Contacts of the helix formed by residues 383 - 392 (chain F) in PDB entry 7KHC
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 ASN 383 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379F MET* 3.6 30.5 + - - +
380F VAL* 2.7 12.7 + - - +
382F ALA* 1.3 85.9 - - - +
384F LEU* 1.3 63.8 + - - +
385F ARG* 4.4 1.3 - - - +
386F LEU* 3.9 21.1 - - + +
412F LEU* 3.2 36.6 - - + +
416F VAL* 4.6 9.9 - - - +
427F PHE* 4.7 21.3 - - - -
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Residues in contact with LEU 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ILE* 5.7 9.4 - - + -
380F VAL* 2.8 29.3 + - + +
381F GLU* 4.2 15.9 - - + +
382F ALA 3.6 2.0 - - - -
383F ASN* 1.3 73.7 - - - +
385F ARG* 1.3 76.9 + - + +
386F LEU 2.7 16.5 + - - -
387F VAL* 2.8 22.5 + - - +
388F ILE* 3.8 18.5 + - + +
409F ASN* 5.9 2.5 - - - +
412F LEU* 5.3 0.2 - - - -
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Residues in contact with ARG 385 (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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381F GLU 4.0 7.3 + - - -
382F ALA 3.1 31.3 + - - -
383F ASN* 4.4 1.2 - - - +
384F LEU* 1.3 98.3 - - + +
386F LEU* 1.3 61.5 + - + +
387F VAL 3.3 0.2 - - - -
388F ILE* 3.1 15.1 + - + +
389F SER* 2.9 29.1 + - - -
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Residues in contact with LEU 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F ASN* 3.9 21.7 - - + +
384F LEU 2.7 5.9 + - - -
385F ARG* 1.3 81.3 - - + +
387F VAL* 1.3 62.1 + - - +
389F SER* 2.4 30.1 + - - +
390F ILE* 3.0 28.2 + - + +
412F LEU* 5.0 5.6 - - + -
427F PHE* 6.3 2.9 - - + -
428F SER* 5.6 4.3 - - - +
431F ALA* 4.8 11.7 - - + -
432F THR* 4.7 12.6 - - + -
435F ILE* 4.4 15.5 - - + -
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Residues in contact with VAL 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384F LEU 2.8 15.7 + - - +
386F LEU* 1.3 73.6 - - - +
388F ILE* 1.3 59.5 + - + +
390F ILE* 3.4 2.9 + - - +
391F ALA* 2.9 31.2 + - + +
405F ILE* 3.4 28.5 - - + +
408F GLY* 3.6 24.7 - - - +
409F ASN* 3.3 30.3 - - - +
412F LEU* 3.8 26.9 - - + -
435F ILE* 4.3 14.8 - - + +
439F ILE* 5.8 0.4 - - + -
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Residues in contact with ILE 388 (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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384F LEU* 3.8 22.6 + - + +
385F ARG* 3.1 14.3 + - + +
387F VAL* 1.3 79.0 - - + +
389F SER* 1.3 63.7 + - - +
391F ALA* 3.1 15.6 + - - +
392F LYS* 3.2 33.1 + - + +
401F PHE* 4.7 14.8 - - + -
405F ILE* 4.7 24.2 - - + -
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Residues in contact with SER 389 (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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385F ARG* 2.9 11.4 + - - -
386F LEU* 2.4 42.8 + - - +
388F ILE* 1.3 81.0 - - - +
390F ILE* 1.3 63.2 + - - +
392F LYS* 3.4 27.1 + - - +
393F LYS 4.5 1.6 + - - -
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Residues in contact with ILE 390 (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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386F LEU* 3.0 21.3 + - + +
387F VAL 4.1 2.7 - - - +
389F SER* 1.3 86.2 + - - +
391F ALA* 1.3 63.7 + - - +
393F LYS* 3.3 20.7 + - + +
394F TYR* 4.3 8.5 - - + -
432F THR* 3.6 35.9 - - + -
435F ILE* 3.7 40.8 - - + -
436F ARG* 4.7 19.7 - - + +
439F ILE* 5.0 2.7 - - + -
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Residues in contact with ALA 391 (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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387F VAL 2.9 19.9 + - - +
388F ILE* 3.1 8.7 + - - +
390F ILE* 1.3 73.6 - - - +
392F LYS* 1.3 54.7 + - - +
393F LYS 2.7 17.9 + - - -
394F TYR* 2.9 26.2 + - - +
401F PHE* 4.4 7.9 - - + -
404F LEU* 4.7 8.4 - - + +
405F ILE* 4.2 28.7 - - + +
439F ILE* 4.7 13.0 - - + -
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Residues in contact with LYS 392 (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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388F ILE* 3.2 35.8 + - + +
389F SER* 3.4 21.0 - - - +
390F ILE 3.3 1.0 - - - -
391F ALA* 1.3 75.4 - - - +
393F LYS* 1.3 58.5 + - - +
395F THR* 2.3 26.0 + - - +
401F PHE* 4.1 20.2 - - + -
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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