 + - - +
395C GLN* 4.0 9.3 + - - +
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Residues in contact with TRP 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C MET* 3.7 29.4 - - + +
385C ASP* 3.6 25.0 - - + +
388C PHE* 4.0 20.9 - - + -
389C GLY 3.3 20.3 + - - +
390C LYS 3.4 8.2 - - - -
391C TYR* 1.3 73.7 - - - +
393C LEU* 1.3 86.7 + - + +
394C SER 3.3 0.2 - - - -
395C GLN* 3.3 23.2 + - - +
396C CYS* 3.4 48.9 + - - -
410C MET* 5.4 1.6 - - + +
414C LEU* 4.0 16.8 - - + -
424C TYR* 3.6 37.7 + - + -
425C GLU* 5.0 4.8 + - - +
428C ALA* 4.2 3.7 - - + +
429C PRO* 3.6 27.8 - - + -
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Residues in contact with LEU 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390C LYS 6.0 0.9 - - - +
391C TYR* 3.2 1.9 - - - -
392C TRP* 1.3 113.0 - - + +
394C SER* 1.3 62.9 + - - +
395C GLN 3.2 0.2 + - - -
396C CYS* 4.4 1.6 - - - -
397C PHE* 3.0 51.4 + - + +
421C PHE* 3.8 28.0 - - + +
422C ARG* 4.1 30.7 - - - +
424C TYR* 3.9 2.2 - - + -
425C GLU* 4.0 29.2 - - + +
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Residues in contact with SER 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C TYR* 3.2 25.7 + - - +
393C LEU* 1.3 79.3 - - - +
395C GLN* 1.3 65.3 + - - +
397C PHE 3.9 10.1 - - - +
422C ARG* 5.6 1.6 + - - +
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Residues in contact with GLN 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388C PHE* 3.1 48.9 + - - +
391C TYR 4.2 4.8 + - - +
392C TRP* 3.3 16.4 + - - +
393C LEU 3.2 0.6 - - - -
394C SER* 1.3 83.8 - - - +
396C CYS* 1.3 60.1 + - + +
397C PHE 3.9 1.0 + - - -
404C ILE* 4.2 1.7 - - - +
406C THR* 3.8 30.8 + - + +
410C MET* 3.9 7.5 - - + +
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Residues in contact with CYS 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C MET* 4.8 0.2 - - - -
392C TRP* 3.4 46.0 - - - +
393C LEU 3.3 0.8 + - - -
395C GLN* 1.3 78.3 - - - +
397C PHE* 1.3 64.3 + - - +
398C ASP 4.2 0.4 - - - -
403C TYR* 3.4 22.7 - - + -
404C ILE* 2.7 46.6 + - - +
406C THR* 4.9 0.2 - - - +
410C MET* 3.8 26.0 - - + -
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Residues in contact with PHE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C TRP* 4.7 0.2 - + - -
393C LEU* 3.0 35.7 + - + +
394C SER* 3.9 9.9 - - - +
395C GLN 5.2 0.9 - - - -
396C CYS* 1.3 85.9 - - - +
398C ASP* 1.3 64.0 + - - +
401C GLY 3.4 26.2 - - - -
402C ARG 3.3 5.8 - - - -
403C TYR* 3.7 29.4 - + + -
414C LEU* 4.0 26.2 - - + -
416C GLN* 6.2 0.2 - - - -
421C PHE* 3.6 56.1 - + + -
424C TYR* 4.4 7.9 - + - -
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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