Contacts of the helix formed by residues 105 - 118 (chain A) in PDB entry 1U9C
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 ASN 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.7 34.5 - - + +
79A LEU* 4.8 0.2 - - - +
101A ASP 3.5 19.1 + - - +
102A PHE 3.3 9.3 + - - +
103A PRO 3.5 0.4 - - - -
104A ASP* 1.3 74.7 - - - +
106A GLU* 1.3 65.5 + - - +
107A THR* 3.0 15.9 + - - -
108A LEU* 2.8 32.5 + - + +
109A GLN* 3.0 24.6 + - - +
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LYS* 2.9 35.1 + - - -
104A ASP 3.3 6.5 + - - +
105A ASN* 1.3 74.6 + - - +
107A THR* 1.3 83.3 + - - +
109A GLN* 3.7 14.2 - - - +
110A TYR* 3.0 28.8 + - - +
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Residues in contact with THR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.8 26.5 + - + +
80A SER* 3.6 31.2 - - - +
81A LYS* 3.7 10.5 - - + +
105A ASN* 3.0 12.1 + - - -
106A GLU* 1.3 97.2 + - - +
108A LEU* 1.3 62.8 + - - +
110A TYR* 3.2 5.9 + - - +
111A VAL* 2.9 27.3 + - + +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.5 4.5 - - + -
47A ILE* 4.6 3.1 - - + -
79A LEU* 3.9 21.7 - - + +
90A ILE* 4.4 10.3 - - + -
92A LEU* 4.3 16.8 - - + -
102A PHE* 3.6 55.2 - - + +
105A ASN* 2.8 25.2 + - + +
107A THR* 1.3 72.6 - - - +
109A GLN* 1.3 57.1 + - - +
111A VAL* 3.3 3.4 + - + -
112A LEU* 2.9 48.9 + - + +
131A GLY* 4.0 10.1 - - - +
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PHE 5.3 1.1 - - - +
103A PRO 2.9 28.5 + - - +
104A ASP* 3.6 16.4 + - - +
105A ASN 3.0 18.9 + - - +
106A GLU* 3.7 11.8 - - - +
107A THR 3.3 0.2 - - - -
108A LEU* 1.3 75.4 - - - +
110A TYR* 1.3 58.5 + - - +
112A LEU* 3.4 2.3 + - - +
113A GLN* 2.9 29.7 + - - +
131A GLY 5.1 4.0 - - - +
134A ASN* 3.7 33.8 - - - +
135A ALA* 4.5 15.2 - - + +
136A THR 5.2 0.2 + - - -
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Residues in contact with TYR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LYS* 3.7 49.8 - - + -
84A ALA* 3.9 22.9 - - + -
85A HIS* 4.9 5.8 - + - -
106A GLU* 3.0 17.7 + - - +
107A THR 3.5 4.3 - - - +
109A GLN* 1.3 74.4 - - - +
111A VAL* 1.3 65.7 + - - +
113A GLN* 3.3 15.6 + - - +
114A GLN* 3.1 45.1 + - + +
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.3 4.3 - - + -
79A LEU* 4.5 11.0 - - + -
80A SER 3.7 22.9 - - - +
81A LYS* 4.4 5.4 - - - -
83A ASP 4.1 7.9 - - - +
84A ALA* 4.0 19.5 - - + +
90A ILE* 3.8 18.6 - - + -
107A THR* 2.9 22.1 + - + +
108A LEU* 3.7 7.6 - - + +
110A TYR* 1.3 74.9 - - - +
112A LEU* 1.3 62.0 + - - +
114A GLN* 3.1 3.8 + - - +
115A PHE* 3.0 51.9 + - + -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ILE* 4.1 24.0 - - + -
92A LEU* 4.3 10.8 - - + -
108A LEU* 2.9 39.4 + - + +
109A GLN 3.9 3.1 - - - +
111A VAL* 1.3 70.6 - - - +
113A GLN* 1.3 63.6 + - - +
115A PHE* 3.3 5.0 + - - +
116A ALA* 2.9 24.8 + - - +
122A ILE* 3.8 31.2 - - + +
131A GLY* 3.2 36.3 - - - +
132A LEU* 4.3 5.2 - - + +
135A ALA* 4.1 15.3 - - + -
143A ILE* 3.7 7.3 - - + +
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLN 2.9 19.3 + - - +
110A TYR* 3.5 16.0 - - - +
112A LEU* 1.3 77.1 - - - +
114A GLN* 1.3 66.7 + - - +
116A ALA* 3.3 2.4 + - - +
117A GLU* 2.8 40.1 + - + +
136A THR* 2.8 40.5 + - - +
137A TYR* 3.3 11.9 + - - -
138A LYS* 3.6 43.4 + - - +
143A ILE* 4.1 4.0 - - - +
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Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA* 3.8 29.2 - - + +
85A HIS* 3.1 25.7 + - + +
110A TYR* 3.1 36.1 + - + +
111A VAL 3.1 6.5 + - - +
113A GLN* 1.3 92.6 + - - +
115A PHE* 1.3 65.7 + - - +
117A GLU* 3.3 9.9 + - - +
118A ASP* 2.9 38.9 + - - +
138A LYS* 5.0 6.1 - - - +
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.3 4.9 - - + -
83A ASP 3.5 22.2 - - - -
84A ALA 3.8 12.3 - - - -
87A PHE* 3.6 35.0 - - + -
89A ALA* 3.4 24.2 - - - -
90A ILE* 3.5 25.6 - - + -
111A VAL* 3.0 39.5 + - + +
112A LEU 3.7 6.7 - - - +
114A GLN* 1.3 76.5 - - - +
116A ALA* 1.3 60.6 + - - +
118A ASP* 3.3 2.2 + - - -
119A GLY 3.2 2.9 + - - -
120A ARG* 3.0 49.2 + - + +
121A ILE 3.8 4.9 - - - -
122A ILE* 3.9 16.4 - - + -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU 2.9 17.0 + - - +
113A GLN 3.6 3.8 - - - +
115A PHE* 1.3 72.4 - - - +
117A GLU* 1.3 68.4 + - - +
118A ASP 3.0 1.2 + - - -
119A GLY* 3.1 12.5 + - - -
120A ARG 5.3 1.3 - - - -
122A ILE* 3.9 12.1 - - + +
137A TYR* 3.7 32.0 + - + +
143A ILE* 3.8 24.2 - - + -
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLN* 2.8 38.9 + - + +
114A GLN* 3.6 15.7 - - - +
116A ALA* 1.3 74.2 - - - +
118A ASP* 1.3 68.1 + - - +
119A GLY 3.7 0.3 + - - -
137A TYR* 3.4 20.7 - - + +
138A LYS* 2.8 42.4 + - + +
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Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA 4.7 0.9 - - - +
85A HIS* 3.5 31.7 + - - -
114A GLN* 2.9 26.0 + - - +
115A PHE* 4.0 2.4 - - - +
116A ALA 3.1 0.2 - - - -
117A GLU* 1.3 89.5 - - - +
119A GLY* 1.3 60.7 + - - +
120A ARG* 3.3 26.1 + - - +
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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