Contacts of the helix formed by residues 253 - 262 (chain D) in PDB entry 2Y1M
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 253 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213D HIS* 4.5 1.3 - - - -
250D PRO* 2.9 14.3 + - - +
252D SER* 1.3 80.3 + - - +
254D LEU* 1.3 52.0 + - - +
255D LEU 3.7 1.3 - - - -
256D ARG* 3.4 25.7 + - - -
257D ASN* 2.4 70.1 + - - -
352D LEU 3.9 13.2 + - - -
354D GLU 5.5 4.0 - - - -
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Residues in contact with LEU 254 (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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209D LEU* 4.7 8.7 - - + -
213D HIS* 3.6 14.1 - - + +
241D PHE* 5.9 0.2 - - + -
244D PHE* 4.0 21.5 - - + -
245D THR* 4.1 23.1 - - + +
248D PHE* 3.4 31.7 - - + +
250D PRO 3.9 0.9 - - - -
251D TRP* 3.3 54.2 + - + +
253D SER* 1.3 73.3 - - - +
255D LEU* 1.3 73.0 + - + +
257D ASN* 3.5 7.1 + - - +
258D TRP* 3.3 21.7 + - - +
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Residues in contact with LEU 255 (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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209D LEU* 4.6 5.8 - - + -
213D HIS* 3.4 45.5 + - + +
214D PRO 4.0 7.2 - - - +
215D ILE* 3.7 23.3 - - + -
220D GLU* 4.9 9.9 - - - +
224D LEU* 3.9 34.5 - - + -
244D PHE* 4.7 2.9 - - + -
254D LEU* 1.3 89.6 - - + +
256D ARG* 1.3 65.0 + - - +
257D ASN 3.2 0.2 - - - -
258D TRP* 4.0 12.4 - - + +
259D ASN* 3.1 32.5 + - - +
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Residues in contact with ARG 256 (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 HIS* 5.6 0.4 + - - -
253D SER* 3.4 25.5 + - - +
255D LEU* 1.3 80.4 - - - +
257D ASN* 1.3 61.1 + - - +
259D ASN* 3.9 5.3 + - - +
260D SER* 3.3 33.0 + - - -
351D GLY* 3.6 26.6 + - - -
352D LEU* 3.8 29.0 - - + +
354D GLU 5.5 4.4 + - - -
359D ASP 3.8 8.5 + - - -
360D HIS* 3.1 62.6 + - + +
361D ILE* 4.3 15.5 - - + +
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Residues in contact with ASN 257 (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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248D PHE* 3.4 21.7 + - + +
249D GLN 3.6 11.1 + - - +
250D PRO 3.4 12.3 + - - -
253D SER* 2.4 48.9 + - - +
254D LEU 4.0 0.2 - - - +
255D LEU 3.2 0.4 - - - -
256D ARG* 1.3 75.2 - - - +
258D TRP* 1.3 60.8 + - - +
260D SER 3.3 0.7 + - - -
261D LEU* 2.9 50.1 + - + +
325D PHE* 3.9 7.6 - - + -
352D LEU* 2.4 39.6 - - + +
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Residues in contact with TRP 258 (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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220D GLU* 3.8 22.7 - - + -
223D ALA* 3.5 21.5 - - + -
224D LEU* 3.2 45.3 - - + -
227D THR* 3.2 18.0 + - - -
244D PHE* 4.0 13.0 - + + -
248D PHE* 3.7 34.5 - + + -
254D LEU 3.3 15.4 + - - +
255D LEU* 3.4 19.5 + - + +
257D ASN* 1.3 77.3 - - - +
259D ASN* 1.3 86.5 + - - +
262D ALA* 2.8 38.9 + - + +
263D VAL* 3.3 21.6 + - + -
368D TYR* 4.2 2.2 - + - -
371D TYR* 3.5 10.4 + + - -
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Residues in contact with ASN 259 (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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220D GLU* 3.3 19.9 + - - -
255D LEU* 3.1 24.1 + - - +
256D ARG* 4.0 5.6 - - - +
258D TRP* 1.3 97.6 - - - +
260D SER* 1.3 58.1 + - - +
263D VAL* 3.4 12.4 + - - +
264D THR* 3.0 33.0 + - - -
361D ILE* 4.0 21.1 + - + +
363D VAL* 4.0 10.2 - - + +
368D TYR* 3.0 20.8 + - - -
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Residues in contact with SER 260 (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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256D ARG* 3.3 20.9 + - - -
257D ASN 3.3 4.3 + - - -
258D TRP 3.3 0.6 - - - -
259D ASN* 1.3 77.1 - - - +
261D LEU* 1.3 60.0 + - - +
264D THR* 4.0 9.3 + - - +
265D HIS* 3.6 23.1 + - - +
347D PRO* 5.6 1.0 - - - +
349D LEU* 3.9 22.3 - - - +
352D LEU* 4.1 9.8 - - - +
361D ILE* 3.2 26.8 - - - +
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Residues in contact with LEU 261 (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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247D LEU 5.2 2.2 - - - +
248D PHE* 4.2 19.5 - - + -
249D GLN 5.7 1.1 - - - +
257D ASN* 2.9 30.8 + - + +
260D SER* 1.3 79.4 - - - +
262D ALA* 1.3 60.3 + - - +
265D HIS* 3.6 6.1 - - - +
268D TYR* 3.2 20.8 - - - +
293D PHE* 3.3 20.6 - - + -
324D LEU* 4.5 14.4 - - + -
325D PHE* 3.8 35.9 - - + +
328D LEU* 4.0 21.3 - - + -
349D LEU* 3.7 28.0 - - + -
352D LEU* 4.9 0.2 - - + -
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Residues in contact with ALA 262 (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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248D PHE* 4.0 13.9 - - + -
258D TRP* 2.8 33.1 + - + +
261D LEU* 1.3 80.0 - - - +
263D VAL* 1.3 65.7 + - - +
264D THR 3.4 1.3 + - - -
265D HIS 3.8 4.7 + - - +
268D TYR* 3.5 34.1 - - + +
371D TYR* 3.6 20.3 - - - +
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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