Contacts of the helix formed by residues 287 - 293 (chain W) in PDB entry 6NE3
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 TYR 287 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235W LEU* 3.9 33.0 - - + -
236W VAL 3.6 15.7 - - - -
237W PRO* 3.4 29.4 - - + +
238W LYS 5.4 0.2 - - - -
286W SER* 1.3 81.6 + - - +
288W GLU* 1.3 56.9 + - - +
290W LEU* 2.9 21.5 + - - +
291W ILE* 3.0 17.4 + - - +
307W ILE* 4.4 7.0 - - + -
308W ASP 2.8 24.8 + - - -
309W GLU* 3.0 15.1 + - + +
312W ARG* 3.3 47.8 - - + +
320W LEU* 3.7 28.2 - - + +
564W LEU* 5.5 3.1 - - + -
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Residues in contact with GLU 288 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J T 4.8 22.9 - - - +
58J A 3.3 35.8 - - - +
267W ARG* 4.5 0.2 + - - -
286W SER* 4.4 3.2 + - - +
287W TYR* 1.3 79.7 - - - +
289W MET* 1.3 59.9 + - - +
291W ILE* 3.2 15.3 + - + +
292W LYS* 2.9 58.6 + - - +
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Residues in contact with MET 289 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J A 3.3 36.3 - - - +
260W LEU* 3.9 26.2 - - + +
261W ILE* 3.7 10.5 - - + -
262W GLY* 3.3 33.4 - - - +
267W ARG* 2.9 39.5 - - - +
285W THR* 3.7 21.1 - - + -
286W SER* 3.7 8.2 + - - +
287W TYR 3.2 0.2 - - - -
288W GLU* 1.3 79.0 - - + +
290W LEU* 1.3 57.2 + - - +
292W LYS* 3.3 1.6 + - - -
293W GLU* 2.9 34.7 + - - +
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Residues in contact with LEU 290 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233W MET* 4.7 5.8 - - - -
235W LEU* 3.7 36.3 - - + -
285W THR* 4.1 6.0 - - + +
286W SER 3.4 9.8 + - - +
287W TYR* 2.9 11.2 + - - +
289W MET* 1.3 75.6 - - - +
291W ILE* 1.3 62.3 + - + +
293W GLU 4.3 0.2 - - - +
294W LYS* 2.9 34.7 + - + +
297W PHE* 3.7 24.2 - - + -
320W LEU* 5.7 4.7 - - + -
323W ILE* 4.7 16.3 - - + +
324W VAL* 5.3 4.0 - - + -
327W PHE* 3.6 39.5 - - + -
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Residues in contact with ILE 291 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152I G 5.3 17.3 - - - +
287W TYR 3.0 14.8 + - - +
288W GLU* 3.2 22.2 + - + +
290W LEU* 1.3 77.9 - - + +
292W LYS* 1.3 63.8 + - + +
294W LYS* 3.7 22.0 - - + +
319W LYS* 4.7 7.6 - - + +
320W LEU* 3.8 44.2 - - + +
323W ILE* 3.8 16.4 - - + -
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Residues in contact with LYS 292 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J A 4.8 2.7 - - - -
59J A 3.1 29.9 + - - +
264W LYS* 5.1 5.1 - - - +
267W ARG* 3.6 18.4 - - - +
288W GLU* 2.9 46.4 + - - +
289W MET 3.8 3.1 - - - +
291W ILE* 1.3 84.8 - - + +
293W GLU* 1.3 79.5 + - - +
294W LYS* 3.5 3.3 + - - +
295W SER* 5.0 2.4 + - - -
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Residues in contact with GLU 293 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260W LEU* 4.3 11.2 - - + -
267W ARG* 3.1 41.5 + - + +
271W VAL* 5.7 3.6 - - - +
289W MET 2.9 18.6 + - - +
290W LEU 3.5 2.7 - - - -
292W LYS* 1.3 93.4 - - - +
294W LYS* 1.3 59.9 + - - +
295W SER* 3.2 3.6 - - - +
296W VAL* 3.2 25.8 + - + +
297W PHE* 2.9 45.0 + - + -
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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