Contacts of the helix formed by residues 221 - 235 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129K ILE* 3.8 10.7 - - - +
130K ALA 3.0 21.5 + - - -
132K SER* 3.3 10.7 + - - -
198K LEU* 3.3 29.2 + - - +
199K ILE* 3.1 24.1 + - - -
200K GLY* 3.9 4.3 - - - +
219K ILE 3.5 1.8 + - - -
220K PRO* 1.3 68.4 - - - +
222K ASN* 1.4 50.9 + - - +
224K ALA* 3.7 8.7 - - - +
225K ARG* 2.8 35.7 + - - +
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Residues in contact with ASN 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K ALA 3.4 1.2 + - - -
131K ASP* 2.8 24.1 + - - +
132K SER* 3.1 31.1 + - - +
133K ASP* 3.2 22.4 - - - +
220K PRO* 5.6 0.2 - - + -
221K SER* 1.4 69.8 - - - +
223K MET* 1.3 58.0 + - - +
225K ARG* 3.2 37.3 + - - +
226K THR* 2.8 38.0 + - - +
304K ARG* 6.1 1.6 - - - +
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Residues in contact with MET 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K SER* 5.0 7.6 - - - -
172K LEU* 5.3 6.3 - - - +
174K ASN* 3.6 39.5 - - + +
219K ILE* 4.0 18.4 - - + -
220K PRO* 3.0 20.6 + - + +
222K ASN* 1.3 76.9 - - - +
224K ALA* 1.3 63.9 + - - +
226K THR* 3.9 1.9 - - - -
227K LEU* 3.1 39.3 + - + +
303K SER* 3.8 27.4 - - - +
304K ARG* 4.6 4.9 - - + +
307K THR* 3.5 33.7 - - + +
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Residues in contact with ALA 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78K LEU* 3.8 25.6 - - + +
113K ILE* 3.7 22.4 - - + -
198K LEU* 5.5 0.4 - - + -
201K ILE* 3.9 17.0 - - + -
219K ILE* 4.1 4.9 - - + +
220K PRO 3.0 12.3 + - - +
221K SER* 3.7 9.4 - - - +
222K ASN 3.4 0.2 - - - -
223K MET* 1.3 76.9 - - - +
225K ARG* 1.4 55.5 + - - +
227K LEU* 3.9 1.2 - - - +
228K ALA* 2.9 31.2 + - - +
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Residues in contact with ARG 225 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K ILE* 4.8 8.1 - - + -
78K LEU* 4.8 0.2 - - - +
129K ILE* 3.6 39.9 + - + +
130K ALA 3.4 18.0 + - - -
131K ASP* 4.4 3.2 - - - +
221K SER 2.8 20.9 + - - +
222K ASN* 3.2 46.7 + - - +
224K ALA* 1.4 68.7 - - - +
226K THR* 1.3 62.6 + - - +
228K ALA* 3.3 7.3 + - - +
229K GLN* 3.0 35.0 + - + +
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Residues in contact with THR 226 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222K ASN* 2.8 19.1 + - - +
223K MET* 3.9 5.4 - - - -
225K ARG* 1.3 78.7 + - - +
227K LEU* 1.4 62.5 + - - +
229K GLN* 3.2 9.4 + - - +
230K GLN* 3.2 32.1 + - + +
307K THR* 3.5 27.6 - - + +
308K THR* 4.9 7.4 - - + -
309K GLU* 5.4 1.8 - - + +
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Residues in contact with LEU 227 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K ASP* 3.7 7.0 - - + +
111K SER* 3.3 21.8 - - - +
113K ILE* 3.7 24.5 - - + -
223K MET* 3.1 32.8 + - + +
224K ALA 3.9 3.1 - - - +
226K THR* 1.4 74.2 - - - +
228K ALA* 1.3 62.4 + - - +
230K GLN* 3.1 18.9 + - - +
231K LEU* 3.1 27.7 + - - +
237K ILE* 3.8 14.6 - - + +
239K ARG* 3.7 23.1 - - - +
307K THR* 3.6 28.7 - - - +
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Residues in contact with ALA 228 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K ILE* 4.2 18.8 - - + -
78K LEU* 4.2 8.3 - - + -
113K ILE* 4.8 1.0 - - - +
115K LEU* 4.1 20.7 - - + +
224K ALA 2.9 19.2 + - - +
225K ARG 3.5 5.6 - - - +
227K LEU* 1.3 75.3 - - - +
229K GLN* 1.4 55.1 + - - +
231K LEU* 3.1 13.3 + - - +
232K ILE* 3.0 36.7 + - + +
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Residues in contact with GLN 229 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225K ARG* 3.0 19.2 + - + +
226K THR* 3.2 11.2 + - - +
228K ALA* 1.4 74.8 - - - +
230K GLN* 1.3 58.0 + - + +
232K ILE* 3.2 23.3 + - - +
233K ASP* 2.9 68.7 + - - +
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Residues in contact with GLN 230 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K THR* 3.2 19.3 + - + +
227K LEU* 3.1 17.0 + - - +
229K GLN* 1.3 75.8 - - + +
231K LEU* 1.3 57.0 + - - +
233K ASP* 5.0 0.2 - - - -
234K PHE* 2.9 31.5 + - + -
236K GLU 2.9 22.9 - - - +
237K ILE* 4.3 8.2 - - + +
238K LYS* 2.9 52.9 + - - +
239K ARG* 5.7 0.2 + - - -
307K THR 3.2 24.1 - - - +
309K GLU* 3.9 25.3 + - + +
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Residues in contact with LEU 231 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K ILE* 3.3 13.0 - - + +
106K GLY* 3.5 26.9 - - - +
107K SER* 3.7 25.1 - - - +
108K ASP* 5.8 0.2 - - + -
113K ILE* 4.3 17.9 - - + +
115K LEU* 3.8 26.2 - - + +
227K LEU 3.1 13.9 + - - +
228K ALA* 3.1 8.3 + - - +
230K GLN* 1.3 76.8 - - - +
232K ILE* 1.3 61.6 + - - +
235K GLY* 3.0 23.3 + - - +
236K GLU* 3.8 28.3 - - - -
237K ILE* 3.9 14.4 - - + +
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Residues in contact with ILE 232 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K ILE* 5.3 4.5 - - + -
74K LYS* 5.7 3.6 - - - +
76K TYR* 3.7 47.7 + - + +
105K ILE* 4.6 4.6 - - - +
115K LEU* 3.5 22.9 - - + -
228K ALA* 3.0 28.2 + - + +
229K GLN* 3.2 28.7 + - - +
231K LEU* 1.3 78.9 - - - +
233K ASP* 1.3 69.5 + - - +
235K GLY 4.5 1.0 + - - -
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Residues in contact with ASP 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLN* 6.0 1.9 + - - -
229K GLN* 2.9 39.4 + - - +
230K GLN* 4.4 0.8 - - - +
232K ILE* 1.3 84.9 - - - +
234K PHE* 1.4 86.0 + - + +
309K GLU* 5.4 2.1 - - - +
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Residues in contact with PHE 234 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230K GLN* 2.9 35.4 + - + +
232K ILE 5.0 0.2 - - - -
233K ASP* 1.4 92.6 - - + +
235K GLY* 1.3 57.9 + - - +
236K GLU* 3.1 29.5 + - + +
238K LYS* 3.6 47.1 - - + -
309K GLU* 3.5 35.7 - - + -
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Residues in contact with GLY 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K ILE* 3.6 12.7 - - - +
106K GLY* 3.5 20.1 - - - -
107K SER 4.7 0.3 + - - -
230K GLN 3.6 0.6 + - - -
231K LEU* 3.0 27.0 + - - -
232K ILE 4.5 0.8 + - - -
233K ASP 3.9 0.4 - - - -
234K PHE* 1.3 74.8 - - - +
236K GLU* 1.3 57.3 + - - +
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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