Contacts of the helix formed by residues 207 - 222 (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 GLU 207 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D HIS* 4.1 17.5 + - + -
206D LYS* 1.3 104.6 + - + +
208D ASP* 1.3 65.4 + - - +
209D SER 3.6 0.4 - - - -
210D ILE* 3.2 13.8 - - + +
211D HIS* 2.5 40.9 + - + -
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Residues in contact with ASP 208 (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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101D THR* 5.0 6.9 - - + +
105D PHE* 3.2 43.6 - - + -
204D TRP* 2.6 31.5 + - + +
205D HIS* 3.8 10.0 - - - +
207D GLU* 1.3 90.2 - - - +
209D SER* 1.3 55.3 + - - +
210D ILE 3.2 0.7 - - - -
211D HIS* 2.9 10.3 + - - +
212D VAL* 2.6 37.8 + - + +
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Residues in contact with SER 209 (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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138D ALA 3.5 5.0 - - - +
139D SER* 4.9 7.2 - - - -
142D GLY* 3.5 9.1 - - - -
143D ARG* 4.1 20.2 + - - +
146D GLU* 2.8 26.4 + - - -
204D TRP* 4.4 4.8 + - - +
205D HIS 5.0 1.4 + - - -
206D LYS* 4.8 11.6 - - - -
208D ASP* 1.3 77.5 - - - +
210D ILE* 1.3 65.4 + - - +
212D VAL* 3.0 10.8 + - - +
213D GLY 2.8 20.3 + - - -
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Residues in contact with ILE 210 (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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135D GLN* 4.7 13.9 - - + +
138D ALA* 3.3 14.9 + - + +
139D SER* 4.5 21.5 - - - +
206D LYS 5.1 5.1 + - - +
207D GLU* 3.2 19.3 - - + +
209D SER* 1.3 74.9 - - - +
211D HIS* 1.3 89.0 + - + +
213D GLY 3.1 1.7 + - - -
214D VAL* 2.7 44.1 + - + +
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Residues in contact with HIS 211 (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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100D PRO 5.8 0.4 - - - +
101D THR* 4.5 27.8 - - + -
102D ALA* 4.2 6.5 - - - +
207D GLU* 2.5 29.7 + - + -
208D ASP* 2.9 9.7 + - - +
210D ILE* 1.3 99.1 - - + +
212D VAL* 1.3 65.8 + - + +
214D VAL* 3.1 19.0 + - + +
215D ARG* 3.3 13.5 + - - +
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Residues in contact with VAL 212 (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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101D THR* 6.4 0.2 - - + -
102D ALA* 4.6 9.4 - - - -
105D PHE* 3.2 34.1 - - + +
106D LEU* 3.3 23.5 - - + +
142D GLY* 3.9 4.0 - - - -
145D ILE* 3.7 18.2 - - + -
204D TRP* 3.2 32.1 - - + -
208D ASP* 2.6 25.2 + - + +
209D SER 3.2 7.4 - - - +
211D HIS* 1.3 74.9 - - + +
213D GLY* 1.3 64.2 + - - +
215D ARG* 3.6 1.2 + - - +
216D CYS* 3.3 23.4 + - - -
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Residues in contact with GLY 213 (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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138D ALA* 3.8 13.7 - - - -
141D ILE* 3.8 23.8 - - - -
142D GLY* 4.0 0.6 - - - -
209D SER 2.8 17.1 + - - -
210D ILE 3.5 2.7 - - - -
212D VAL* 1.3 72.8 - - - +
214D VAL* 1.3 54.3 + - - +
216D CYS* 2.9 2.3 + - - +
217D ILE* 2.7 42.0 + - - +
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Residues in contact with VAL 214 (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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134D VAL* 5.8 7.2 - - + +
138D ALA* 3.8 8.0 - - + +
210D ILE* 2.7 39.0 + - + +
211D HIS* 3.1 11.6 + - + +
213D GLY* 1.3 72.2 - - - +
215D ARG* 1.3 56.5 + - - +
217D ILE* 3.3 9.3 + - + +
218D GLU* 2.8 58.3 + - + +
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Residues in contact with ARG 215 (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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84D ARG* 4.4 0.4 - - - +
88D TRP* 2.9 57.3 - - + +
100D PRO* 5.7 3.6 - - - +
102D ALA* 3.7 22.2 - - + -
106D LEU* 5.0 2.0 - - + -
211D HIS 3.3 4.3 + - - +
212D VAL 4.1 2.2 - - - +
214D VAL* 1.3 76.8 - - - +
216D CYS* 1.3 56.6 + - - +
218D GLU* 3.1 26.1 + - - +
219D MET* 2.6 80.5 + - + +
222D GLU* 3.3 32.3 + - - -
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Residues in contact with CYS 216 (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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81D MET* 4.3 2.6 - - - +
106D LEU* 3.7 31.2 - - - -
114D VAL* 4.2 7.0 - - - -
118D THR* 4.0 18.8 - - + +
141D ILE* 3.7 28.9 - - + -
212D VAL 3.3 21.1 + - - -
213D GLY 2.9 8.9 + - - +
215D ARG* 1.3 78.8 - - - +
217D ILE* 1.3 62.7 + - - +
219D MET* 3.2 13.6 + - - +
220D LEU* 3.0 25.4 + - - +
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Residues in contact with ILE 217 (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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122D THR* 5.2 0.2 - - + -
134D VAL* 3.9 17.7 - - + +
137D VAL* 3.3 33.4 - - + -
138D ALA* 3.4 17.5 - - + +
141D ILE* 3.3 17.3 - - + -
213D GLY 2.7 23.8 + - - +
214D VAL* 3.6 6.5 - - - +
216D CYS* 1.3 72.7 - - - +
218D GLU* 1.3 59.5 + - + +
220D LEU* 3.1 16.7 - - + +
221D ILE* 3.0 37.2 - - + +
227D VAL* 4.5 20.6 - - + -
244D ILE* 4.6 8.7 - - + -
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Residues in contact with GLU 218 (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 VAL* 2.8 54.5 + - + +
215D ARG* 3.1 27.9 + - - +
217D ILE* 1.3 75.0 - - + +
219D MET* 1.3 57.1 + - - +
220D LEU 2.9 5.2 - - - -
221D ILE* 3.3 11.6 + - + +
222D GLU* 2.9 27.9 + - - +
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Residues in contact with MET 219 (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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81D MET* 3.6 10.7 - - + +
84D ARG* 3.7 12.1 - - + +
85D ILE* 3.7 33.9 - - + -
88D TRP* 3.3 39.7 - - + -
89D PHE* 6.3 0.2 - - - -
106D LEU* 5.4 7.9 - - + -
215D ARG* 2.6 61.9 + - + +
216D CYS* 3.4 13.9 - - - +
218D GLU* 1.3 70.7 - - - +
220D LEU* 1.3 57.8 + - - +
222D GLU* 3.5 17.5 - - - +
223D SER* 2.9 21.2 + - - -
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Residues in contact with LEU 220 (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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81D MET* 3.5 18.2 - - + -
118D THR* 3.3 26.0 - - + -
119D ILE* 3.9 14.8 - - + -
122D THR* 3.5 28.3 - - + -
216D CYS 3.1 7.4 - - - +
217D ILE* 3.1 15.3 - - - +
219D MET* 1.3 78.8 - - - +
221D ILE* 1.3 56.0 + - - +
222D GLU 3.0 3.4 - - - -
223D SER* 3.7 1.6 - - - -
224D THR* 2.6 43.4 + - + +
226D MET* 3.9 18.4 - - + -
227D VAL* 3.7 25.1 - - + +
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Residues in contact with ILE 221 (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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217D ILE* 3.0 23.7 + - + +
218D GLU* 3.9 9.6 - - + +
220D LEU* 1.3 75.5 - - - +
222D GLU* 1.3 60.8 + - - +
224D THR* 4.3 10.7 - - - +
225D GLY* 5.0 6.5 - - - +
227D VAL* 3.4 48.7 - - + +
228D SER* 5.3 1.1 - - - -
229D LEU* 4.4 19.3 - - + -
244D ILE* 6.0 0.4 - - + -
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Residues in contact with GLU 222 (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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84D ARG* 3.2 38.0 + - - -
215D ARG* 3.3 34.4 + - - -
218D GLU 2.9 15.2 + - - +
219D MET* 3.5 8.9 - - - -
221D ILE* 1.3 80.7 - - - +
223D SER* 1.3 58.0 + - - +
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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