Contacts of the helix formed by residues 264 - 276 (chain D) in PDB entry 3HH2
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 264 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245D CYS* 5.4 2.9 - - - -
252D GLU 4.1 11.7 + - - -
254D VAL* 3.3 16.7 - - - +
262D TYR* 2.9 4.2 + - - +
263D ALA* 1.3 80.0 - - - +
265D GLU* 1.3 74.3 + - - +
266D CYS* 3.3 15.2 + - - -
267D ALA* 3.8 14.3 - - - +
268D MET 3.3 13.9 + - - -
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Residues in contact with GLU 265 (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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252D GLU 4.6 1.6 + - - -
254D VAL* 4.1 17.1 - - + +
264D SER* 1.3 81.2 + - - +
266D CYS* 1.3 56.6 + - - +
268D MET* 3.2 10.5 - - + +
269D LYS* 3.0 45.1 + - - +
281D VAL* 3.3 29.4 - - + +
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Residues in contact with CYS 266 (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 GLU* 5.8 7.9 - - + +
244D LEU 3.9 7.0 - - - +
245D CYS* 2.0 60.9 - - - -
246D PRO* 4.8 4.0 - - - -
264D SER* 3.3 8.1 + - - -
265D GLU* 1.3 76.1 - - + +
267D ALA* 1.3 57.7 + - - +
268D MET 3.1 0.4 - - - -
269D LYS* 3.5 20.5 - - + +
270D GLU* 2.7 31.4 + - + +
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Residues in contact with ALA 267 (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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245D CYS* 3.3 10.2 - - + -
262D TYR* 4.1 7.4 - - + -
263D ALA* 4.2 15.0 - - + +
264D SER* 3.6 27.8 + - - +
265D GLU 3.4 0.2 - - - -
266D CYS* 1.3 76.6 - - - +
268D MET* 1.3 63.3 + - - +
270D GLU* 3.3 9.8 + - - +
271D ALA* 3.0 22.7 + - - +
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Residues in contact with MET 268 (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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254D VAL* 4.4 4.9 - - + -
256D ALA* 3.6 33.9 - - + -
262D TYR* 3.8 18.8 - - + +
264D SER 3.3 11.7 + - - +
265D GLU* 3.2 22.7 - - + +
267D ALA* 1.3 79.2 - - - +
269D LYS* 1.3 73.0 + - + +
271D ALA* 3.2 4.5 + - - +
272D ALA* 3.0 26.0 + - - +
279D LEU* 3.4 36.0 - - + +
280D GLU* 3.7 20.6 - - - +
281D VAL* 4.0 17.7 - - + +
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Residues in contact with LYS 269 (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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90A LYS* 4.4 18.1 - - - +
243D GLU* 4.7 16.5 + - - +
265D GLU* 3.0 42.0 + - - +
266D CYS* 3.7 18.8 - - + +
267D ALA 3.3 0.2 - - - -
268D MET* 1.3 84.4 - - + +
270D GLU* 1.3 60.9 + - - +
272D ALA* 3.4 7.7 + - - +
273D CYS* 2.9 37.5 + - - -
279D LEU 5.8 0.4 - - - +
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Residues in contact with GLU 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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243D GLU 4.2 15.1 - - - +
244D LEU* 4.3 8.7 - - - +
245D CYS* 4.1 27.6 + - - +
266D CYS 2.7 22.5 + - - +
267D ALA* 3.5 7.8 - - - +
269D LYS* 1.3 74.9 - - - +
271D ALA* 1.3 56.8 + - - +
273D CYS* 3.4 6.5 + - - +
274D SER* 3.0 34.0 + - - +
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Residues in contact with ALA 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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262D TYR* 3.5 37.2 - - + +
267D ALA 3.0 9.4 + - - +
268D MET 3.2 5.4 + - - +
270D GLU* 1.3 76.1 - - - +
272D ALA* 1.3 61.1 + - - +
274D SER* 3.4 6.0 + - - +
275D SER* 2.9 30.0 + - - -
279D LEU* 4.6 2.2 - - + -
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Residues in contact with ALA 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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228D LEU* 3.3 14.5 - - + +
268D MET 3.0 13.4 + - - +
269D LYS* 3.6 12.3 - - - +
271D ALA* 1.3 75.7 - - - +
273D CYS* 1.3 57.2 + - - +
275D SER* 3.7 2.5 - - - -
276D GLY 2.9 27.2 + - - -
277D VAL 3.1 29.7 + - - +
278D LEU* 4.6 1.6 - - - -
279D LEU* 3.9 23.0 - - + +
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Residues in contact with CYS 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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226D LYS* 2.8 33.6 + - - +
228D LEU* 3.8 10.5 - - - -
239D SER* 5.3 0.7 - - - -
241D CYS* 2.1 59.5 - - + +
269D LYS* 2.9 27.8 + - - +
270D GLU* 3.6 7.0 - - - +
272D ALA* 1.3 77.4 - - - +
274D SER* 1.3 57.4 + - - +
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Residues in contact with SER 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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226D LYS* 3.1 13.8 + - - +
270D GLU* 3.0 18.9 + - - +
271D ALA* 3.8 6.7 - - - -
272D ALA 3.3 0.2 - - - -
273D CYS* 1.3 75.9 - - - +
275D SER* 1.3 58.8 + - - +
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Residues in contact with SER 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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226D LYS* 4.0 1.6 - - - -
271D ALA 2.9 21.2 + - - -
272D ALA* 3.3 6.9 + - - -
274D SER* 1.3 79.3 - - - +
276D GLY* 1.3 61.8 + - - +
277D VAL* 3.3 27.3 + - - +
279D LEU* 5.7 0.9 - - - +
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Residues in contact with GLY 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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216D CYS* 4.6 2.8 - - - -
226D LYS* 3.5 14.9 - - - +
227D CYS 3.7 15.1 - - - +
228D LEU* 3.6 5.1 - - - -
229D TRP* 3.0 28.0 + - - +
231D PHE* 5.2 0.2 - - - -
272D ALA 2.9 8.8 + - - -
274D SER 3.4 2.8 - - - -
275D SER* 1.3 78.7 - - - +
277D VAL* 1.3 61.5 + - - +
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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