Contacts of the helix formed by residues 319 - 327 (chain B) in PDB entry 5FJH
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 MET 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B MET* 4.1 11.0 - - + -
298B TRP* 3.4 43.7 - - + -
299B ILE* 3.7 34.1 - - + +
302B GLY* 3.8 24.2 - - - +
303B LYS* 4.0 9.6 - - + +
316B LYS* 5.9 1.6 - - - +
317B ILE* 3.5 8.3 + - - +
318B SER* 1.3 72.9 + - - +
320B ASP* 1.3 64.2 + - - +
321B ILE 3.4 1.8 - - - -
322B PHE* 3.1 18.6 + - + +
323B VAL* 3.1 21.3 + - - +
334B TRP* 4.1 21.2 - - + -
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Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B SER* 3.3 14.9 + - - +
319B MET* 1.3 78.2 - - - +
321B ILE* 1.3 58.8 + - - +
323B VAL* 3.3 0.5 + - - -
324B ARG* 2.8 38.8 + - - +
331B TYR* 3.0 30.5 + - - -
334B TRP* 3.6 19.3 - - + -
335B LYS* 3.6 16.3 - - - +
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Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B VAL* 3.7 25.6 - - + -
166B CYS* 4.0 26.2 - - + -
168B ILE* 3.5 34.5 - - + +
318B SER 4.4 5.8 + - - +
320B ASP* 1.3 79.9 + - - +
322B PHE* 1.3 75.6 + - + +
324B ARG* 3.4 32.8 - - - +
325B LYS* 2.9 44.4 + - + +
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Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B VAL* 3.9 22.9 - - + -
159B LEU* 3.9 26.9 - - + -
162B VAL* 3.4 38.1 - - + -
168B ILE* 6.0 0.7 - - + -
170B ILE* 6.1 2.2 - - + -
298B TRP* 4.3 15.9 - + - -
299B ILE* 4.0 22.5 - - + +
317B ILE* 4.0 18.4 - - + -
318B SER 3.8 20.6 - - - -
319B MET* 3.1 22.9 + - + +
321B ILE* 1.3 84.7 - - + +
323B VAL* 1.3 57.2 + - - +
326B PHE* 2.9 40.0 + + - +
327B GLN 3.6 0.3 + - - -
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE* 4.4 3.8 - - + -
303B LYS* 3.8 33.7 - - + +
319B MET 3.1 17.1 + - - +
320B ASP 3.8 3.4 - - - +
322B PHE* 1.3 75.8 - - - +
324B ARG* 1.3 57.8 + - - +
327B GLN* 2.9 55.8 + - + +
330B ARG 4.6 0.9 - - - -
331B TYR* 3.7 30.5 - - + +
334B TRP* 3.7 30.3 - - + -
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Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B CYS* 5.9 0.4 - - - -
320B ASP* 2.8 28.2 + - - +
321B ILE* 3.4 30.8 - - - +
323B VAL* 1.3 75.9 - - - +
325B LYS* 1.3 84.5 + - - +
328B PRO* 3.9 17.2 - - - +
331B TYR* 3.5 41.8 - - + +
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Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B VAL* 6.1 0.9 - - + -
166B CYS* 4.9 13.2 - - - -
321B ILE* 2.9 34.5 + - + +
324B ARG* 1.3 107.9 - - - +
326B PHE* 1.3 81.7 + - + +
328B PRO* 3.9 9.4 - - - +
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Residues in contact with PHE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B VAL* 3.5 30.3 - - + -
161B VAL* 4.6 16.2 - - + -
162B VAL* 4.5 12.8 - - + -
296B VAL* 3.7 28.8 - - + +
299B ILE* 3.5 24.2 - - + -
322B PHE* 2.9 21.9 + - - +
325B LYS* 1.3 91.3 - - + +
327B GLN* 1.3 62.6 + - - +
328B PRO* 3.3 10.5 - - - +
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Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B VAL* 5.0 4.7 + - + +
299B ILE* 3.5 32.4 - - + +
300B ASP* 2.9 25.1 + - - +
303B LYS* 2.8 29.1 + - - +
322B PHE 3.6 0.6 + - - +
323B VAL* 2.9 27.3 + - + +
326B PHE* 1.3 84.7 - - - +
328B PRO* 1.3 64.7 - - - +
329B ASP* 3.1 2.9 - - - -
330B ARG* 2.9 38.3 + - - +
331B TYR 3.2 6.8 + - - -
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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