Contacts of the helix formed by residues 273 - 279 (chain B) in PDB entry 4K2S
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 CYS 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B GLN* 3.4 5.4 - - - -
267B PHE* 3.9 11.2 - - + -
269B SER 3.9 10.8 - - - -
270B ILE* 3.1 17.9 + - - -
271B HIS 3.3 0.2 - - - -
272B ASP* 1.3 81.4 - - - +
274B ARG* 1.3 66.8 + - - +
275B GLU 3.3 2.5 - - - -
276B LEU* 3.2 8.3 + - + -
277B ILE* 3.0 37.4 + - + +
285B ILE* 3.9 31.2 - - + -
287B MET* 4.4 5.6 - - - -
301B VAL* 4.3 11.2 - - - -
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Residues in contact with ARG 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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246A ASN* 3.0 42.3 + - - +
247A GLN* 4.9 2.2 - - - +
248A GLU* 3.0 37.7 + - - +
247B GLN* 3.7 0.6 + - - -
270B ILE* 2.9 19.8 + - + +
271B HIS* 4.8 11.4 + - - +
273B CYS* 1.3 76.8 - - - +
275B GLU* 1.3 90.8 + - - +
277B ILE* 3.4 1.4 + - - +
278B GLN* 2.9 70.8 + - - +
304B LEU* 4.0 19.7 - - + -
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Residues in contact with GLU 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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248A GLU* 4.5 4.3 - - - +
275A GLU* 3.7 18.7 - - - +
247B GLN* 3.2 36.9 + - + +
271B HIS 4.0 4.7 - - - +
274B ARG* 1.3 116.1 + - - +
276B LEU* 1.3 66.7 + - - +
278B GLN* 4.4 5.4 - - - +
279B ASN* 2.9 46.5 + - - +
281B TRP* 4.4 3.8 - - + -
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Residues in contact with LEU 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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244B ALA* 4.8 3.1 - - + -
247B GLN* 3.1 49.6 + - + +
250B LEU* 3.7 26.2 - - + -
263B ILE* 3.7 18.2 - - + -
267B PHE* 3.6 36.1 - - + -
272B ASP 4.0 5.6 - - - +
273B CYS* 3.2 10.3 + - + +
275B GLU* 1.3 75.7 - - - +
277B ILE* 1.3 59.8 + - - +
280B GLN 3.6 0.2 + - - -
281B TRP* 2.9 38.0 + - + +
282B ILE* 3.8 15.8 + - + -
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Residues in contact with ILE 277 (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 ILE* 6.0 0.2 - - + -
273B CYS* 3.0 35.9 + - + +
274B ARG 3.8 2.9 - - - +
276B LEU* 1.3 76.1 - - - +
278B GLN* 1.3 60.5 + - - +
280B GLN* 3.0 19.1 + - - -
282B ILE* 4.2 20.6 - - + -
285B ILE* 4.7 6.5 - - + -
301B VAL* 4.4 11.0 - - + +
304B LEU* 3.8 27.1 - - + +
305B ALA* 3.7 39.3 - - + +
308B TYR* 3.5 24.3 - - + +
310B VAL* 4.4 8.1 - - + +
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Residues in contact with GLN 278 (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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274B ARG* 2.9 61.9 + - - +
275B GLU* 4.2 4.1 - - - +
277B ILE* 1.3 73.7 - - - +
279B ASN* 1.3 63.8 + - - +
280B GLN* 3.2 3.3 + - - +
304B LEU* 4.0 20.5 - - + +
308B TYR* 3.3 46.5 + - + +
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Residues in contact with ASN 279 (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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275B GLU* 2.9 36.2 + - - +
278B GLN* 1.3 79.2 - - - +
280B GLN* 1.3 72.1 + - - +
281B TRP* 3.3 52.0 + - + +
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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