Contacts of the helix formed by residues 276 - 283 (chain A) in PDB entry 2WFD
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 PRO 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A VAL* 4.3 9.0 - - + -
272A LEU 5.3 0.2 - - - +
274A PRO 4.1 2.9 - - - +
275A TYR* 1.3 92.0 - - + +
277A SER* 1.3 65.9 + - - +
278A LYS 3.3 1.1 - - - +
279A LEU* 3.1 31.8 + - + +
280A SER* 3.7 6.6 + - - -
356A GLU 3.9 20.9 - - - +
357A ILE* 4.5 7.4 - - - -
358A LEU 5.4 3.1 - - - +
360A ALA* 3.9 33.2 - - + -
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TYR 4.0 0.4 + - - -
276A PRO* 1.3 73.8 - - - +
278A LYS* 1.3 71.1 + - - +
279A LEU 3.2 0.2 - - - -
280A SER* 2.9 29.9 + - - +
356A GLU 5.2 0.2 + - - -
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A PRO* 3.3 2.0 + - - +
277A SER* 1.3 85.8 + - - +
279A LEU* 1.3 61.1 + - + +
280A SER* 3.3 1.9 + - - -
281A GLY 4.8 0.5 + - - -
350A LYS* 3.1 38.2 - - + +
351A GLU 5.8 2.2 - - - +
352A LEU* 4.1 19.3 - - + -
356A GLU* 3.6 53.8 + - + +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL* 4.4 11.9 - - + -
275A TYR* 3.8 13.4 - - + -
276A PRO* 3.1 35.0 + - + +
278A LYS* 1.3 84.3 - - + +
280A SER* 1.3 62.3 + - - +
281A GLY 3.2 2.9 - - - -
282A LEU* 3.1 33.3 + - + +
283A LYS 3.6 6.2 + - - -
287A ILE* 4.1 19.7 - - + -
325A ILE* 4.0 25.4 - - + -
350A LYS* 5.0 2.5 - - + +
352A LEU* 3.9 31.0 - - + -
357A ILE* 4.3 7.9 - - + -
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TYR* 5.4 0.9 - - - -
276A PRO 3.7 4.0 + - - -
277A SER* 2.9 25.9 + - - -
278A LYS 3.3 1.9 - - - -
279A LEU* 1.3 77.2 - - - +
281A GLY* 1.3 59.0 + - - +
283A LYS* 3.1 42.4 + - - +
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Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A LYS 4.8 2.4 + - - -
279A LEU 3.2 1.0 - - - -
280A SER* 1.3 80.5 + - - +
282A LEU* 1.3 62.0 + - - +
283A LYS 3.3 4.5 + - - +
285A LYS* 5.9 0.3 - - - +
350A LYS* 5.5 6.9 - - - +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TYR* 4.2 3.0 - - - -
279A LEU* 3.1 36.2 + - + +
281A GLY* 1.3 78.5 - - - +
283A LYS* 1.3 68.4 + - - +
284A GLY 3.4 0.2 + - - -
285A LYS* 3.0 42.1 + - + +
287A ILE* 3.7 14.1 - - + -
315A GLY* 6.0 0.7 - - - -
323A ILE* 3.3 33.9 - - + -
349A VAL* 3.4 24.2 - - + -
350A LYS* 4.3 26.9 - - + -
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A GLU* 3.3 29.3 + - - +
275A TYR* 3.8 28.5 - - + +
279A LEU 3.6 1.8 + - - -
280A SER* 3.1 31.8 + - - +
281A GLY 3.3 4.1 - - - +
282A LEU* 1.3 80.4 - - - +
284A GLY* 1.3 59.3 + - - +
285A LYS* 3.4 4.0 + - - +
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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