Contacts of the helix formed by residues 227 - 236 (chain A) in PDB entry 3PM0
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 HIS 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLU* 3.0 46.7 + - - -
224A LEU* 4.7 7.8 + - - +
225A LEU 3.3 1.2 - - - -
226A SER* 1.3 90.4 + - - +
228A ASN* 1.3 69.3 + - - +
229A GLU 3.1 4.2 + - - +
230A GLU* 3.2 37.4 + - - +
231A PHE* 3.4 7.0 + - - +
260A GLU* 5.8 3.4 - - + +
264A LEU* 3.5 40.3 - - + +
267A ASN* 5.3 5.3 + - - -
800A BHF 5.1 1.8 - - + -
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Residues in contact with ASN 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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198A VAL* 3.9 14.3 - - - +
224A LEU 5.1 0.9 - - - +
225A LEU* 3.8 20.2 + - - +
226A SER 3.8 0.4 - - - -
227A HIS* 1.3 78.9 + - - +
229A GLU* 1.3 61.4 + - - +
231A PHE* 3.3 10.4 + - - +
232A GLY* 3.3 10.4 + - - -
268A PHE* 5.2 0.2 - - - -
332A GLN* 2.6 32.4 + - - +
333A ASP* 3.0 33.7 + - - +
336A SER* 5.1 0.2 - - - -
510A THR* 5.5 0.2 + - - -
512A LYS* 3.6 20.4 - - - +
800A BHF 3.5 22.8 - - - -
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Residues in contact with GLU 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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227A HIS 3.1 0.8 - - - -
228A ASN* 1.3 74.8 - - - +
230A GLU* 1.3 74.8 + - - +
231A PHE 3.0 2.1 + - - -
232A GLY* 3.3 1.8 + - - -
233A ARG* 3.0 47.7 + - + +
506A SER* 3.2 34.9 + - - +
512A LYS* 4.3 16.3 - - + +
514A LYS* 3.8 18.3 + - - +
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Residues in contact with GLU 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 SER 4.5 1.7 - - - +
227A HIS* 3.2 42.0 + - - +
229A GLU* 1.3 84.3 - - - +
231A PHE* 1.3 59.3 + - - +
233A ARG* 4.0 13.0 - - - +
234A THR* 3.0 28.4 + - - -
257A VAL* 3.6 13.9 - - + +
260A GLU* 3.1 45.8 - - + +
261A PHE* 3.8 2.3 - - - +
264A LEU* 3.9 12.8 - - + -
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Residues in contact with PHE 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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126A VAL* 4.2 8.5 - - + -
134A PHE* 3.6 33.7 - + - -
227A HIS 3.4 5.5 + - - +
228A ASN 3.3 4.6 + - - +
229A GLU 3.0 1.2 - - - -
230A GLU* 1.3 79.5 - - - +
232A GLY* 1.3 65.0 + - - +
234A THR* 3.5 3.6 + - - -
235A VAL* 3.2 30.3 + - + +
261A PHE* 3.7 22.9 - + - -
264A LEU* 4.0 7.4 - - + +
265A ASN* 3.5 21.1 - - - -
333A ASP* 4.9 2.0 - - - -
509A LEU* 4.3 7.6 - - + -
800A BHF 3.3 76.7 - + + -
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Residues in contact with GLY 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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228A ASN 3.3 6.5 + - - -
229A GLU* 3.3 5.3 + - - -
231A PHE* 1.3 79.6 - - - +
233A ARG* 1.3 61.0 + - - +
234A THR 3.2 0.2 - - - -
235A VAL* 4.2 2.5 - - - -
236A GLY* 2.7 31.2 + - - -
333A ASP* 5.8 1.8 - - - -
508A GLY* 3.1 27.5 - - - -
509A LEU* 3.9 10.5 - - - -
510A THR* 5.8 0.2 - - - -
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Residues in contact with ARG 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 GLU* 3.0 47.5 + - + +
230A GLU* 4.1 7.7 - - - +
232A GLY* 1.3 77.3 - - - +
234A THR* 1.3 57.4 + - - +
236A GLY* 4.8 0.2 - - - -
239A SER* 2.8 26.9 + - - -
241A VAL* 4.7 0.9 - - - +
253A PRO* 4.7 15.4 + - - +
256A THR* 5.8 1.6 - - - +
257A VAL* 3.6 46.0 - - + +
260A GLU* 3.9 12.5 + - - -
506A SER* 4.6 3.4 - - - +
507A TYR 4.1 16.2 - - - +
508A GLY* 4.4 4.3 - - - -
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Residues in contact with THR 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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122A SER* 3.8 17.0 - - - +
230A GLU 3.0 15.0 + - - -
231A PHE 3.8 0.2 - - - -
232A GLY 3.2 0.4 - - - -
233A ARG* 1.3 79.5 - - - +
235A VAL* 1.3 58.1 + - - +
239A SER* 2.9 19.6 + - - -
241A VAL* 4.1 19.0 - - + +
242A ASP* 4.0 11.3 - - - +
257A VAL* 3.7 15.0 + - - +
261A PHE* 3.3 55.0 - - + +
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Residues in contact with VAL 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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120A PHE* 5.8 0.5 - - - -
122A SER* 4.0 3.1 - - - +
123A PHE* 3.8 35.2 - - + -
126A VAL* 5.1 1.6 - - + -
134A PHE* 4.1 17.5 - - + -
231A PHE* 3.2 31.4 - - + +
232A GLY* 4.2 0.7 - - - -
234A THR* 1.3 76.9 - - - +
236A GLY* 1.3 70.4 + - - +
237A ALA 3.4 1.4 + - - -
239A SER* 4.5 0.2 - - - -
242A ASP* 5.3 0.2 - - - -
261A PHE* 4.0 24.9 - - + -
400A PRO* 3.6 21.5 - - + +
509A LEU* 3.9 20.1 - - + +
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Residues in contact with GLY 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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232A GLY 2.7 26.0 + - - -
233A ARG 4.2 0.8 + - - -
234A THR 3.5 0.8 - - - -
235A VAL* 1.3 74.9 - - - +
237A ALA* 1.3 62.3 + - - -
238A GLY 3.1 0.2 + - - -
239A SER* 2.9 31.0 + - - -
508A GLY* 4.2 3.4 - - - -
509A LEU* 3.7 23.6 - - - -
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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