Contacts of the helix formed by residues 269 - 276 (chain B) in PDB entry 5KX8
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 SER 269 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B GLY* 1.4 73.7 - - - -
270B LEU* 1.3 63.5 + - - +
271B LEU* 3.5 7.6 + - - +
272B ASP* 3.2 33.1 + - - +
273B ARG* 3.2 25.1 + - - +
314B SER 4.0 2.5 - - - -
315B ALA* 3.7 25.5 - - - +
317B ILE 3.4 6.7 - - - -
318B LEU* 4.1 6.5 - - - +
319B LEU* 4.3 1.1 - - - -
501B 6YE 4.3 14.1 + - - -
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Residues in contact with LEU 270 (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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269B SER* 1.3 69.4 - - - +
271B LEU* 1.3 56.1 + - - +
273B ARG* 3.2 1.4 + - - +
274B LEU* 2.8 60.8 + - + +
283B LEU* 3.9 19.5 - - + -
288B ARG* 5.9 0.4 - - + -
291B ILE* 4.1 25.4 - - + -
314B SER* 3.2 17.2 + - - +
317B ILE* 2.9 28.9 + - + +
319B LEU* 4.1 8.9 - - + +
376B VAL* 4.1 16.4 - - + +
380B ILE* 3.9 30.7 - - + -
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Residues in contact with LEU 271 (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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269B SER* 3.6 7.4 - - - +
270B LEU* 1.3 76.4 - - - +
272B ASP* 1.3 72.9 + - - +
274B LEU* 3.1 5.6 + - + +
275B SER* 3.0 26.8 + - - +
314B SER* 3.1 33.0 + - - +
315B ALA* 3.8 24.7 - - + +
354B TYR* 4.3 5.4 - - - +
379B GLU* 3.9 10.8 - - - +
385B PRO* 5.1 13.9 - - + -
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Residues in contact with ASP 272 (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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192B MET 4.9 2.4 - - - +
269B SER* 3.2 22.5 + - - +
271B LEU* 1.3 86.6 - - - +
273B ARG* 1.3 73.1 + - - +
275B SER* 3.3 7.2 + - - -
276B CYS* 3.0 6.9 + - - -
277B LEU* 2.9 60.8 + - + +
501B 6YE 3.7 19.4 + - - -
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Residues in contact with ARG 273 (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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266B PRO 5.4 0.6 + - - -
267B ASN* 2.9 45.3 + - - +
268B GLY* 4.0 7.3 - - - +
269B SER 3.2 11.2 + - - +
270B LEU 3.2 2.4 + - - +
272B ASP* 1.3 94.3 + - - +
274B LEU* 1.4 64.9 + - - +
276B CYS* 3.3 17.4 + - - +
277B LEU* 3.0 30.1 + - - +
278B ASP* 5.2 2.0 + - - +
280B THR* 2.9 35.4 + - - +
281B PRO 4.8 4.4 - - - +
283B LEU* 3.6 34.8 + - + +
319B LEU* 3.7 12.6 - - + -
323B PHE* 4.3 16.8 - - + -
501B 6YE 5.4 2.6 - - - -
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Residues in contact with LEU 274 (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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270B LEU* 2.8 48.8 + - + +
271B LEU* 3.7 5.2 - - + +
273B ARG* 1.4 73.5 - - - +
275B SER* 1.3 58.7 + - - +
276B CYS* 3.7 1.7 + - - -
283B LEU* 4.3 12.6 - - + +
288B ARG* 3.8 34.4 + - + +
314B SER* 4.8 3.6 - - - -
379B GLU* 3.7 40.6 - - + +
380B ILE* 4.0 9.6 - - - +
383B GLY* 4.0 23.5 - - - +
415B ASP* 4.8 1.2 - - - +
417B LYS* 4.2 17.3 + - - -
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Residues in contact with SER 275 (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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271B LEU* 3.0 18.4 + - - +
272B ASP* 3.3 13.5 + - - -
274B LEU* 1.3 77.4 - - - +
276B CYS* 1.4 67.8 + - - +
277B LEU* 3.4 10.8 + - - +
383B GLY 5.3 2.7 - - - -
417B LYS* 5.6 1.3 - - - +
416C LYS* 5.6 4.9 - - - +
417C LYS* 3.3 17.0 - - - +
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Residues in contact with CYS 276 (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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272B ASP 3.0 5.8 + - - -
273B ARG 3.3 10.3 + - - -
274B LEU 4.3 1.3 - - - -
275B SER* 1.4 78.9 - - - +
277B LEU* 1.3 67.1 + - - +
278B ASP 3.3 0.3 + - - -
279B GLY 3.1 13.7 + - - -
280B THR* 3.3 26.0 - - - +
282B PRO* 3.7 41.1 - - - -
417B LYS* 4.1 16.6 - - - -
282C PRO* 4.2 4.0 - - + -
417C LYS* 3.4 25.0 - - + +
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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