Contacts of the helix formed by residues 234 - 242 (chain E) in PDB entry 3PB1
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 234 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91E HIS* 4.2 11.7 - + - -
101E ASN* 3.4 37.0 - - - -
103E ILE* 3.9 38.4 - - + -
179E LYS* 3.6 40.4 - - + -
229E THR* 3.6 17.9 - - + -
230E ARG 3.0 27.8 - - - -
231E VAL* 2.9 8.2 + - - +
233E HIS* 1.3 85.1 - - + +
235E LEU* 1.3 58.9 + - - +
236E PRO* 3.4 4.7 - - - -
237E TRP* 3.1 13.9 + - + +
238E ILE* 3.0 30.1 + - + +
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Residues in contact with LEU 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E SO4 4.4 1.1 - - - +
123E LEU* 4.1 28.7 - - + -
124E PRO* 3.1 29.8 - - + +
125E SER* 3.5 4.0 - - - +
126E MET* 3.3 33.9 - - + +
231E VAL 4.2 6.7 - - - +
232E SER* 4.0 14.5 + - - +
234E PHE* 1.3 74.6 - - - +
236E PRO* 1.4 67.9 - - + +
238E ILE* 4.3 8.3 - - + -
239E ARG* 2.8 69.5 + - + +
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Residues in contact with PRO 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E MET* 3.6 26.7 - - + -
127E TYR* 5.8 4.9 - - + +
232E SER 5.9 0.4 - - - +
233E HIS 4.9 3.6 - - - +
234E PHE* 3.6 6.5 - - - +
235E LEU* 1.4 93.4 - - + +
237E TRP* 1.3 60.6 + - - +
239E ARG* 4.2 4.2 - - + +
240E SER* 3.1 27.7 + - - -
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Residues in contact with TRP 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ILE* 3.9 23.6 - - + -
90E LEU 4.1 0.4 + - - -
91E HIS* 3.3 57.2 - + - +
92E LYS* 5.1 2.4 - - - +
103E ILE* 3.7 39.3 - - + -
104E ALA* 4.0 6.3 - - - -
105E LEU* 3.5 34.1 - - + -
234E PHE* 3.1 16.2 + - + +
236E PRO* 1.3 75.9 - - - +
238E ILE* 1.3 87.1 + - + +
240E SER* 3.3 4.2 + - - -
241E HIS* 3.0 55.5 + + - +
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Residues in contact with ILE 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E ILE* 4.0 25.4 - - + -
53E ILE* 3.7 28.9 - - + -
103E ILE* 4.2 5.4 - - + -
105E LEU* 4.1 5.3 - - + +
123E LEU* 4.1 16.6 - - + -
231E VAL* 4.0 20.2 - - + -
234E PHE 3.0 28.2 + - - +
235E LEU* 3.8 12.8 - - + +
237E TRP* 1.3 91.7 - - + +
239E ARG* 1.3 58.6 + - + +
241E HIS 3.7 0.5 - - - -
242E THR* 2.7 45.1 + - + +
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Residues in contact with ARG 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E SO4 3.0 41.8 + - - -
123E LEU* 6.1 1.6 - - + -
124E PRO 5.5 0.6 + - - -
125E SER* 6.0 0.2 - - - +
126E MET* 3.2 27.9 - - - +
235E LEU* 2.8 46.3 + - + +
236E PRO* 4.2 4.2 - - + +
238E ILE* 1.3 77.4 - - + +
240E SER* 1.3 61.7 + - - +
242E THR* 3.2 15.5 + - - -
243E LYS* 3.3 23.3 - - - +
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Residues in contact with SER 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E PRO 3.1 18.8 + - - -
237E TRP* 3.3 6.8 + - - -
239E ARG* 1.3 75.7 - - - +
241E HIS* 1.3 75.3 + - - +
243E LYS* 3.5 25.1 + - - +
244E GLU 4.1 2.1 + - - -
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Residues in contact with HIS 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E TRP* 3.7 2.8 - - - -
89E ILE* 3.6 36.4 - - + +
90E LEU 5.8 0.4 + - - -
92E LYS* 6.0 6.8 + - + +
105E LEU* 3.7 19.1 - - + -
237E TRP* 3.0 61.2 + + - +
240E SER* 1.3 85.7 + - - +
242E THR* 1.3 58.3 + - - +
243E LYS 3.2 3.1 - - - -
244E GLU 3.0 28.7 - - - -
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Residues in contact with THR 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E SO4 4.6 5.2 + - - -
47E ILE* 4.2 15.5 - - + -
48E SER* 5.4 1.3 - - - +
51E TRP* 3.4 53.9 + - + -
105E LEU* 4.2 12.3 - - + -
238E ILE* 2.7 26.7 + - + +
239E ARG* 3.2 15.1 + - - -
241E HIS* 1.3 73.8 - - - +
243E LYS* 1.3 64.1 + - - +
244E GLU* 3.3 0.7 - - - +
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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
------------------------------------------------------------
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