Contacts of the helix formed by residues 225 - 235 (chain A) in PDB entry 1I3J
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 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ALA* 4.1 0.7 - - - -
224A ILE* 1.3 80.7 - - - +
226A SER* 1.3 66.0 + - - +
227A GLY 4.1 3.1 - - - -
228A LEU* 3.0 23.4 + - - +
229A VAL* 3.4 7.8 + - - +
34C T 2.6 59.0 + - - +
35C A 4.3 12.3 - - - -
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Residues in contact with SER 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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215A ALA* 5.7 4.1 - - - +
216A ALA* 5.5 9.2 - - - -
219A ALA* 4.1 15.6 - - - +
224A ILE 4.0 0.8 + - - -
225A SER* 1.3 73.4 - - - +
227A GLY* 1.3 62.8 + - - +
229A VAL* 3.0 21.3 + - - +
230A THR* 3.3 10.0 + - - -
15B G 5.3 9.0 + - - +
16B T 3.9 23.5 + - - +
36C A 5.2 2.8 + - - -
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Residues in contact with GLY 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A SER* 3.1 3.8 + - - -
226A SER* 1.3 82.0 + - - +
228A LEU* 1.3 55.7 + - - +
230A THR* 3.3 5.5 + - - -
231A TYR* 3.0 25.1 + - - +
16B T 4.2 1.7 - - - +
17B T 3.7 32.8 - - - +
18B T 5.2 0.8 - - - +
34C T 3.9 14.3 - - - +
35C A 4.4 4.4 + - - +
36C A 5.2 1.6 - - - +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ILE* 3.7 18.8 - - + -
225A SER* 3.0 15.3 + - - +
227A GLY* 1.3 75.4 - - - +
229A VAL* 1.3 58.2 + - - +
231A TYR* 3.2 25.6 + - + +
232A ARG* 2.9 63.7 + - - +
32C A 4.7 2.0 - - + -
33C T 3.9 45.3 - - + +
34C T 3.6 26.3 - - + +
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 3.8 28.3 - - + -
215A ALA* 3.8 36.6 - - + +
218A ALA* 4.7 1.6 - - + -
219A ALA* 3.9 13.5 - - + +
224A ILE* 3.8 20.4 - - + -
225A SER 3.4 7.8 + - - +
226A SER* 3.0 11.7 + - - +
228A LEU* 1.3 75.5 - - - +
230A THR* 1.3 63.3 + - - +
232A ARG* 3.2 2.8 + - - +
233A VAL* 3.0 28.2 + - - +
240A TRP* 4.2 15.3 - - + -
242A TYR* 4.3 4.3 - - - +
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ALA* 6.1 0.2 - - - +
226A SER 3.3 7.9 + - - -
227A GLY 3.3 8.7 + - - -
228A LEU 3.3 0.2 - - - -
229A VAL* 1.3 78.3 - - - +
231A TYR* 1.3 64.7 + - - +
233A VAL* 3.2 8.0 + - + +
234A LYS* 3.1 41.3 + - + +
242A TYR* 4.2 0.4 + - + -
15B G 4.2 0.3 - - - +
16B T 2.4 69.6 + - + +
17B T 3.9 11.4 - - + +
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Residues in contact with TYR 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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227A GLY 3.0 13.5 + - - +
228A LEU* 3.3 23.3 - - + +
230A THR* 1.3 78.6 - - - +
232A ARG* 1.3 65.9 + - + +
234A LYS* 3.3 6.9 + - + +
235A SER* 3.0 35.2 + - - -
238A TRP* 5.5 4.5 - - - -
18B T 6.6 0.2 - - + -
31C A 4.2 2.9 + - - -
32C A 3.2 47.9 + + + -
33C T 3.6 33.0 - - + -
34C T 5.7 0.7 - - + -
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Residues in contact with ARG 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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222A PHE* 4.1 9.9 - - - -
224A ILE* 3.8 16.2 - - - +
228A LEU* 2.9 41.6 + - + +
229A VAL 3.2 0.2 + - - -
231A TYR* 1.3 80.7 - - + +
233A VAL* 1.3 66.4 + - - +
235A SER* 3.2 17.4 + - - +
238A TRP* 3.2 75.9 - - + +
240A TRP* 3.5 48.6 - - + +
33C T 3.4 23.8 + - - -
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 3.8 27.8 - - + -
229A VAL 3.0 21.7 + - - +
230A THR* 3.5 8.5 - - + +
232A ARG* 1.3 77.8 - - - +
234A LYS* 1.3 66.1 + - + +
235A SER 3.7 3.1 + - - +
238A TRP 5.6 0.2 - - - +
240A TRP* 3.4 29.8 - - + +
241A PHE* 4.5 4.7 - - - +
242A TYR* 3.8 34.8 - - + +
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Residues in contact with LYS 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 THR* 3.1 33.6 + - + +
231A TYR* 3.9 6.3 - - + +
232A ARG 3.2 0.2 - - - -
233A VAL* 1.3 82.6 - - + +
235A SER* 1.3 61.8 + - - +
236A ASP* 3.7 5.2 + - - +
17B T 3.1 26.4 + - - +
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Residues in contact with SER 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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231A TYR* 3.0 27.6 + - - -
232A ARG* 3.2 12.1 + - - +
233A VAL 4.3 2.6 - - - +
234A LYS* 1.3 78.0 - - - +
236A ASP* 1.3 61.4 + - - +
237A LYS* 2.8 30.9 + - - +
238A TRP* 3.3 30.9 + - - +
32C A 5.5 1.0 + - - -
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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