Contacts of the strand formed by residues 280 - 285 (chain C) in PDB entry 1ZKK
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 LYS 280 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A ASP* 3.5 23.1 + - - +
225A GLY* 3.9 4.3 - - - -
251C GLU* 6.5 0.2 - - + -
276C GLN* 3.4 4.0 - - - +
277C TYR 2.8 34.9 + - - +
278C LEU* 3.8 9.6 - - + +
279C SER* 1.3 91.2 + - - +
281C THR* 1.3 64.3 + - - +
282C TYR* 3.7 22.5 - - + +
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Residues in contact with THR 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 5.3 5.2 - - + -
223A ILE 3.7 4.0 + - - -
224A ASP* 2.8 18.5 + - - +
225A GLY 2.8 13.5 + - - -
227A GLY* 5.2 0.2 - - - -
251C GLU* 3.9 3.6 - - - +
252C ILE* 3.2 49.8 + - + +
274C TYR* 4.5 12.1 - - + -
275C PHE 3.5 11.9 - - - +
276C GLN* 2.6 28.3 + - - +
280C LYS* 1.3 73.4 - - - +
282C TYR* 1.3 74.5 + - - +
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Residues in contact with TYR 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C LEU* 4.0 15.7 - - + -
250C ILE 3.4 15.7 - - - +
251C GLU* 3.7 31.0 + - + +
252C ILE 5.0 1.8 - - - -
274C TYR* 3.4 5.1 - - - +
275C PHE* 2.8 52.7 + + + +
277C TYR* 3.4 52.2 + + + -
278C LEU* 5.8 1.2 - - - +
280C LYS* 3.7 26.3 - - + +
281C THR* 1.3 80.7 - - - +
283C CYS* 1.3 62.0 + - - +
316C PRO* 4.8 4.3 - - + -
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Residues in contact with CYS 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ASP 3.4 2.6 - - - +
249C LEU* 3.5 2.4 - - - +
250C ILE* 2.8 38.1 + - + +
255C ALA* 3.8 20.6 - - + -
272C MET* 3.6 33.7 - - - -
273C TYR 3.2 26.9 - - - -
274C TYR* 4.0 13.7 - - + -
275C PHE* 4.3 2.0 - - - -
282C TYR* 1.3 76.7 - - - +
284C VAL* 1.3 70.3 + - - +
285C ASP* 4.1 1.6 - - - -
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Residues in contact with VAL 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C TYR* 3.5 34.6 - - + +
247C GLY* 3.4 37.0 - - - +
248C ASP 3.7 4.0 - - - +
249C LEU* 4.4 9.9 - - + -
271C TYR 3.4 2.8 - - - +
273C TYR 2.8 35.7 + - - +
275C PHE* 3.8 20.8 - - + -
283C CYS* 1.3 72.1 - - - +
285C ASP* 1.3 59.3 + - - +
286C ALA 3.4 5.5 + - - -
316C PRO 6.0 0.9 - - - +
317C HIS* 6.1 0.7 - - - -
318C LEU* 4.0 19.1 - - + +
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Residues in contact with ASP 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ASP* 2.8 43.5 + - - +
250C ILE* 3.9 12.3 - - + -
258C ARG* 2.8 32.4 + - - +
262C TYR* 2.6 23.6 + - - -
271C TYR 4.3 1.1 - - - -
272C MET* 3.6 19.4 - - + +
283C CYS* 3.5 1.8 + - - -
284C VAL* 1.3 70.7 - - - +
286C ALA* 1.3 57.6 + - - +
287C THR* 2.6 30.1 + - - -
288C ARG 5.0 1.4 + - - -
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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