Contacts of the helix formed by residues 221 - 235 (chain D) in PDB entry 3STJ
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 221 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D ILE* 3.7 14.3 - - - +
130D ALA 2.9 20.1 + - - -
132D SER* 3.3 12.6 + - - -
198D LEU* 3.4 30.3 + - - +
199D ILE* 3.0 17.1 + - - -
200D GLY* 4.0 2.9 - - - -
219D ILE 3.6 1.2 + - - -
220D PRO* 1.3 70.0 - - - +
222D ASN* 1.4 53.3 + - - +
224D ALA* 3.6 7.9 - - - +
225D ARG* 2.7 39.1 + - - +
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Residues in contact with ASN 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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130D ALA 3.4 1.8 + - - -
131D ASP* 2.7 25.0 + - - +
132D SER* 3.1 32.9 + - - +
133D ASP* 3.2 20.5 - - - +
220D PRO* 5.5 0.2 - - + -
221D SER* 1.4 74.3 + - - +
223D MET* 1.3 58.1 + - - +
225D ARG* 3.2 37.7 + - - +
226D THR* 2.8 34.9 + - - +
304D ARG* 5.8 2.9 - - - +
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Residues in contact with MET 223 (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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111D SER* 5.1 8.7 - - - -
172D LEU* 5.2 7.4 - - - +
174D ASN* 3.6 30.5 - - + +
219D ILE* 4.0 17.7 - - + -
220D PRO* 3.1 18.8 + - + +
222D ASN* 1.3 76.2 - - - +
224D ALA* 1.3 63.9 + - - +
226D THR* 3.6 1.2 + - - -
227D LEU* 3.1 43.2 + - + +
303D SER* 3.5 27.8 - - - +
304D ARG* 4.5 6.5 - - + +
307D THR* 3.6 36.8 - - + +
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Residues in contact with ALA 224 (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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78D LEU* 3.9 26.0 - - + +
113D ILE* 3.7 23.1 - - + -
198D LEU* 5.5 1.3 - - + -
201D ILE* 4.1 15.3 - - + -
219D ILE* 4.2 2.2 - - + +
220D PRO 3.0 15.7 + - - +
221D SER* 3.7 8.3 - - - +
223D MET* 1.3 77.3 - - - +
225D ARG* 1.4 54.5 + - - +
227D LEU* 3.9 1.4 - - - +
228D ALA* 2.9 30.8 + - - +
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Residues in contact with ARG 225 (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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70D ILE* 4.9 7.4 - - + -
78D LEU* 4.8 0.4 - - - +
129D ILE* 3.5 39.2 + - + +
130D ALA 3.4 17.8 + - - -
131D ASP* 4.4 3.0 - - - +
221D SER 2.7 20.2 + - - +
222D ASN* 3.2 47.3 + - - +
224D ALA* 1.4 68.8 - - - +
226D THR* 1.3 62.0 + - - +
228D ALA* 3.3 8.0 + - - +
229D GLN* 3.0 36.1 + - + +
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Residues in contact with THR 226 (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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222D ASN* 2.8 17.8 + - - +
223D MET 3.8 4.3 - - - -
225D ARG* 1.3 80.9 + - - +
227D LEU* 1.3 61.8 + - - +
229D GLN* 3.3 9.1 + - - +
230D GLN* 3.1 39.0 + - - +
307D THR* 3.9 22.9 - - + +
308D THR* 4.8 6.1 - - + -
309D GLU* 5.4 1.1 - - + +
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Residues in contact with LEU 227 (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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108D ASP* 3.7 6.5 - - + +
111D SER* 3.3 28.7 - - - +
113D ILE* 3.7 26.5 - - + -
223D MET* 3.1 34.4 + - + +
224D ALA 3.9 2.7 - - - +
226D THR* 1.3 73.9 - - - +
228D ALA* 1.4 62.7 + - - +
230D GLN* 3.2 9.5 + - - +
231D LEU* 3.1 28.0 + - - +
237D ILE* 3.8 15.6 - - + +
239D ARG* 3.6 27.1 - - - +
307D THR* 4.3 22.9 - - + +
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Residues in contact with ALA 228 (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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70D ILE* 4.1 24.0 - - + -
78D LEU* 4.2 13.7 - - + -
113D ILE* 4.8 0.6 - - - +
115D LEU* 4.2 11.7 - - + +
224D ALA 2.9 19.2 + - - +
225D ARG 3.3 6.0 + - - +
227D LEU* 1.4 75.7 - - - +
229D GLN* 1.4 55.8 + - - +
231D LEU* 3.1 12.7 + - - +
232D ILE* 2.9 34.2 + - + +
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Residues in contact with GLN 229 (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 ARG* 3.0 20.2 + - + +
226D THR* 3.3 12.1 + - - +
228D ALA* 1.4 74.4 - - - +
230D GLN* 1.3 57.1 + - + +
232D ILE* 3.2 26.2 + - - +
233D ASP* 2.9 66.9 + - - +
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Residues in contact with GLN 230 (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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226D THR* 3.1 26.7 + - - +
227D LEU* 3.2 12.4 + - - +
229D GLN* 1.3 75.5 - - + +
231D LEU* 1.3 56.6 - - - +
234D PHE* 2.8 49.4 + - + -
236D GLU 3.1 19.0 - - - +
237D ILE* 3.5 15.4 - - + +
238D LYS 2.8 40.9 + - - +
239D ARG* 5.4 0.2 - - - +
306D ALA 5.4 0.4 + - - -
307D THR 2.9 23.9 + - - +
309D GLU* 4.1 20.5 + - + +
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Residues in contact with LEU 231 (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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105D ILE* 3.4 11.5 - - + +
106D GLY* 3.6 26.0 - - - +
107D SER* 3.6 31.2 - - - +
108D ASP 5.0 0.4 - - - +
113D ILE* 4.2 18.4 - - + +
115D LEU* 3.9 24.5 - - + +
227D LEU 3.1 15.2 + - - +
228D ALA* 3.1 7.6 + - - +
230D GLN* 1.3 75.5 - - - +
232D ILE* 1.4 63.9 + - - +
235D GLY* 3.1 22.9 + - - +
236D GLU* 3.8 27.6 - - - -
237D ILE* 4.1 9.9 - - + +
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Residues in contact with ILE 232 (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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70D ILE* 6.2 1.1 - - + -
71D ASN* 6.1 1.1 - - - +
74D LYS* 5.6 4.7 - - - +
76D TYR* 3.9 40.6 + - + +
105D ILE* 4.6 3.7 - - - +
115D LEU* 3.4 24.0 - - + -
228D ALA* 2.9 22.8 + - + +
229D GLN* 3.2 37.7 + - - +
231D LEU* 1.4 75.6 - - - +
233D ASP* 1.4 73.4 + - - +
235D GLY 4.8 0.5 + - - -
229G GLN* 6.1 1.6 - - - +
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Residues in contact with ASP 233 (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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229D GLN* 2.9 41.2 + - - +
232D ILE* 1.4 86.5 - - - +
234D PHE* 1.4 90.6 + - + +
235D GLY 3.8 0.2 - - - -
309D GLU* 5.2 1.7 - - - +
74G LYS* 4.5 13.7 + - - -
232G ILE* 5.5 7.4 - - - +
233G ASP* 5.0 7.3 - - - +
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Residues in contact with PHE 234 (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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230D GLN* 2.8 40.3 + - + +
233D ASP* 1.4 95.6 - - + +
235D GLY* 1.3 58.9 + - - +
236D GLU* 3.0 31.1 + - + +
238D LYS* 3.6 46.0 - - + -
309D GLU* 3.7 34.3 - - - -
74G LYS* 5.8 2.9 - - - -
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Residues in contact with GLY 235 (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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105D ILE* 3.9 21.2 - - - +
106D GLY* 4.1 6.6 - - - -
107D SER 5.2 0.2 + - - -
230D GLN 3.6 0.4 + - - -
231D LEU* 3.1 26.6 + - - -
232D ILE 4.7 0.6 + - - -
233D ASP 3.8 0.6 - - - -
234D PHE* 1.3 76.0 - - - +
236D GLU* 1.3 57.9 + - - +
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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