Contacts of the helix formed by residues 113 - 126 (chain C) in PDB entry 1XPM
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 ALA 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C ALA* 3.5 11.4 - - + +
78C THR 4.6 0.4 - - - +
107C MET* 3.4 36.8 - - + +
108C LYS* 4.0 0.9 - - - -
109C GLU* 3.6 17.6 + - - +
111C SCY 3.7 1.4 - - - -
112C TYR* 1.3 78.7 - - - +
114C ALA* 1.3 61.1 + - - +
115C THR 3.1 1.0 + - - -
116C PRO* 3.3 21.5 - - - +
117C ALA* 3.4 10.9 + - - +
278C THR* 4.1 10.1 - - + +
105D PHE* 5.9 0.7 - - + -
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Residues in contact with ALA 114 (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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77C ALA* 3.4 17.1 - - + +
112C TYR 3.0 4.2 + - - -
113C ALA* 1.3 74.5 - - - +
115C THR* 1.3 58.3 + - - +
117C ALA* 3.3 6.7 - - - +
118C ILE* 3.1 32.1 + - - +
135C VAL* 4.8 3.1 - - + -
137C ALA* 4.1 10.5 - - + -
160C MET* 4.6 7.0 - - + -
278C THR* 3.7 18.0 + - - +
282C TYR* 3.7 25.6 - - + -
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Residues in contact with THR 115 (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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112C TYR* 3.0 8.4 + - + -
114C ALA* 1.3 75.0 - - - +
116C PRO* 1.3 73.0 - - - +
117C ALA 3.0 1.3 + - - -
118C ILE* 3.3 3.4 + - - +
119C GLN* 3.0 28.6 + - + +
282C TYR* 2.8 21.8 + - - +
304C SER* 2.6 30.8 + - - -
312C GLU* 3.5 32.8 - - - +
314C TYR* 3.7 20.9 - - + -
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Residues in contact with PRO 116 (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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107C MET* 4.0 9.2 - - - -
112C TYR* 3.2 42.4 - - + +
113C ALA* 3.3 16.2 - - - +
115C THR* 1.3 92.7 - - - +
117C ALA* 1.3 54.1 + - - +
119C GLN* 4.3 6.5 - - + -
120C LEU* 2.8 37.6 + - + +
103D ARG* 4.3 11.2 - - - +
105D PHE* 3.9 33.9 - - + -
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Residues in contact with ALA 117 (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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75C ILE* 3.8 19.6 - - + +
77C ALA* 5.1 2.2 - - + -
107C MET* 3.6 19.9 - - - -
113C ALA 3.4 14.5 + - - +
114C ALA* 3.3 11.9 - - - +
115C THR 3.0 0.2 - - - -
116C PRO* 1.3 79.9 - - - +
118C ILE* 1.3 58.5 + - - +
120C LEU* 4.4 0.2 - - - +
121C ALA* 3.0 28.2 + - - +
135C VAL* 3.7 23.2 - - + +
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Residues in contact with ILE 118 (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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5C ILE* 4.7 6.5 - - + -
114C ALA 3.1 12.8 + - - +
115C THR* 3.4 10.3 - - - +
117C ALA* 1.3 73.0 - - - +
119C GLN* 1.3 67.4 + - + +
121C ALA* 3.4 7.2 - - - +
122C LYS* 3.0 26.5 + - - +
135C VAL* 3.9 17.0 - - + -
160C MET* 3.7 25.8 - - + -
162C ILE* 4.0 20.7 - - + +
171C LEU* 4.0 21.5 - - + +
282C TYR* 3.6 18.2 - - + +
314C TYR* 3.5 27.4 - - + +
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Residues in contact with GLN 119 (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 THR* 3.0 22.7 + - + +
116C PRO* 4.1 1.3 - - + +
118C ILE* 1.3 80.5 - - + +
120C LEU* 1.3 61.5 + - - +
122C LYS* 3.3 17.5 + - - +
123C ASP* 3.2 26.2 + - - +
171C LEU* 4.1 14.5 - - - +
172C ASN 4.7 9.6 + - - +
175C ALA* 4.4 7.1 - - - +
312C GLU* 3.6 8.3 - - - +
314C TYR* 3.3 45.9 - - - +
103D ARG* 3.4 36.2 + - - +
128D ARG* 6.0 0.2 + - - -
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Residues in contact with LEU 120 (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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73C MET* 5.0 0.9 - - - -
75C ILE* 5.9 0.9 - - + -
107C MET* 4.0 11.0 - - + -
116C PRO* 2.8 23.8 + - + +
117C ALA 4.4 0.9 - - - +
119C GLN* 1.3 70.1 - - - +
121C ALA* 1.3 60.8 + - - +
123C ASP* 3.2 20.6 + - + +
124C TYR* 2.9 30.0 + - - +
73D MET* 4.0 13.0 - - + -
75D ILE* 5.0 0.9 - - + -
103D ARG* 4.0 16.8 - - - +
105D PHE* 3.7 31.9 - - + -
107D MET* 4.5 2.9 - - + -
120D LEU* 4.1 34.6 - - + +
124D TYR* 4.0 19.1 - - + -
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Residues in contact with ALA 121 (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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73C MET* 4.1 13.9 - - + +
75C ILE* 5.2 0.4 - - - +
117C ALA 3.0 20.1 + - - +
118C ILE* 3.4 11.4 - - - +
120C LEU* 1.3 76.4 - - - +
122C LYS* 1.3 63.1 + - - +
124C TYR* 3.3 3.3 + - - +
125C LEU* 3.0 29.9 + - - +
133C VAL* 3.6 31.1 - - + +
135C VAL* 4.4 0.4 - - + -
162C ILE* 4.1 10.3 - - + -
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Residues in contact with LYS 122 (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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3C ILE* 3.8 45.6 - - + +
118C ILE 3.0 13.2 + - - +
119C GLN* 3.4 17.3 - - - +
121C ALA* 1.3 77.4 - - - +
123C ASP* 1.3 67.9 + - - +
125C LEU* 3.2 11.8 + - - +
126C ALA* 3.3 10.0 + - - +
162C ILE* 4.3 2.0 - - + +
171C LEU* 3.3 48.0 - - + -
172C ASN 4.9 7.0 - - - +
173C GLU* 5.3 5.8 - - - +
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Residues in contact with ASP 123 (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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119C GLN 3.2 15.3 + - - +
120C LEU* 3.2 27.0 + - + +
122C LYS* 1.3 84.1 - - - +
124C TYR* 1.3 63.5 + - - +
126C ALA* 3.3 20.4 + - - +
103D ARG* 4.8 1.4 + - - -
123D ASP* 3.7 32.4 - - + +
124D TYR* 3.5 23.6 - - - +
127D THR* 5.6 0.5 + - - -
128D ARG* 4.1 13.5 + - - -
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Residues in contact with TYR 124 (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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72C GLY* 4.1 11.3 + - - -
73C MET* 3.6 28.3 - - + -
103C ARG* 3.6 31.3 - - + +
120C LEU 2.9 17.5 + - - +
121C ALA 3.4 3.6 - - - +
122C LYS 3.2 0.2 - - - -
123C ASP* 1.3 78.2 - - - +
125C LEU* 1.3 73.1 + - + +
126C ALA 3.3 1.0 + - - -
127C THR* 4.1 1.6 + - - -
128C ARG* 2.8 66.6 + - - +
131C GLU* 2.7 29.3 + - - -
133C VAL* 3.7 21.1 - - + -
120D LEU* 3.8 4.9 - - + -
123D ASP* 3.5 15.6 - - - +
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Residues in contact with LEU 125 (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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3C ILE* 4.1 6.7 - - + -
121C ALA 3.0 19.6 + - - +
122C LYS 3.2 5.8 + - - +
124C TYR* 1.3 91.1 - - + +
126C ALA* 1.3 59.5 + - - +
127C THR 3.2 0.4 - - - -
128C ARG* 2.9 14.5 + - + +
131C GLU* 3.5 38.1 - - + +
133C VAL* 3.9 13.2 - - + -
162C ILE* 3.5 43.5 - - + +
163C ALA* 3.9 10.1 - - - -
164C HIS* 2.6 33.8 + - + +
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Residues in contact with ALA 126 (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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2B ALA* 5.1 5.6 + - + +
165B ASN* 3.4 21.2 - - - +
3C ILE* 4.0 13.5 - - + -
122C LYS 3.3 8.5 + - - +
123C ASP* 3.5 16.2 - - - +
124C TYR 3.2 2.4 - - - -
125C LEU* 1.3 75.8 - - - +
127C THR* 1.3 66.8 + - + +
128C ARG 3.6 0.3 + - - -
164C HIS* 4.0 7.3 - - - -
126D ALA* 6.1 4.9 - - + -
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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