Contacts of the helix formed by residues 221 - 235 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ILE* 3.7 14.4 - - - +
130A ALA 2.8 20.4 + - - -
132A SER* 3.3 13.0 + - - -
198A LEU* 3.4 30.0 + - - +
199A ILE* 2.9 16.1 + - - -
200A GLY* 4.1 2.7 - - - +
219A ILE 3.6 1.0 + - - -
220A PRO* 1.3 67.6 - - - +
222A ASN* 1.3 56.9 + - - +
224A ALA* 3.7 7.7 - - - +
225A ARG* 2.7 38.1 + - - +
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Residues in contact with ASN 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ALA 3.4 2.0 + - - -
131A ASP* 2.8 25.0 + - - +
132A SER* 3.1 30.6 + - - +
133A ASP* 3.2 22.5 - - - +
220A PRO* 5.4 0.2 - - + -
221A SER* 1.3 75.3 + - - +
223A MET* 1.3 59.2 + - - +
225A ARG* 3.2 36.2 + - - +
226A THR* 2.8 34.4 + - - +
304A ARG* 6.0 1.8 - - - +
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Residues in contact with MET 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 5.1 7.4 - - - -
172A LEU* 5.3 6.7 - - - +
174A ASN* 3.6 39.5 - - + +
219A ILE* 4.0 17.0 - - + -
220A PRO* 3.2 20.8 + - + +
222A ASN* 1.3 77.6 - - - +
224A ALA* 1.4 63.9 + - - +
226A THR* 3.6 1.6 + - - -
227A LEU* 3.1 40.8 + - + +
303A SER* 4.0 26.0 - - - +
304A ARG* 4.6 7.0 - - + +
307A THR* 3.5 28.2 - - + +
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 3.9 23.7 - - + +
113A ILE* 3.7 24.1 - - + +
198A LEU* 5.5 1.1 - - + -
201A ILE* 4.1 15.0 - - + -
219A ILE* 4.2 2.6 - - + +
220A PRO 2.9 16.8 + - - +
221A SER* 3.7 8.1 - - - +
223A MET* 1.4 76.0 - - - +
225A ARG* 1.4 54.2 + - - +
227A LEU* 3.5 1.6 + - - +
228A ALA* 2.9 31.7 + - - +
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Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 4.8 6.9 - - + +
78A LEU* 4.9 0.4 - - - +
129A ILE* 3.6 39.3 + - + +
130A ALA 3.4 18.0 + - - -
131A ASP* 4.4 2.6 - - - +
221A SER 2.7 21.5 + - - +
222A ASN* 3.2 46.3 + - - +
224A ALA* 1.4 67.7 - - - +
226A THR* 1.3 63.7 + - - +
228A ALA* 3.3 8.0 + - - +
229A GLN* 3.0 34.3 + - + +
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Residues in contact with THR 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ASN 2.8 18.6 + - - -
223A MET 3.9 3.4 - - - -
225A ARG* 1.3 81.9 + - - +
227A LEU* 1.3 60.7 + - - +
229A GLN* 3.2 9.1 + - - +
230A GLN* 3.2 30.2 + - + +
307A THR* 3.2 30.1 - - + +
308A THR* 4.9 5.4 - - + -
309A GLU* 5.3 1.8 - - + +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ASP* 3.7 6.7 - - + +
111A SER* 3.3 28.5 - - - +
113A ILE* 3.8 26.7 - - + -
223A MET* 3.1 34.6 + - + +
224A ALA 3.9 2.7 - - - +
226A THR* 1.3 73.7 - - - +
228A ALA* 1.4 61.9 + - - +
230A GLN* 3.3 14.3 + - - +
231A LEU* 3.1 28.3 + - - +
237A ILE* 3.8 14.2 - - + +
239A ARG* 3.4 28.9 - - - +
307A THR* 3.8 17.7 - - + +
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 4.1 24.2 - - + -
78A LEU* 4.2 13.9 - - + -
113A ILE* 4.7 0.8 - - - +
115A LEU* 4.2 11.8 - - + +
224A ALA 2.9 18.4 + - - +
225A ARG 3.3 5.6 + - - +
227A LEU* 1.4 75.5 - - - +
229A GLN* 1.4 56.6 + - - +
231A LEU* 3.1 12.9 + - - +
232A ILE* 2.9 34.7 + - + +
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Residues in contact with GLN 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ARG* 3.0 20.0 + - + +
226A THR* 3.2 11.8 + - - +
228A ALA* 1.4 73.2 - - - +
230A GLN* 1.3 59.3 + - + +
232A ILE* 3.1 26.6 + - - +
233A ASP* 2.9 65.9 + - - +
233K ASP* 6.0 1.8 + - - -
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Residues in contact with GLN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A THR* 3.2 21.8 + - - +
227A LEU* 3.5 15.7 - - - +
229A GLN* 1.3 78.4 - - + +
231A LEU* 1.3 57.2 + - - +
233A ASP* 5.0 0.2 - - - -
234A PHE* 2.9 46.3 + - + -
236A GLU 3.0 20.4 - - - +
237A ILE* 3.5 14.5 - - - +
238A LYS 2.9 41.1 + - - +
239A ARG* 5.2 1.0 - - - +
307A THR 3.3 21.9 + - - +
309A GLU* 4.1 23.2 + - + +
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 3.4 11.6 - - + +
106A GLY* 3.7 25.4 - - - +
107A SER* 3.5 31.4 - - - +
108A ASP* 4.9 0.7 - - + +
113A ILE* 4.2 18.2 - - + +
115A LEU* 3.9 25.1 - - + +
227A LEU 3.1 15.6 + - - +
228A ALA* 3.1 7.4 + - - +
230A GLN* 1.3 74.9 - - - +
232A ILE* 1.4 61.4 + - - +
235A GLY* 3.0 24.6 + - - +
236A GLU* 3.8 28.7 - - - -
237A ILE* 4.1 9.0 - - + +
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Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 6.1 1.3 - - + -
71A ASN* 6.0 1.8 - - - +
74A LYS* 5.6 5.2 - - - +
76A TYR* 3.9 39.0 + - + +
105A ILE* 4.6 4.7 - - - +
115A LEU* 3.4 24.7 - - + -
228A ALA* 2.9 22.8 + - + +
229A GLN* 3.4 37.5 - - - +
231A LEU* 1.4 77.3 - - - +
233A ASP* 1.4 71.8 + - - +
235A GLY 4.7 0.7 + - - -
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Residues in contact with ASP 233 (chain A).
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* 2.9 41.2 + - - +
230A GLN* 5.0 0.2 - - - -
232A ILE* 1.4 85.9 - - - +
234A PHE* 1.4 90.6 + - + +
309A GLU* 5.2 3.1 - - - +
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Residues in contact with PHE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLN* 2.9 34.3 + - + +
233A ASP* 1.4 100.9 - - + +
235A GLY* 1.3 59.8 + - - +
236A GLU* 3.0 32.2 + - + +
238A LYS* 3.6 47.6 - - + -
309A GLU* 3.9 28.3 - - - -
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Residues in contact with GLY 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 3.8 21.7 - - - +
106A GLY* 3.9 8.5 - - - -
107A SER 4.9 0.3 + - - -
230A GLN 3.7 0.2 + - - -
231A LEU* 3.0 26.3 + - - -
232A ILE 4.7 0.8 + - - -
233A ASP 3.9 0.2 - - - -
234A PHE* 1.3 75.9 - - - +
236A GLU* 1.3 57.8 + - - +
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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