Contacts of the helix formed by residues 283 - 296 (chain A) in PDB entry 2YTZ
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 ASP 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ASP* 5.8 4.0 - - - +
217A VAL 4.0 7.6 - - - +
218A ILE* 2.9 19.2 + - - +
282A LYS* 1.3 72.1 - - - +
284A GLU* 1.3 53.8 + - - +
285A LYS* 3.5 11.1 + - - +
286A ILE* 2.7 65.0 + - + +
287A VAL* 2.9 12.0 + - - +
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Residues in contact with GLU 284 (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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282A LYS* 3.1 44.8 + - - +
283A ASP* 1.3 71.0 + - - +
285A LYS* 1.3 63.4 + - - +
287A VAL* 3.7 7.1 - - - +
288A SER* 2.9 31.1 + - - -
313A ASP* 2.7 33.9 - - - +
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Residues in contact with LYS 285 (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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283A ASP* 3.0 10.5 + - - +
284A GLU* 1.3 77.5 - - - +
286A ILE* 1.3 64.9 + - + +
288A SER* 3.6 5.0 + - - -
289A LYS* 3.3 44.1 + - - +
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Residues in contact with ILE 286 (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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42A LEU* 4.0 15.9 - - + -
45A ILE* 3.8 17.0 - - + +
46A LEU* 4.1 18.6 - - + -
218A ILE* 4.0 29.6 - - + +
283A ASP* 2.7 44.1 + - + +
285A LYS* 1.3 74.4 - - + +
287A VAL* 1.3 66.0 + - + +
289A LYS* 3.0 20.6 + - + +
290A MET* 3.1 14.9 + - + +
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Residues in contact with VAL 287 (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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218A ILE 4.0 7.2 - - - +
219A LEU* 3.9 26.7 - - + -
282A LYS* 4.0 17.3 - - + -
283A ASP 2.9 14.2 + - - +
284A GLU* 3.7 11.2 - - - +
286A ILE* 1.3 75.8 - - + +
288A SER* 1.3 62.8 + - - +
290A MET* 3.1 27.7 + - + +
291A VAL* 3.2 8.9 + - + +
309A LEU* 4.2 11.7 - - + +
312A ILE* 4.2 8.5 - - + -
313A ASP* 3.9 33.0 - - + +
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Residues in contact with SER 288 (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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284A GLU* 2.9 23.6 + - - -
285A LYS* 3.8 7.0 - - - -
286A ILE 3.1 0.2 - - - -
287A VAL* 1.3 77.0 - - - +
289A LYS* 1.3 63.7 + - - +
291A VAL* 3.1 15.1 + - - +
292A LYS* 3.3 10.2 + - - +
313A ASP* 2.8 27.8 + - - -
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Residues in contact with LYS 289 (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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45A ILE* 3.6 27.4 - - + -
285A LYS* 3.3 36.8 - - - +
286A ILE* 3.0 7.5 + - - +
288A SER* 1.3 77.1 - - - +
290A MET* 1.3 52.3 + - - +
292A LYS* 2.9 12.3 + - + +
293A GLU* 2.6 35.9 + - - +
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Residues in contact with MET 290 (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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38A ILE* 3.6 31.4 - - + +
41A VAL* 3.3 14.9 - - + +
42A LEU* 3.6 42.6 - - + +
45A ILE* 3.3 22.0 - - + -
219A LEU* 4.1 17.7 - - + -
286A ILE* 3.1 15.7 + - + +
287A VAL* 3.1 22.0 + - - +
289A LYS* 1.3 77.2 - - - +
291A VAL* 1.3 53.8 + - - +
293A GLU* 4.3 0.4 - - - -
294A ALA* 2.7 37.8 + - - +
309A LEU* 4.0 17.7 - - + -
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Residues in contact with VAL 291 (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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287A VAL 3.4 15.0 - - - +
288A SER 3.4 7.9 - - - +
289A LYS 3.1 0.6 - - - -
290A MET* 1.3 76.1 - - - +
292A LYS* 1.3 61.3 + - - +
294A ALA* 3.6 5.5 + - - +
295A GLU* 2.9 36.6 + - - +
306A LEU* 4.0 2.0 - - + +
309A LEU* 3.9 21.1 - - + +
310A LYS* 3.7 39.7 - - + +
313A ASP* 3.8 30.7 - - + +
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Residues in contact with LYS 292 (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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288A SER 3.3 7.9 + - - +
289A LYS* 2.9 12.9 + - + +
291A VAL* 1.3 80.2 - - - +
293A GLU* 1.3 64.1 + - - +
295A GLU* 3.3 24.5 + - - +
296A SER* 3.5 13.4 + - - +
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Residues in contact with GLU 293 (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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41A VAL* 4.0 11.2 - - + +
44A ASN* 3.3 41.6 - - + +
45A ILE* 4.6 6.3 - - + -
289A LYS 2.6 19.0 + - - +
290A MET* 3.8 4.9 - - - +
292A LYS* 1.3 72.9 - - - +
294A ALA* 1.3 60.9 + - - +
296A SER* 2.8 33.6 + - - -
297A LEU* 3.3 36.7 - - + +
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Residues in contact with ALA 294 (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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41A VAL* 3.9 18.8 - - + +
290A MET 2.7 22.4 + - - +
291A VAL 3.8 4.7 - - - +
293A GLU* 1.3 72.8 - - - +
295A GLU* 1.3 62.1 + - - +
297A LEU* 3.4 13.3 + - - +
299A LEU* 4.0 13.8 - - + +
302A LYS* 3.4 14.4 - - - -
306A LEU* 3.8 12.9 - - + +
309A LEU* 3.8 22.4 - - + -
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Residues in contact with GLU 295 (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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291A VAL* 2.9 27.7 + - - +
292A LYS* 3.5 20.2 - - - +
293A GLU 3.1 0.8 - - - -
294A ALA* 1.3 78.4 - - - +
296A SER* 1.3 55.9 + - - +
297A LEU 3.3 0.7 - - - -
302A LYS* 2.7 26.5 + - - +
306A LEU* 3.3 17.7 - - + +
310A LYS* 3.0 25.4 + - - -
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Residues in contact with SER 296 (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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292A LYS* 3.5 10.8 + - - +
293A GLU* 2.8 27.1 + - - -
295A GLU* 1.3 78.2 - - - +
297A LEU* 1.3 65.2 + - - +
302A LYS* 4.5 0.2 - - - -
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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