Contacts of the helix formed by residues 128 - 138 (chain C) in PDB entry 4X4R
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 ASP 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C CYS* 3.5 8.4 - - - +
115C TYR* 3.2 37.9 + - - +
117C LEU* 3.7 23.8 - - + +
120C PRO* 4.6 0.9 - - - +
123C ILE* 3.9 12.1 - - + -
124C LYS 3.4 7.6 + - - -
125C SER* 2.7 41.4 + - - +
126C ALA 3.5 2.6 - - - -
127C VAL* 1.3 77.0 - - - +
129C ARG* 1.3 59.4 + - - +
130C THR 3.3 0.4 - - - -
131C PRO* 3.4 10.4 - - - +
132C PHE* 3.4 23.0 - - - -
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Residues in contact with ARG 129 (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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120C PRO* 5.0 4.9 - - + -
123C ILE* 3.9 40.9 - - + +
126C ALA* 4.1 17.1 + - - +
127C VAL* 3.1 1.9 - - - -
128C ASP* 1.3 77.9 - - - +
130C THR* 1.3 59.2 + - - +
131C PRO 3.4 0.7 - - - -
132C PHE* 3.3 9.5 + - - +
133C HIS* 2.8 48.5 + - + +
218C ASP* 4.0 7.9 - - - -
220C VAL* 4.8 4.0 - - + -
221C ASP* 3.5 29.8 + - - -
224C ARG* 3.4 50.8 - - - +
34D C 4.5 14.8 + - - -
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Residues in contact with THR 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 3.7 21.1 - - + +
50C ARG* 4.4 0.7 + - - +
63C PHE* 3.6 14.4 - - + -
127C VAL* 3.2 14.8 + - - -
129C ARG* 1.3 76.6 - - - +
131C PRO* 1.3 68.4 - - - +
133C HIS* 3.3 11.1 + - - +
134C HIS* 3.3 20.8 + - - +
501C APC 3.6 25.2 - - - +
37D C 2.7 35.0 + - - +
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Residues in contact with PRO 131 (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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43C VAL* 4.9 7.6 - - + -
45C VAL* 4.4 9.9 - - + -
63C PHE* 4.1 10.1 - - + -
65C LEU* 4.7 14.6 - - + -
114C CYS* 4.0 24.5 - - - -
115C TYR 5.3 3.1 - - - +
127C VAL 3.6 6.7 - - - +
128C ASP* 3.4 16.4 - - - +
130C THR* 1.3 95.6 - - - +
132C PHE* 1.3 64.6 + - + +
134C HIS* 3.2 4.9 + - - +
135C LYS* 3.2 41.4 + - - +
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Residues in contact with PHE 132 (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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115C TYR 5.7 0.9 - - - -
117C LEU* 3.1 41.1 - - + -
118C LYS* 4.8 0.7 - - + -
119C GLU* 3.6 17.7 - - - -
120C PRO* 3.5 36.1 - - + -
128C ASP 3.4 20.9 - - - -
129C ARG 3.3 3.0 + - - +
131C PRO* 1.3 78.0 - - + +
133C HIS* 1.3 65.9 + - - +
135C LYS* 3.8 26.6 - - + +
136C TRP* 3.1 26.3 + - - +
220C VAL* 3.4 24.4 - - + +
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Residues in contact with HIS 133 (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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50C ARG* 4.0 4.7 - - - +
129C ARG* 2.8 39.9 + - + +
130C THR* 3.4 13.2 - - - +
131C PRO 3.2 0.2 - - - -
132C PHE* 1.3 78.5 - - - +
134C HIS* 1.3 60.3 + - - +
136C TRP* 3.9 1.3 - - - +
137C LEU* 3.1 30.0 + - - +
173C TYR* 3.2 36.5 - + + -
218C ASP* 2.8 23.6 + - - -
220C VAL* 3.6 15.9 - - + +
501C APC 3.1 50.2 + + - +
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Residues in contact with HIS 134 (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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43C VAL* 4.7 9.2 - - + -
44C PHE 3.6 15.0 + - - -
45C VAL* 3.7 24.8 - - + -
49C ALA* 3.3 38.3 + - + +
50C ARG* 3.2 35.2 + - + +
130C THR 3.3 1.0 + - - -
131C PRO 3.2 6.9 + - - +
133C HIS* 1.3 79.5 - - - +
135C LYS* 1.3 64.4 + - + +
138C GLU* 3.2 43.4 + - + +
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Residues in contact with LYS 135 (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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43C VAL* 6.3 3.4 - - - -
65C LEU* 5.6 6.2 - - - +
117C LEU 5.0 4.2 + - - -
118C LYS* 5.7 5.1 - - - +
131C PRO* 3.2 29.4 + - - +
132C PHE* 3.9 33.8 - - + +
134C HIS* 1.3 81.4 - - + +
136C TRP* 1.3 60.5 + - - +
138C GLU* 3.4 28.5 - - - +
139C GLY 4.9 0.3 + - - -
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Residues in contact with TRP 136 (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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132C PHE 3.1 18.2 + - - +
133C HIS* 3.9 2.7 - - - +
134C HIS 3.3 0.2 - - - -
135C LYS* 1.3 79.5 - - - +
137C LEU* 1.3 89.3 + - + +
139C GLY 4.6 1.1 + - - -
140C ARG* 3.1 78.4 + - - +
173C TYR* 5.0 2.7 - - - -
177C LEU* 3.7 11.7 - - + -
180C VAL* 4.5 7.9 - - + -
203C VAL* 4.0 18.8 - - + -
204C ALA* 5.1 7.8 - - - +
219C PRO* 3.3 42.0 - - + +
220C VAL* 4.1 14.1 - - + -
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Residues in contact with LEU 137 (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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50C ARG* 4.0 20.4 - - - +
133C HIS 3.1 16.7 + - - +
135C LYS 3.4 0.2 - - - -
136C TRP* 1.3 106.1 - - + +
138C GLU* 1.3 59.2 + - - +
139C GLY 3.1 3.3 + - - -
140C ARG* 3.8 1.3 - - + +
141C ILE* 2.8 42.0 + - + +
173C TYR* 3.4 33.2 - - + -
176C GLU* 3.9 26.7 - - + +
177C LEU* 4.1 8.7 - - + -
180C VAL* 4.1 20.4 - - + -
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Residues in contact with GLU 138 (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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50C ARG* 5.1 5.1 - - + +
134C HIS* 3.2 39.1 + - + +
135C LYS* 3.4 24.8 - - - +
137C LEU* 1.3 78.1 - - - +
139C GLY* 1.3 64.2 + - - +
141C ILE* 4.3 6.4 - - - +
142C LYS* 3.6 25.5 + - - +
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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