Contacts of the helix formed by residues 226 - 241 (chain A) in PDB entry 3IH9
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 PRO 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A VAL* 4.0 22.0 - - + -
214A GLY 3.9 0.2 - - - -
223A ARG* 4.2 7.4 - - - +
225A LEU* 1.3 89.7 - - + +
227A SER* 1.3 65.4 + - - +
228A ILE* 4.3 5.4 - - + +
229A VAL* 3.2 28.3 + - + +
230A ALA* 3.1 20.3 + - - +
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Residues in contact with SER 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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214A GLY* 3.0 25.8 - - - -
223A ARG* 3.5 17.1 - - - +
226A PRO* 1.3 71.9 - - - +
228A ILE* 1.3 60.9 + - - +
230A ALA* 3.5 1.7 + - - +
231A ARG* 3.0 29.7 + - - +
336A ARG* 6.0 4.0 - - - -
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Residues in contact with ILE 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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80A PHE* 3.4 30.0 - - + -
226A PRO* 3.1 5.5 - - + +
227A SER* 1.3 85.2 + - - +
229A VAL* 1.3 63.0 + - + +
231A ARG* 3.4 41.7 + - - +
232A ARG* 3.1 21.1 + - - +
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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
----------------------------------------------------------
72A ALA* 3.8 38.1 - - + +
75A LEU* 4.2 14.4 - - + +
76A VAL* 4.0 15.0 - - + +
80A PHE* 4.1 22.0 - - + -
225A LEU* 4.6 5.6 - - + -
226A PRO* 3.2 31.9 + - + +
228A ILE* 1.3 76.7 - - + +
230A ALA* 1.3 67.4 + - - +
232A ARG* 3.1 4.0 + - - +
233A VAL* 3.0 21.9 + - + +
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Residues in contact with ALA 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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211A LEU* 4.1 22.7 - - + +
214A GLY* 3.7 33.9 - - - -
215A GLY* 3.9 7.0 - - - +
225A LEU* 4.7 4.7 - - + +
226A PRO 3.1 8.9 + - - +
227A SER 3.9 1.6 - - - +
229A VAL* 1.3 80.0 - - - +
231A ARG* 1.3 63.4 + - - +
233A VAL* 3.4 6.3 + - - +
234A VAL* 3.0 30.0 + - - +
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Residues in contact with ARG 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLY* 5.8 0.2 - - - -
227A SER 3.0 18.5 + - - +
228A ILE* 3.4 33.4 + - - +
229A VAL 3.1 0.2 - - - -
230A ALA* 1.3 77.5 - - - +
232A ARG* 1.3 58.2 + - - +
234A VAL* 3.3 5.0 + - - +
235A SER* 2.7 38.6 + - - +
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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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71A TYR* 3.1 28.9 + - + +
75A LEU* 3.9 15.1 - - + +
80A PHE* 3.4 34.1 - - + -
84A ASP* 3.0 39.2 + - - -
89A LEU* 3.5 30.1 - - - +
228A ILE 3.1 10.4 + - - +
229A VAL 3.1 7.4 + - - +
231A ARG* 1.3 79.5 - - - +
233A VAL* 1.3 64.9 + - - +
235A SER* 2.9 21.3 + - - -
236A VAL* 3.0 16.1 + - - +
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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
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68A PRO* 3.4 48.5 - - + +
71A TYR* 4.0 17.4 - - + -
72A ALA* 3.8 25.6 - - + +
75A LEU* 4.5 2.7 - - + -
112A MET* 5.5 0.2 - - - +
211A LEU* 4.2 20.6 - - + -
229A VAL* 3.0 18.2 + - + +
230A ALA* 3.7 9.9 - - - +
232A ARG* 1.3 78.4 - - - +
234A VAL* 1.3 61.9 + - - +
236A VAL* 3.4 2.9 + - - +
237A MET* 3.0 23.4 + - - +
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Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.8 39.0 - - + +
212A ALA 5.0 0.2 - - - +
230A ALA 3.0 18.3 + - - +
231A ARG* 3.9 4.5 - - - +
233A VAL* 1.3 72.9 - - - +
235A SER* 1.3 64.4 + - - +
237A MET* 3.6 7.6 - - - +
238A THR* 3.1 23.2 + - - +
256A PRO* 3.7 29.6 - - + -
268A ALA* 3.9 11.4 - - + +
270A PRO* 4.1 19.3 - - + -
306A LEU* 5.9 0.2 - - + -
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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 ARG* 2.7 30.1 + - - +
232A ARG* 3.1 18.1 - - - -
234A VAL* 1.3 77.8 - - - +
236A VAL* 1.3 59.2 + - - +
238A THR* 3.3 6.0 + - - -
239A SER* 3.0 28.0 + - - -
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Residues in contact with VAL 236 (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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71A TYR* 3.9 23.3 - - + +
89A LEU* 3.9 30.1 - - + +
110A ASN* 4.3 12.3 - - + +
111A ALA* 4.4 6.5 - - + +
112A MET* 3.6 24.6 - - + +
232A ARG* 3.0 16.6 + - - +
233A VAL 3.9 3.6 - - - +
235A SER* 1.3 75.0 - - - +
237A MET* 1.3 60.6 - - - +
238A THR 3.2 0.2 - - - -
239A SER* 3.8 7.2 - - - +
240A SER* 2.8 38.3 + - - +
241A GLY 3.4 0.7 + - - -
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Residues in contact with MET 237 (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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68A PRO* 4.1 20.0 - - + -
112A MET* 4.4 12.1 - - + -
211A LEU* 4.1 22.7 - - - -
233A VAL* 3.0 20.3 + - - +
234A VAL* 3.6 15.9 - - - +
235A SER 3.3 0.2 - - - -
236A VAL* 1.3 75.6 - - - +
238A THR* 1.3 59.9 + - - +
241A GLY* 2.7 33.5 + - - +
242A MET* 4.4 0.9 + - - +
256A PRO* 3.7 26.7 - - + +
257A ALA* 3.7 25.1 + - - +
258A LYS* 4.1 2.5 - - + +
266A LEU* 3.7 27.6 - - + +
268A ALA* 4.7 8.1 - - + -
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Residues in contact with THR 238 (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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234A VAL* 3.1 13.1 + - - +
235A SER* 3.5 10.0 - - - -
237A MET* 1.3 81.3 - - - +
239A SER* 1.3 61.8 + - - +
241A GLY 4.6 0.2 + - - -
242A MET* 5.4 0.7 + - - +
246A ALA* 3.9 17.3 - - - +
249A TRP* 5.4 7.7 - - + -
250A LEU* 4.0 31.6 - - + +
256A PRO* 3.1 30.6 - - + +
306A LEU* 4.1 14.0 - - + +
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Residues in contact with SER 239 (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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89A LEU 4.5 9.4 + - - -
91A PRO* 3.2 28.6 - - - +
235A SER 3.0 16.1 + - - -
236A VAL* 3.8 7.1 + - - +
238A THR* 1.3 80.5 - - - +
240A SER* 1.3 68.7 + - - +
246A ALA* 3.3 15.7 - - - +
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Residues in contact with SER 240 (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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89A LEU 4.8 1.2 + - - -
90A ASN 4.2 0.2 - - - -
91A PRO* 3.6 15.4 - - - +
92A SER 5.0 1.5 - - - +
110A ASN* 3.1 41.9 + - - +
112A MET* 3.7 10.2 - - - +
236A VAL* 2.8 17.2 + - - +
239A SER* 1.3 90.0 + - - +
241A GLY* 1.3 64.8 + - - +
242A MET 3.2 3.4 - - - -
243A TYR* 2.9 22.7 + - - +
246A ALA* 4.7 0.2 - - - -
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Residues in contact with GLY 241 (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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112A MET* 3.8 4.0 - - - +
236A VAL 3.4 2.8 + - - -
237A MET* 2.7 28.9 + - - -
238A THR 4.5 0.2 - - - -
240A SER* 1.3 72.7 - - - +
242A MET* 1.3 65.8 + - - +
243A TYR* 3.7 7.8 - - - -
257A ALA 3.6 12.6 - - - -
258A LYS* 3.3 35.6 + - - +
287A ASN* 5.5 0.2 - - - +
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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