Contacts of the helix formed by residues 250 - 261 (chain D) in PDB entry 1DS5
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 GLY 250 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246D ALA 2.5 24.1 + - - -
248D VAL 3.2 3.2 + - - -
249D LEU* 1.3 82.0 - - - +
251D THR* 1.3 64.0 + - - -
252D ASP* 3.4 3.8 - - - -
253D GLY 3.3 9.2 + - - -
276D HIS 3.3 11.4 - - - -
277D SER 3.5 1.1 - - - -
278D ARG* 3.4 17.5 - - - -
307D TYR* 3.2 12.2 + - - -
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Residues in contact with THR 251 (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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246D ALA* 3.9 12.1 - - + -
250D GLY* 1.3 66.0 - - - -
252D ASP* 1.3 54.6 + - - -
253D GLY 2.8 7.9 + - - -
254D LEU* 2.8 27.4 + - + -
255D ASN* 2.9 29.9 + - - -
273D VAL* 3.8 20.9 - - + -
274D GLY 3.0 25.6 - - - +
275D ARG* 3.6 8.5 - - - +
276D HIS* 2.8 37.1 + - + +
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Residues in contact with ASP 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D GLY 3.4 2.1 + - - +
251D THR* 1.3 78.6 + - - +
253D GLY* 1.3 57.9 + - - +
255D ASN* 4.2 5.0 - - - +
256D VAL* 3.0 24.1 + - - +
275D ARG* 4.9 14.5 + - - -
276D HIS 4.3 6.7 + - - +
277D SER* 5.4 4.1 - - - -
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Residues in contact with GLY 253 (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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249D LEU 4.9 2.0 + - - -
250D GLY 3.3 7.4 + - - -
251D THR 2.9 0.8 - - - -
252D ASP* 1.3 79.3 - - - +
254D LEU* 1.3 66.5 + - - +
255D ASN 2.9 3.5 + - - -
256D VAL* 3.2 7.5 + - - +
257D TYR* 3.0 23.2 + - - +
307D TYR* 3.6 13.9 - - - +
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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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200D PRO* 5.6 0.2 - - + -
204D VAL* 4.6 7.9 - - + -
242D LEU* 4.4 27.1 - - + -
246D ALA* 4.6 3.8 - - + -
251D THR* 2.8 13.7 + - + +
253D GLY* 1.3 75.4 - - - +
255D ASN* 1.3 62.4 + - - +
257D TYR* 3.3 13.1 - - + +
258D LEU* 3.1 45.6 + - + +
265D LEU* 4.5 8.5 - - + -
273D VAL* 3.7 30.3 - - + -
307D TYR* 3.2 47.0 - - + +
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Residues in contact with ASN 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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251D THR* 2.9 31.1 + - - +
252D ASP* 4.7 5.6 - - - +
253D GLY 2.9 2.2 - - - -
254D LEU* 1.3 84.1 - - - +
256D VAL* 1.3 66.7 + - + +
257D TYR 3.0 1.6 - - - -
258D LEU* 3.2 13.0 + - - +
259D ASN* 3.0 33.4 + - - +
275D ARG* 6.0 2.6 + - - -
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Residues in contact with VAL 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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252D ASP 3.0 22.9 - - - +
253D GLY* 3.7 7.6 - - - +
255D ASN* 1.3 78.0 - - + +
257D TYR* 1.3 55.4 + - - +
259D ASN* 3.4 5.9 + - - +
260D LYS* 3.0 32.4 + - + +
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Residues in contact with TYR 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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200D PRO* 4.5 7.6 - - + -
201D GLU* 3.6 21.6 - - - +
204D VAL* 3.9 22.6 - - + +
206D LEU* 3.3 23.9 - - + +
253D GLY 3.0 12.3 + - - +
254D LEU* 3.3 19.3 - - + +
256D VAL* 1.3 75.3 - - - +
258D LEU* 1.3 77.7 + - + +
260D LYS* 3.1 10.0 + - - +
261D TYR* 3.1 43.4 + + + +
263D ILE* 5.8 1.6 - - + -
307D TYR* 3.1 47.7 + - + -
308D ASP* 3.7 14.8 - - + -
309D HIS* 3.8 3.5 + - - -
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Residues in contact with LEU 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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204D VAL* 4.3 7.9 - - + -
254D LEU* 3.1 24.8 + - + +
255D ASN* 3.6 17.9 - - - +
257D TYR* 1.3 94.4 - - + +
259D ASN* 1.3 66.3 + - - +
261D TYR 3.2 1.2 + - - -
262D ARG* 2.9 18.4 + - - -
263D ILE* 2.9 53.4 + - + +
265D LEU* 3.4 41.3 - - + +
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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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255D ASN* 3.0 26.1 + - - +
256D VAL* 3.9 5.8 - - - +
258D LEU* 1.3 78.2 - - - +
260D LYS* 1.3 67.8 + - - +
262D ARG* 2.7 19.5 + - - +
263D ILE 5.4 2.4 + - - -
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Residues in contact with LYS 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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6D MET* 5.6 6.2 - - - +
256D VAL* 3.0 17.6 + - + +
257D TYR* 3.1 12.5 + - - +
259D ASN* 1.3 76.0 - - - +
261D TYR* 1.3 98.4 + - + +
262D ARG* 3.5 6.1 + - - +
308D ASP* 3.2 22.8 + - - +
310D GLN* 4.4 8.7 - - - +
311D GLU* 4.3 7.0 - - - +
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Residues in contact with TYR 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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6D MET* 3.3 39.9 + - + +
7D SER* 4.2 3.4 - - - -
206D LEU* 4.0 13.2 - - + -
257D TYR* 3.1 34.1 + + + +
259D ASN 3.0 0.6 - - - -
260D LYS* 1.3 105.8 + - + +
262D ARG* 1.3 86.3 + - - +
263D ILE* 2.8 26.9 + - + +
308D ASP* 2.9 38.7 + - - -
309D HIS* 3.6 21.0 + + - -
310D GLN* 3.2 18.5 + - - +
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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