Contacts of the helix formed by residues 269 - 278 (chain D) in PDB entry 2W93
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 LYS 269 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260D GLY 5.3 0.8 + - - -
261D GLY* 5.2 8.1 - - - -
262D VAL 4.9 3.4 + - - +
268D SER* 1.3 70.6 - - - +
270D PRO* 1.3 76.0 - - + +
271D GLU* 4.3 5.2 - - + +
272D VAL* 2.8 42.7 + - + +
273D LYS 3.0 10.0 + - - -
351D ALA 4.1 17.0 + - - +
352D ARG* 4.9 1.8 - - - +
353D THR* 3.2 37.2 + - - +
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Residues in contact with PRO 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D SER 3.3 6.5 - - - +
269D LYS* 1.3 83.8 - - + +
271D GLU* 1.3 58.3 + - + +
273D LYS* 3.5 11.7 + - + +
274D GLU* 3.2 29.3 + - - +
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Residues in contact with GLU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D LYS* 2.9 5.9 + - + +
270D PRO* 1.3 77.5 - - + +
272D VAL* 1.3 61.9 + - + +
274D GLU* 3.7 5.0 + - - +
275D ALA* 3.1 27.5 + - - +
350D PRO* 3.5 28.9 - - + +
351D ALA* 4.1 9.4 + - - +
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Residues in contact with VAL 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D PHE* 3.7 22.9 - - + -
260D GLY 3.6 20.2 - - - +
261D GLY* 4.5 3.4 - - - -
262D VAL 3.7 23.8 - - - +
263D TYR* 3.9 13.9 - - + -
268D SER* 4.2 4.9 - - - -
269D LYS* 2.8 42.7 + - + +
271D GLU* 1.3 70.1 - - + +
273D LYS* 1.3 64.2 + - - +
275D ALA* 3.3 1.4 + - - +
276D VAL* 3.1 24.3 + - - +
350D PRO* 4.0 14.1 - - + -
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Residues in contact with LYS 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D TYR* 4.2 10.3 - - + -
265D GLY 3.8 15.0 - - - +
266D THR* 3.7 39.2 - - - +
268D SER* 3.9 5.2 - - - +
269D LYS 3.0 11.0 + - - +
270D PRO* 3.7 13.2 - - + +
272D VAL* 1.3 76.8 - - - +
274D GLU* 1.3 61.7 + - + +
276D VAL* 4.1 0.3 - - - +
277D GLU* 2.7 72.0 + - - +
300D SER* 4.4 8.3 - - - -
302D LYS* 4.6 2.8 - - - +
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Residues in contact with GLU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D PRO 3.2 15.0 + - - +
271D GLU* 4.1 5.6 - - - +
272D VAL 3.2 0.2 - - - -
273D LYS* 1.3 82.9 + - + +
275D ALA* 1.3 58.9 + - - +
277D GLU* 4.7 11.6 - - - +
278D SER* 2.8 49.8 + - - -
302D LYS* 5.2 4.7 + - - +
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Residues in contact with ALA 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ASN* 4.3 4.2 + - - +
215D VAL* 3.5 16.9 - - - +
241D PRO* 6.2 0.4 - - + -
243D PHE* 3.6 23.8 - - + -
271D GLU 3.1 20.3 + - - +
272D VAL 3.3 2.4 + - - +
274D GLU* 1.3 76.7 - - - +
276D VAL* 1.3 61.9 + - - +
278D SER* 3.7 10.9 + - - -
279D ALA 4.0 2.1 + - - -
348D ALA 5.5 4.0 - - - +
350D PRO* 3.8 12.6 - - + -
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Residues in contact with VAL 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D VAL* 4.1 15.2 - - + +
217D LEU* 5.1 6.7 - - + -
243D PHE* 3.6 38.4 - - + -
263D TYR* 3.9 46.4 - - + -
272D VAL 3.1 16.3 + - - +
275D ALA* 1.3 76.2 - - - +
277D GLU* 1.3 59.4 + - - +
279D ALA* 3.1 26.3 - - - +
282D ILE* 4.1 6.4 - - + +
301D TYR* 4.2 14.8 - - + -
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Residues in contact with GLU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D TYR* 2.6 34.0 + - + +
265D GLY* 4.4 1.4 - - - -
273D LYS* 2.7 58.1 + - - +
274D GLU* 4.6 9.2 - - - +
276D VAL* 1.3 77.2 - - + +
278D SER* 1.3 57.8 + - - +
279D ALA 3.3 3.2 + - - +
282D ILE* 5.5 0.7 - - - -
298D SER 4.3 1.6 - - - +
299D TYR* 4.0 1.4 - - - -
300D SER* 3.1 34.6 + - - +
301D TYR* 4.3 4.0 - - - +
302D LYS* 3.2 48.1 + - + +
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Residues in contact with SER 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ASN* 3.1 23.7 + - - +
274D GLU* 2.8 37.1 + - - -
275D ALA* 3.7 5.5 + - - -
277D GLU* 1.3 75.6 - - - +
279D ALA* 1.3 65.5 + - - +
280D ASP* 3.7 2.1 + - - +
302D LYS* 5.1 3.1 - - - -
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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