Contacts of the helix formed by residues 392 - 396 (chain F) in PDB entry 6CP3
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 392 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408B PHE* 5.3 12.3 - - - -
387F ILE* 3.5 6.2 + - - +
388F ILE* 3.3 31.1 + - - +
391F LEU* 1.3 81.5 - - - +
393F MET* 1.3 65.2 + - - -
394F ASP* 3.2 6.0 + - - -
395F GLU* 3.8 9.1 + - - +
396F LEU* 4.9 1.6 - - - +
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Residues in contact with MET 393 (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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408B PHE* 6.0 1.6 - - - -
388F ILE* 3.7 29.8 - - + -
392F GLY* 1.3 72.7 - - - -
394F ASP* 1.3 68.2 + - - +
395F GLU 3.2 1.7 + - - -
396F LEU* 3.4 18.7 + - + +
401F LYS* 3.9 22.4 - - + +
404F VAL* 3.8 27.4 - - + -
405F GLU* 4.0 26.5 - - + +
408F ARG* 3.5 30.1 - - - +
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Residues in contact with ASP 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PHE* 5.9 3.6 - - - -
392F GLY* 3.2 3.4 - - - -
393F MET* 1.3 81.5 - - - +
395F GLU* 1.3 63.3 + - + +
396F LEU 3.4 7.6 + - - +
401F LYS* 3.6 23.7 + - - +
85G GLY* 3.8 26.5 - - - +
86G SER* 3.4 34.0 + - - -
88G HIS* 5.8 1.9 - - - -
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Residues in contact with GLU 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C PHE* 5.2 7.9 - - + +
387F ILE* 4.9 9.1 - - + +
391F LEU* 4.2 31.2 - - + -
392F GLY 3.8 7.3 + - - +
393F MET 3.2 2.0 - - - -
394F ASP* 1.3 82.5 - - + +
396F LEU* 1.3 68.2 + - - +
82G GLY* 5.1 0.2 - - - -
83G LEU* 3.3 45.5 + - + +
84G CYS 3.6 0.2 + - - -
85G GLY* 3.1 33.5 + - - +
88G HIS* 5.0 2.8 - - - -
236G ALA* 5.6 1.1 - - + +
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Residues in contact with LEU 396 (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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408C PHE 5.6 4.1 - - - +
384F LEU* 4.6 20.4 - - + -
387F ILE* 4.9 13.2 - - + -
388F ILE* 3.8 28.7 - - + -
392F GLY 5.0 0.9 - - - +
393F MET* 3.4 22.4 - - + +
394F ASP 3.4 6.5 + - - +
395F GLU* 1.3 86.6 - - - +
397F SER* 1.3 70.5 + - - +
398F GLU* 5.1 1.6 - - - +
400F ASP* 4.4 3.6 - - + +
401F LYS* 4.0 21.3 - - + +
404F VAL* 3.9 24.9 - - + -
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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