Contacts of the helix formed by residues 143 - 149 (chain C) in PDB entry 4PHZ
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 THR 143 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C PHE* 4.3 1.8 - - - -
129C ASP* 4.3 0.2 + - - -
132C TRP* 3.8 18.4 - - + +
133C HIS* 6.0 0.6 - - + -
136C VAL* 5.1 1.8 - - + -
138C ARG* 4.0 31.0 - - + +
139C ASP 5.6 0.4 - - - +
140C THR* 3.6 22.4 - - + +
141C ASP 3.3 3.8 + - - -
142C PHE* 1.3 76.5 - - - +
144C PRO* 1.4 78.4 - - - +
145C SER* 3.5 3.3 + - - -
146C HIS* 3.4 24.4 + - - +
147C ILE* 3.1 21.7 + - - +
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Residues in contact with PRO 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B TRP* 4.7 9.4 - - + -
42C GLU* 5.3 0.4 - - - -
46C GLY* 5.1 0.7 - - - -
50C GLY* 3.5 34.5 - - - +
58C PHE* 4.0 8.7 - - + -
62C TRP* 3.9 41.8 - - + +
132C TRP* 3.5 24.0 - - + +
143C THR* 1.4 85.4 - - - +
145C SER* 1.3 58.1 + - - +
147C ILE* 3.0 21.3 + - + +
148C ILE* 3.1 16.8 + - - +
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Residues in contact with SER 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B TRP* 4.7 4.5 - - - -
42C GLU* 5.1 0.2 - - - -
125C PHE* 4.1 3.1 + - - +
128C GLN* 3.4 21.8 + - - +
129C ASP* 3.2 40.2 + - - +
132C TRP* 4.2 15.4 - - - -
143C THR* 3.3 4.2 + - - -
144C PRO* 1.3 76.3 - - - +
146C HIS* 1.3 55.7 + - - +
148C ILE* 3.2 7.3 + - - +
149C GLU* 2.6 39.6 + - - +
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Residues in contact with HIS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ASP* 3.0 27.0 + - - -
133C HIS* 3.6 3.4 + - - -
138C ARG* 3.3 24.9 - - - -
141C ASP* 2.6 35.8 + - + +
142C PHE* 4.6 0.9 - - - -
143C THR* 3.4 14.8 + - - +
145C SER* 1.3 72.0 - - - +
147C ILE* 1.3 64.4 + - - +
149C GLU* 4.1 1.1 - - - -
150C PHE* 3.1 43.6 + + + +
151C TYR* 3.0 23.1 - - + -
301C CU 1.9 30.2 - - - -
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PHE* 4.4 2.2 - - + -
62C TRP* 3.3 44.0 - - + +
63C MET* 4.5 2.7 - - - +
65C ILE* 3.8 22.7 - - + -
66C LEU* 3.9 22.4 - - + +
69C GLU* 3.0 31.7 - - - +
142C PHE* 4.2 22.0 - - + +
143C THR 3.1 20.8 + - - +
144C PRO* 3.0 10.6 + - + +
146C HIS* 1.3 75.6 - - - +
148C ILE* 1.3 69.4 + - + +
151C TYR* 3.3 15.5 - - - +
152C MET 3.4 1.7 + - - -
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Residues in contact with ILE 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C VAL* 3.8 19.7 - - + -
41C TYR* 6.5 0.4 - - + -
42C GLU* 3.6 19.7 - - - +
62C TRP* 4.2 14.6 - - + -
65C ILE* 4.6 9.9 - - + -
125C PHE* 3.5 39.5 - - + -
128C GLN* 5.3 0.2 - - - +
144C PRO 3.1 11.2 + - - +
145C SER* 3.7 6.3 - - - +
147C ILE* 1.3 86.0 - - + +
149C GLU* 1.3 59.1 + - - +
152C MET* 3.0 34.8 + - + +
153C SER* 2.8 32.1 + - - -
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Residues in contact with GLU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B MET* 5.5 0.5 - - - +
121C GLY 4.7 1.6 - - - +
125C PHE* 3.5 26.0 - - + +
126C THR* 2.9 39.7 + - - +
129C ASP* 3.3 23.8 - - - +
145C SER 2.6 18.8 + - - +
146C HIS* 4.1 1.6 - - - -
148C ILE* 1.3 77.4 - - - +
150C PHE* 1.3 98.5 + - + +
151C TYR 3.1 0.2 + - - -
153C SER* 3.3 8.9 + - - -
154C TYR* 3.2 30.8 + - + -
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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