Contacts of the helix formed by residues 267 - 277 (chain D) in PDB entry 1Y9D
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 GLN 267 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248D LYS* 4.7 1.2 + - - -
253D ASP* 5.3 0.2 - - - +
258D TYR* 4.5 7.4 + - - -
259D LEU 3.9 14.0 + - - +
260D GLY* 3.4 22.3 - - - +
261D SER 2.9 12.0 + - - +
266D ALA* 1.3 74.6 - - - +
268D LYS* 1.3 66.3 + - - +
269D PRO 3.5 0.2 - - - -
270D ALA 3.3 2.8 + - - -
271D ASN* 3.1 21.3 + - - +
356D TRP* 2.7 40.2 - - - +
360D LEU* 4.3 3.6 - - - +
402D ASN* 3.4 36.7 + - - +
403D ARG* 3.8 27.3 + - + +
552D ALA* 4.0 2.0 - - - -
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Residues in contact with LYS 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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267D GLN* 1.3 68.9 - - - +
269D PRO* 1.3 72.0 - - + +
270D ALA 3.2 0.5 + - - -
271D ASN* 3.2 2.7 + - - +
272D GLU* 2.6 62.4 + - - +
352D ASN* 2.6 25.7 + - - -
355D ASN* 4.7 1.4 + - - -
356D TRP* 3.5 40.4 - - + +
552D ALA* 3.8 15.7 - - + +
555D LEU* 4.2 15.9 - - + -
557D LEU* 3.8 18.4 - - - -
579D LEU* 4.1 13.9 - - + -
580D GLN 2.8 22.8 + - - -
582D LEU 3.8 0.4 - - - +
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Residues in contact with PRO 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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259D LEU* 3.4 27.5 - - + +
267D GLN 3.6 3.6 - - - -
268D LYS* 1.3 93.7 - - + +
270D ALA* 1.3 56.4 + - - +
272D GLU* 4.0 1.0 - - - +
273D ALA* 3.1 30.5 + - - +
349D ASN* 4.8 1.0 - - - +
352D ASN* 3.8 22.9 + - + +
353D VAL* 4.1 22.9 - - + -
356D TRP* 3.5 41.7 - - + +
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Residues in contact with ALA 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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242D MET* 3.9 17.1 - - - +
259D LEU* 3.2 17.1 + - + +
260D GLY 3.5 21.1 - - - +
261D SER 3.4 27.4 - - - +
262D ALA* 3.8 3.5 - - - +
267D GLN 3.3 0.6 + - - +
268D LYS 3.3 0.8 - - - -
269D PRO* 1.3 75.2 - - - +
271D ASN* 1.3 66.4 + - - +
273D ALA 3.6 0.3 + - - -
274D LEU* 3.1 26.7 + - - +
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Residues in contact with ASN 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 ALA* 4.4 8.6 - - - +
263D ASN 4.7 13.0 + - - +
266D ALA* 4.7 8.0 - - + +
267D GLN 3.1 18.5 + - - +
268D LYS* 3.7 3.6 - - - +
270D ALA* 1.3 78.7 - - - +
272D GLU* 1.3 64.8 + - - +
274D LEU* 3.7 8.5 + - - +
275D ALA* 3.7 11.1 + - - +
552D ALA* 3.0 33.1 + - + +
553D GLU* 4.2 14.3 - - - +
555D LEU* 4.7 5.9 - - - +
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Residues in contact with GLU 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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268D LYS* 2.6 57.8 + - - +
269D PRO 4.0 2.2 - - - +
271D ASN* 1.3 75.8 - - - +
273D ALA* 1.3 65.5 + - - +
274D LEU 3.4 0.3 + - - -
275D ALA* 3.6 14.0 + - - +
276D GLN* 3.6 14.9 - - - +
352D ASN* 2.7 18.2 + - - +
555D LEU* 3.7 21.8 - - + +
557D LEU* 5.1 0.2 - - - +
581D PRO* 3.5 6.8 - - - +
582D LEU* 3.0 36.9 + - + +
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Residues in contact with ALA 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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216D LEU* 4.2 5.8 - - + -
259D LEU* 3.7 16.6 - - + -
269D PRO 3.1 19.2 + - - +
270D ALA 4.2 1.3 - - - +
272D GLU* 1.3 76.3 - - - +
274D LEU* 1.3 63.6 + - - +
276D GLN* 3.0 12.5 + - - +
277D ALA* 3.0 14.2 + - - +
345D TRP* 3.7 15.8 - - + -
349D ASN* 3.6 21.5 - - - +
582D LEU* 3.9 10.0 - - - +
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Residues in contact with LEU 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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216D LEU* 3.9 5.1 - - + +
218D TYR* 4.7 4.3 - - + -
242D MET* 3.6 24.7 - - + -
262D ALA* 3.9 19.5 - - + -
270D ALA 3.1 17.7 + - - +
271D ASN* 3.9 5.6 - - - +
272D GLU 3.2 0.2 - - - -
273D ALA* 1.3 77.4 - - - +
275D ALA* 1.3 65.3 + - - +
276D GLN 3.0 0.9 + - - -
277D ALA* 3.3 10.9 + - - +
280D VAL* 4.1 24.2 - - + -
282D PHE* 5.9 2.2 - - + -
287D TYR* 3.9 32.8 - - + +
299D THR* 4.6 5.9 + - - +
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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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271D ASN 3.7 7.7 + - - +
272D GLU* 3.6 11.8 + - - +
273D ALA 3.4 0.2 - - - -
274D LEU* 1.3 78.6 - - - +
276D GLN* 1.3 63.4 - - + +
298D ASN* 3.5 27.0 + - - +
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Residues in contact with GLN 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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214D ARG* 3.0 43.7 + - - +
272D GLU 3.6 15.3 - - - +
273D ALA 3.0 8.0 + - - +
275D ALA* 1.3 80.0 - - + +
277D ALA* 1.3 67.2 + - - +
278D ASP* 4.5 0.7 - - - +
298D ASN* 4.0 13.3 + - - +
345D TRP* 3.7 16.6 - - + -
582D LEU* 4.1 14.6 - - + -
586D LEU* 3.3 16.5 - - + +
593D ASP* 2.8 37.5 + - - +
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Residues in contact with ALA 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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214D ARG* 3.2 20.0 - - - +
216D LEU* 3.8 31.4 - - + -
273D ALA 3.0 7.1 + - - +
274D LEU 3.3 7.2 + - - +
276D GLN* 1.3 80.2 - - - +
278D ASP* 1.3 60.0 - - - +
279D VAL 4.4 1.1 - - - +
280D VAL* 3.9 18.2 - - + -
298D ASN* 3.2 12.5 - - - +
299D THR* 3.1 15.2 + - - +
345D TRP* 4.3 1.6 - - + -
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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