Contacts of the strand formed by residues 279 - 284 (chain C) in PDB entry 2ATW
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 279 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277C VAL* 3.6 2.4 - - - +
278C VAL* 1.3 89.3 - - - +
280C VAL* 1.3 67.8 + - - +
281C SER* 4.3 7.6 + - - -
291C ARG 4.1 0.2 - - - +
292C VAL* 3.4 3.6 - - - +
293C VAL* 2.8 51.7 + - - +
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Residues in contact with VAL 280 (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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265C ALA* 3.7 48.5 - - + +
268C VAL* 4.5 3.8 - - + -
269C ALA* 3.8 22.7 - - + +
277C VAL* 4.0 5.4 - - + -
279C SER* 1.3 82.3 - - - +
281C SER* 1.3 66.2 + - - +
282C VAL* 4.3 1.0 + - + +
290C ALA* 4.2 15.0 - - + -
291C ARG 3.6 8.1 - - - +
292C VAL* 3.8 20.2 - - + -
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Residues in contact with SER 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C SER* 4.3 7.6 + - - -
280C VAL* 1.3 76.4 + - - +
282C VAL* 1.3 64.0 + - - +
283C ILE* 3.3 13.8 + - - +
290C ALA* 3.3 4.3 - - - +
291C ARG* 2.9 42.6 + - - +
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Residues in contact with VAL 282 (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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264C PRO* 5.5 1.6 - - + -
265C ALA* 4.5 22.2 - - + +
280C VAL 4.2 0.8 + - - +
281C SER* 1.3 73.0 - - - +
283C ILE* 1.3 66.7 + - - +
284C ASP 3.9 0.9 - - - +
285C GLN* 3.6 42.8 - - + +
289C ALA 3.9 2.9 - - - -
290C ALA* 4.6 2.2 - - + +
319C TRP* 3.8 24.5 - - + -
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Residues in contact with ILE 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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281C SER* 3.3 8.5 + - - +
282C VAL* 1.3 80.2 - - - +
284C ASP* 1.3 68.3 + - + +
285C GLN 4.2 0.2 - - - -
289C ALA* 2.8 18.9 + - + +
290C ALA 4.3 2.0 - - - -
291C ARG* 3.6 64.4 - - + +
322C ASP* 6.4 0.4 - - + -
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Residues in contact with ASP 284 (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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282C VAL* 4.0 1.8 - - - -
283C ILE* 1.3 86.9 - - + +
285C GLN* 1.3 53.4 + - - +
286C THR* 3.1 11.8 + - - -
287C ALA* 2.7 41.1 + - + +
288C ARG 2.7 29.3 + - - -
289C ALA* 2.7 23.0 + - + -
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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