Contacts of the helix formed by residues 231 - 238 (chain A) in PDB entry 5PKI
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 PHE 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.6 19.1 - - + -
86A PHE 3.8 10.1 - - - -
87A THR* 3.6 26.9 - - + -
227A ALA* 2.9 21.2 + - + +
228A ARG 3.8 2.5 - - - -
230A LEU* 1.3 88.0 - - + +
232A PRO* 1.4 65.4 - - - +
233A GLY 3.4 2.0 - - - -
234A SER* 3.3 11.8 + - - +
235A SER* 3.0 21.8 + - - -
241A PHE* 3.8 24.0 - + + -
247A ALA* 3.8 15.3 - - + -
248A LEU 3.6 22.2 - - - -
249A ILE* 4.0 20.0 - - + -
411A EDO 3.7 22.2 - - - +
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Residues in contact with PRO 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 ARG 3.5 15.0 - - - +
229A GLU* 3.6 10.8 - - - +
230A LEU 3.3 9.0 - - - +
231A PHE* 1.4 87.7 - - - +
233A GLY* 1.3 63.3 - - - +
235A SER* 3.3 3.4 + - - -
236A ARG* 3.1 43.9 + - - +
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Residues in contact with GLY 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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231A PHE 3.4 0.6 - - - -
232A PRO* 1.3 78.4 - - - +
234A SER* 1.3 66.5 + - - +
236A ARG* 3.3 20.3 + - - +
237A GLY* 3.0 19.1 + - - -
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Residues in contact with SER 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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87A THR* 5.4 5.7 - - - +
231A PHE* 3.3 20.4 + - - +
233A GLY* 1.3 76.6 - - - +
235A SER* 1.3 62.1 + - - +
237A GLY* 3.1 11.1 + - - -
238A CYS* 3.2 12.6 + - - +
241A PHE* 3.8 32.0 - - - +
244A HIS* 5.5 1.6 - - - -
411A EDO 5.7 0.7 + - - -
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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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228A ARG* 3.1 40.6 + - - +
231A PHE 3.0 16.0 + - - -
232A PRO* 3.7 4.9 - - - -
233A GLY 3.2 0.2 - - - -
234A SER* 1.3 76.0 - - - +
236A ARG* 1.3 62.0 + - - +
238A CYS 3.1 18.9 + - - +
239A GLY* 4.6 2.4 - - - -
241A PHE* 3.6 22.6 - - - -
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Residues in contact with ARG 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 PRO* 3.1 25.4 + - - +
233A GLY* 3.3 33.2 + - - +
235A SER* 1.3 77.3 - - - +
237A GLY* 1.3 58.9 + - - +
238A CYS* 3.5 0.7 + - - -
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Residues in contact with GLY 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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233A GLY 3.0 13.2 + - - -
234A SER* 3.1 5.1 + - - -
236A ARG* 1.3 76.4 - - - +
238A CYS* 1.4 62.5 + - - +
312A CYS* 3.8 14.5 - - - +
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Residues in contact with CYS 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 SER 3.2 7.0 + - - +
235A SER* 3.1 16.6 + - - +
236A ARG 3.3 0.8 + - - -
237A GLY* 1.4 81.1 - - - +
239A GLY* 1.3 62.1 + - - +
240A ALA* 3.1 24.0 + - - -
241A PHE* 3.5 15.2 + - + +
244A HIS* 3.6 12.8 - - + +
309A GLN 5.3 0.4 - - - -
310A CYS* 3.9 10.3 - - - -
311A SER 4.8 0.7 - - - -
312A CYS* 3.8 10.8 - - - -
401A ZN 2.4 36.1 - - - -
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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