Contacts of the helix formed by residues 283 - 293 (chain B) in PDB entry 6E8Y
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 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277B PHE* 4.2 7.0 - - - -
281B GLY 3.7 2.4 + - - -
282B LYS* 1.3 79.2 - - - +
284B ILE* 1.3 65.0 + - - +
285B GLU* 3.5 8.8 + - - +
286B GLN* 3.0 29.0 + - - +
287B LEU* 3.0 22.2 + - - +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 5.9 1.8 - - + -
213B PHE* 5.8 2.2 - - + -
273B VAL* 3.9 22.1 - - + +
274B ALA* 5.6 2.5 - - - -
277B PHE* 3.8 28.4 - - + -
282B LYS 3.9 0.2 + - - -
283B SER* 1.3 73.0 - - - +
285B GLU* 1.3 55.2 + - - +
287B LEU* 2.8 6.7 + - - +
288B GLU* 2.7 57.9 + - + +
297B LEU* 4.6 6.1 - - + -
300B PRO* 4.4 21.5 - - + -
329B CYS* 4.1 36.6 - - + +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B SER* 3.3 7.8 + - - +
284B ILE* 1.3 78.8 - - - +
286B GLN* 1.3 63.9 + - - +
288B GLU* 3.1 19.5 + - - +
289B LYS* 3.0 21.9 + - + +
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Residues in contact with GLN 286 (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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282B LYS* 3.9 31.1 - - + +
283B SER* 3.0 24.3 + - - +
285B GLU* 1.3 77.3 - - - +
287B LEU* 1.3 57.9 + - - +
289B LYS* 3.2 10.1 + - + +
290B GLU* 2.7 53.4 + - + +
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Residues in contact with LEU 287 (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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273B VAL* 3.6 29.7 - - + +
276B ALA* 3.9 17.7 - - + -
277B PHE* 3.6 35.0 - - + +
282B LYS* 3.8 35.0 - - + +
283B SER 3.0 18.7 + - - +
284B ILE 2.8 7.4 + - - +
286B GLN* 1.3 74.8 - - - +
288B GLU* 1.3 65.1 + - - +
290B GLU* 4.1 3.4 - - - +
291B LEU* 3.1 52.1 + - + +
292B LEU* 4.9 0.2 - - - +
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Residues in contact with GLU 288 (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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273B VAL* 5.4 1.5 - - + +
284B ILE* 2.7 39.6 + - + +
285B GLU* 3.4 22.5 - - - +
287B LEU* 1.3 73.2 - - - +
289B LYS* 1.3 56.4 + - - +
292B LEU* 2.9 40.1 + - + -
293B ASN 3.1 15.3 - - - +
296B LYS* 3.4 15.9 - - - +
297B LEU* 2.7 40.8 + - + +
301B GLU* 5.6 0.7 - - - +
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Residues in contact with LYS 289 (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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285B GLU* 3.0 12.5 + - + +
286B GLN* 3.2 12.5 + - + +
288B GLU* 1.3 79.6 - - - +
290B GLU* 1.3 65.1 + - + +
291B LEU 3.4 0.2 + - - -
293B ASN* 3.8 20.5 + - - -
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Residues in contact with GLU 290 (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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282B LYS* 2.6 33.0 + - - +
286B GLN* 2.7 54.0 + - + +
287B LEU* 3.3 6.3 + - - +
289B LYS* 1.3 80.0 - - + +
291B LEU* 1.3 70.6 + - + +
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Residues in contact with LEU 291 (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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272B LYS* 4.3 25.4 - - + -
273B VAL* 4.9 9.4 - - + -
276B ALA* 5.7 3.8 - - + -
287B LEU* 3.1 51.0 + - + +
290B GLU* 1.3 90.4 - - + +
292B LEU* 1.3 76.9 + - + +
293B ASN 3.7 1.6 - - - -
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Residues in contact with LEU 292 (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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269B ARG* 3.7 43.9 + - + +
273B VAL* 4.4 9.0 - - + -
288B GLU* 2.9 32.5 + - + +
291B LEU* 1.3 102.0 - - + +
293B ASN* 1.3 74.2 + - - +
296B LYS 5.1 8.0 + - - +
297B LEU* 3.6 34.8 - - + +
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Residues in contact with ASN 293 (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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288B GLU* 3.1 17.0 + - - +
289B LYS* 3.8 16.4 + - - -
290B GLU 5.1 0.2 - - - -
291B LEU 3.7 1.8 - - - -
292B LEU* 1.3 86.7 - - - +
296B LYS 5.7 2.4 + - - -
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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