Contacts of the helix formed by residues 105 - 119 (chain C) in PDB entry 4HRE
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 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C ASN* 3.8 5.6 - - - +
69C GLN* 3.8 25.7 - - + +
104C LYS* 1.3 74.2 - - - +
106C PRO* 1.3 65.2 - - - +
107C ALA* 3.5 6.5 + - - +
108C GLN* 2.9 35.5 + - + +
109C TYR* 2.8 30.8 + - - +
146C VAL* 5.3 1.9 - - - +
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Residues in contact with PRO 106 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C ASN* 3.6 24.9 - - + +
104C LYS 4.7 0.4 - - - +
105C THR* 1.3 88.2 - - - +
107C ALA* 1.3 62.9 + - - +
109C TYR* 3.4 5.2 + - + +
110C ASP* 3.1 32.8 + - - +
297C GLU* 6.5 1.1 - - + -
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Residues in contact with ALA 107 (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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105C THR* 3.2 5.3 + - - +
106C PRO* 1.3 77.5 - - - +
108C GLN* 1.3 61.3 + - - +
110C ASP* 3.3 2.0 + - - +
111C ALA* 2.8 32.4 + - - +
139C GLU 5.4 0.4 - - - +
142C GLU* 3.8 27.6 - - + +
143C ILE* 4.4 11.9 - - + +
145C ARG* 5.0 2.5 - - - +
146C VAL* 3.6 25.9 - - + +
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Residues in contact with GLN 108 (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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69C GLN* 5.4 1.0 + - - +
103C LEU 5.1 1.0 - - - +
104C LYS* 4.0 27.9 - - + +
105C THR* 2.9 37.4 + - - +
107C ALA* 1.3 77.7 - - - +
109C TYR* 1.3 51.7 + - - +
111C ALA* 3.6 0.9 - - - +
112C SER* 2.6 37.1 + - - -
146C VAL* 3.9 15.0 - - + +
150C MET* 3.7 25.1 - - + +
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Residues in contact with TYR 109 (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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97C THR 5.3 2.2 + - - -
101C GLY* 3.7 31.3 - - - +
104C LYS* 3.8 17.2 - - + +
105C THR 2.8 16.8 + - - +
106C PRO* 3.7 7.2 - - + +
108C GLN* 1.3 76.7 - - - +
110C ASP* 1.3 67.4 + - - +
112C SER* 3.0 10.1 + - - -
113C GLU* 2.8 61.5 + - + +
289C ILE* 4.4 7.8 - - - +
290C ARG* 3.4 40.2 + - + +
293C VAL* 3.8 31.9 - - + +
294C SER* 4.5 8.3 - - - -
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Residues in contact with ASP 110 (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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106C PRO* 3.1 20.0 + - - +
107C ALA* 3.9 1.7 - - - +
109C TYR* 1.3 87.9 - - - +
111C ALA* 1.3 57.2 + - - +
113C GLU* 3.2 6.6 + - - +
114C LEU* 2.9 36.2 + - - +
131C ILE* 3.9 9.8 - - + +
135C ARG* 3.1 43.5 + - - +
139C GLU* 5.6 1.4 - - - +
143C ILE* 3.7 27.0 - - + +
290C ARG* 6.1 0.5 - - - +
294C SER* 4.4 3.2 - - - -
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Residues in contact with ALA 111 (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 ALA 2.8 21.4 + - - +
108C GLN* 3.6 4.5 - - - +
110C ASP* 1.3 71.2 - - - +
112C SER* 1.3 63.5 + - - +
114C LEU* 3.2 8.7 + - - +
115C LYS* 3.1 19.8 + - - +
143C ILE* 4.4 7.0 - - + +
146C VAL* 4.4 1.3 - - + -
147C TYR* 3.8 45.5 - - + +
150C MET* 4.2 13.0 - - - -
151C TYR* 4.4 2.5 - - + -
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Residues in contact with SER 112 (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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104C LYS* 3.4 27.8 + - - +
108C GLN 2.6 25.9 + - - -
109C TYR* 3.0 11.3 + - - -
111C ALA* 1.3 72.3 - - - +
113C GLU* 1.3 60.2 + - - +
115C LYS* 3.5 2.4 + - - +
116C ALA* 3.1 22.9 + - - +
150C MET* 4.1 7.4 - - - +
151C TYR* 3.4 20.9 + - - -
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Residues in contact with GLU 113 (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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109C TYR* 2.8 60.4 + - + +
110C ASP* 3.6 5.2 - - - +
112C SER* 1.3 72.7 - - - +
114C LEU* 1.3 63.2 + - - +
116C ALA* 3.2 12.1 + - - +
117C SER* 3.1 21.0 + - - -
127C SER* 5.2 6.4 - - - -
131C ILE* 3.9 16.2 - - + -
286C LYS* 6.0 1.2 - - - +
290C ARG* 3.8 28.6 + - + -
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Residues in contact with LEU 114 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C ASP 2.9 20.3 + - - +
111C ALA* 3.2 8.0 + - - +
113C GLU* 1.3 76.3 - - - +
115C LYS* 1.3 61.4 + - - +
117C SER* 2.5 23.2 + - - -
118C MET* 3.1 17.9 + - + +
128C LEU* 3.5 38.1 - - + +
131C ILE* 3.8 27.4 - - + -
132C ILE* 4.3 11.9 - - + -
140C LEU* 6.3 0.2 - - + -
143C ILE* 3.6 29.8 - - + -
147C TYR* 4.1 8.3 - - + -
155C LEU* 4.2 17.7 - - + -
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Residues in contact with LYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111C ALA 3.1 6.4 + - - +
112C SER 3.7 6.3 - - - +
114C LEU* 1.3 78.9 - - - +
116C ALA* 1.3 62.9 + - - +
118C MET* 3.5 4.3 + - + +
119C LYS* 3.2 63.3 + - - +
147C TYR* 3.3 23.3 - - - +
151C TYR* 3.6 55.2 - - + +
153C THR* 5.8 0.4 - - - -
158C ASP* 4.2 10.1 - - - +
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Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C SER 3.1 15.4 + - - +
113C GLU* 3.4 16.8 - - - +
114C LEU 3.2 0.2 - - - -
115C LYS* 1.3 76.9 - - - +
117C SER* 1.3 62.1 + - - +
119C LYS* 3.7 14.3 + - - +
124C ASP* 5.2 0.9 - - - +
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Residues in contact with SER 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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113C GLU 3.1 8.7 + - - -
114C LEU* 2.5 27.5 + - - -
116C ALA* 1.3 80.0 - - - +
118C MET* 1.3 65.5 + - - +
119C LYS 3.2 8.9 + - - +
123C THR* 3.2 6.9 - - - +
124C ASP* 2.8 54.9 + - - +
127C SER* 4.5 5.8 - - - -
128C LEU* 4.1 17.3 + - - +
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Residues in contact with MET 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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114C LEU* 3.1 27.8 + - + +
115C LYS* 3.5 4.7 + - + +
117C SER* 1.3 81.8 + - - +
119C LYS* 1.3 65.2 + - - +
120C GLY 3.2 1.7 + - - -
123C THR* 3.8 7.2 - - + -
128C LEU* 4.2 12.8 - - + -
147C TYR* 3.0 33.0 - - + +
155C LEU* 4.1 6.7 - - + -
158C ASP* 3.6 35.2 - - + +
159C ILE* 3.7 16.2 - - - -
162C ASP* 2.7 47.6 - - + +
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Residues in contact with LYS 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 LYS* 3.2 41.8 + - - +
116C ALA* 4.0 10.6 - - - +
117C SER 3.2 9.1 - - - +
118C MET* 1.3 78.2 - - - +
120C GLY* 1.3 60.3 + - - +
122C GLY 4.1 6.2 - - - +
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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