Contacts of the helix formed by residues 247 - 263 (chain D) in PDB entry 1S77
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 ALA 247 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225D GLY 3.5 11.4 - - - +
226D MET 2.8 24.8 + - - +
228D SER* 3.7 10.1 - - - +
245D GLU* 4.4 0.9 - - - -
246D LEU* 1.3 85.0 - - - +
248D PRO* 1.3 69.4 - - + +
249D GLU* 3.0 23.6 - - - +
250D TYR* 3.8 15.9 - - + -
251D ALA* 3.2 19.4 + - - +
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Residues in contact with PRO 248 (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 SER* 4.9 6.1 - - - +
245D GLU* 5.8 4.7 - - - +
246D LEU 4.5 0.7 - - - +
247D ALA* 1.3 86.5 - - + +
249D GLU* 1.3 77.7 + - - +
251D ALA* 4.0 1.6 - - + +
252D GLU* 2.9 46.7 + - + +
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Residues in contact with GLU 249 (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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225D GLY 5.0 0.2 - - - +
247D ALA* 3.0 29.1 - - - +
248D PRO* 1.3 87.8 - - - +
250D TYR* 1.3 79.0 + - + +
251D ALA 3.4 0.4 - - - -
252D GLU* 4.2 7.2 - - - +
253D ALA* 3.2 22.3 + - - +
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Residues in contact with TYR 250 (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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73D LEU* 3.3 35.5 - - + +
76D THR* 6.0 3.4 - - + -
77D LEU* 4.5 19.8 - - + +
80D LYS* 5.6 3.5 + - - -
224D THR 5.2 1.7 - - - -
225D GLY* 3.8 24.3 + - - -
226D MET* 3.7 21.1 - - + -
246D LEU* 3.7 21.8 - - + +
247D ALA* 3.8 14.0 + - + -
248D PRO 3.4 0.6 - - - -
249D GLU* 1.3 94.2 - - + +
251D ALA* 1.3 61.4 + - - +
253D ALA* 3.8 6.3 - - + +
254D ILE* 3.6 23.6 + - - +
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Residues in contact with ALA 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 LEU* 3.4 25.8 - - + +
247D ALA 3.2 18.8 + - - +
248D PRO* 4.0 2.7 - - + +
250D TYR* 1.3 78.3 - - - +
252D GLU* 1.3 61.1 + - + +
253D ALA 2.8 9.1 + - - -
254D ILE* 3.3 4.5 + - - +
255D ALA* 3.0 23.5 + - - +
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Residues in contact with GLU 252 (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 PRO* 2.9 34.1 + - + +
249D GLU* 4.4 5.5 - - - -
251D ALA* 1.3 76.0 - - + +
253D ALA* 1.3 53.2 + - - +
255D ALA* 3.9 7.5 - - - +
256D THR* 2.4 38.1 + - - +
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Residues in contact with ALA 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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73D LEU* 5.2 8.3 - - + -
249D GLU 3.2 21.5 + - - +
250D TYR* 3.8 11.2 - - + +
251D ALA 2.8 1.6 - - - -
252D GLU* 1.3 75.3 - - - +
254D ILE* 1.3 58.2 + - + +
255D ALA 2.9 1.1 - - - -
256D THR* 2.9 5.5 + - - -
257D ARG* 2.7 36.1 + - - +
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Residues in contact with ILE 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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55D PHE* 4.5 10.1 - - + -
64D VAL* 4.2 18.6 - - + -
69D ALA* 3.4 33.5 - - + +
70D ALA* 3.7 24.9 - - + -
73D LEU* 3.6 28.7 - - + +
123D LEU* 4.2 14.1 - - + -
127D THR* 6.0 2.2 - - + -
246D LEU* 4.6 10.8 - - + -
250D TYR 3.6 13.6 + - - +
251D ALA* 3.3 5.9 + - - +
253D ALA* 1.3 77.7 - - - +
255D ALA* 1.3 57.4 + - - +
257D ARG* 3.5 0.2 - - - +
258D ALA* 3.1 23.4 + - - +
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Residues in contact with ALA 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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52D ARG* 4.4 4.8 + - - +
55D PHE* 5.5 3.6 - - - -
251D ALA 3.0 17.7 + - - +
252D GLU* 3.9 8.7 - - - +
253D ALA 2.9 0.6 - - - -
254D ILE* 1.3 77.6 - - - +
256D THR* 1.3 64.2 + - - +
258D ALA* 3.4 7.5 + - - +
259D GLY* 3.3 17.5 + - - -
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Residues in contact with THR 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 GLU* 2.4 25.1 + - - +
253D ALA* 2.9 7.2 + - - -
255D ALA* 1.3 73.3 - - - +
257D ARG* 1.3 67.8 + - - +
258D ALA 3.0 0.7 + - - -
259D GLY* 3.1 3.2 + - - -
260D ALA* 2.8 29.7 + - + +
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Residues in contact with ARG 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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68D ALA* 4.4 4.0 + - - +
69D ALA* 3.0 39.0 - - - +
71D LYS* 6.0 2.0 - - - +
72D PRO* 3.5 33.1 - - + +
253D ALA 2.7 15.1 + - - +
254D ILE 3.5 2.2 - - - +
256D THR* 1.3 77.6 - - - +
258D ALA* 1.3 58.5 + - - +
260D ALA* 3.1 15.4 + - - +
261D LEU* 2.8 43.6 - - + +
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Residues in contact with ALA 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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51D PHE* 3.9 13.9 - - + -
52D ARG* 3.8 23.6 - - - +
55D PHE* 4.3 10.5 - - + -
69D ALA* 3.8 13.2 - - + +
254D ILE 3.1 14.2 + - - +
255D ALA* 3.5 10.8 - - - +
256D THR 3.1 0.4 - - - -
257D ARG* 1.3 72.3 - - - +
259D GLY* 1.3 58.9 + - - +
261D LEU* 2.6 28.0 + - - +
262D ALA* 2.7 13.6 + - - +
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Residues in contact with GLY 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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44D TYR* 5.6 0.5 + - - -
48D GLU* 5.0 4.8 - - - +
52D ARG* 3.4 15.5 - - - +
255D ALA 3.3 6.7 + - - -
256D THR* 3.1 6.5 + - - -
258D ALA* 1.3 77.9 - - - +
260D ALA* 1.3 56.9 + - - +
261D LEU 3.1 5.0 + - - -
262D ALA* 3.6 10.7 + - - +
263D GLY* 3.9 8.0 + - - -
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Residues in contact with ALA 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 THR* 2.8 24.7 + - + +
257D ARG* 3.1 13.9 + - - +
259D GLY* 1.3 74.6 - - - +
261D LEU* 1.3 61.0 + - - +
263D GLY* 5.0 0.7 - - - -
264D ILE* 5.1 6.1 - - - +
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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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51D PHE* 4.1 22.2 - - + -
68D ALA* 3.2 36.1 - - + -
69D ALA* 3.5 19.5 - - + +
257D ARG* 2.8 34.1 - - + +
258D ALA* 2.6 12.5 + - - +
259D GLY 3.1 1.2 + - - -
260D ALA* 1.3 75.1 - - - +
262D ALA* 1.3 62.1 + - - +
263D GLY 3.1 3.0 - - - +
264D ILE* 3.3 40.9 - - + +
265D SER* 4.9 2.3 + - - -
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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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44D TYR 4.8 0.2 - - - +
47D GLY 4.1 3.1 - - - +
48D GLU* 3.3 47.1 + - + +
51D PHE* 3.2 36.1 - - + +
52D ARG* 4.7 6.3 - - - +
258D ALA 2.7 12.3 + - - +
259D GLY* 4.2 5.6 - - - +
261D LEU* 1.3 79.1 - - - +
263D GLY* 1.3 56.0 + - - +
264D ILE 3.3 4.6 + - - -
265D SER* 4.4 4.4 + - - -
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Residues in contact with GLY 263 (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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44D TYR* 3.0 51.3 + - - -
48D GLU* 3.5 6.8 + - - -
259D GLY 3.9 6.9 + - - -
261D LEU 3.1 2.2 - - - +
262D ALA* 1.3 78.9 - - - +
264D ILE* 1.3 66.8 + - - +
266D PRO* 5.1 0.7 - - - -
292D ARG* 4.6 6.2 - - - +
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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