Contacts of the helix formed by residues 117 - 133 (chain A) in PDB entry 6B3I
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A THR 5.4 1.3 - - - +
116A ARG* 1.3 75.5 - - - +
118A ASN* 1.3 63.2 + - - +
119A LYS* 3.7 7.6 + - - +
120A GLU* 3.1 32.6 + - - +
121A ILE* 2.9 28.5 + - - +
160A ARG* 6.5 1.3 - - - +
162A GLU* 3.6 13.5 - - - +
202A TYR* 4.9 16.2 - - + -
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Residues in contact with ASN 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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117A THR* 1.3 72.6 - - - +
119A LYS* 1.3 62.6 + - - +
121A ILE* 3.3 4.7 + - - +
122A ILE* 3.2 32.3 + - + +
158A ALA* 3.2 40.7 + - + +
159A ASN 4.1 1.0 - - - -
160A ARG* 2.7 46.7 + - - +
162A GLU* 2.8 31.1 + - - +
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 3.3 8.3 + - - +
118A ASN* 1.3 77.8 - - - +
120A GLU* 1.3 64.2 + - + +
122A ILE* 3.8 8.0 + - - +
123A ALA* 3.4 20.8 + - - +
162A GLU* 4.6 1.6 + - - +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER* 5.2 0.4 + - - -
115A THR 4.5 1.2 - - - +
116A ARG* 3.4 28.6 - - + -
117A THR* 3.1 37.8 + - - +
119A LYS* 1.3 81.5 - - + +
121A ILE* 1.3 64.9 + - - +
122A ILE 3.2 0.4 - - - -
123A ALA* 3.4 6.4 + - - +
124A ILE* 3.1 31.3 + - + +
275A ARG* 4.7 3.0 + - - -
278A VAL* 3.8 29.3 - - - +
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Residues in contact with ILE 121 (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 LEU* 4.3 20.9 - - + +
116A ARG* 3.5 31.0 - - + +
117A THR 2.9 20.3 + - - +
118A ASN* 3.9 12.1 - - - +
120A GLU* 1.3 75.9 - - - +
122A ILE* 1.3 62.6 + - - +
124A ILE* 3.4 9.1 + - + +
125A LYS* 3.0 26.8 + - + +
155A LEU* 3.3 33.9 - - + +
156A LEU* 3.9 27.8 - - + +
158A ALA* 4.1 5.8 - - + -
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Residues in contact with ILE 122 (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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118A ASN* 3.2 20.8 + - + +
119A LYS* 4.0 7.4 - - - +
121A ILE* 1.3 77.3 - - - +
123A ALA* 1.3 58.3 + - - +
125A LYS* 3.1 18.6 + - + +
126A GLU* 2.8 32.3 + - + +
158A ALA* 3.7 21.8 - - + +
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Residues in contact with ALA 123 (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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88A SER* 3.3 27.1 - - - +
119A LYS 3.4 15.1 + - - +
120A GLU* 3.9 5.4 - - - +
121A ILE 3.4 0.6 - - - -
122A ILE* 1.3 81.0 - - - +
124A ILE* 1.3 57.2 + - - +
126A GLU* 3.9 9.1 - - - +
127A ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 124 (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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88A SER* 3.9 22.4 - - - +
91A ALA* 3.8 12.1 - - + -
92A ALA* 4.1 13.3 - - - +
95A LEU* 3.9 15.3 - - + -
112A VAL* 3.7 27.1 - - + -
113A LEU* 5.8 4.3 - - + -
116A ARG* 4.2 16.2 - - + +
120A GLU* 3.1 19.7 + - + +
121A ILE* 3.7 7.6 - - + +
123A ALA* 1.3 75.7 - - - +
125A LYS* 1.3 60.9 + - - +
127A ALA* 3.9 0.5 - - - +
128A TYR* 2.8 29.8 + - - +
136A LEU* 3.8 20.4 - - + -
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Residues in contact with LYS 125 (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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121A ILE* 3.0 28.1 + - + +
122A ILE* 3.5 20.2 - - + +
124A ILE* 1.3 75.6 - - - +
126A GLU* 1.3 62.8 + - - +
128A TYR* 3.9 2.9 - - - +
129A GLN* 3.2 22.5 + - - +
136A LEU* 4.1 20.2 + - + +
137A GLU* 5.5 9.8 + - + +
156A LEU* 2.9 48.3 + - + +
157A GLN* 4.4 9.7 + - - +
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Residues in contact with GLU 126 (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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122A ILE* 2.8 23.9 + - + +
123A ALA* 3.9 9.1 - - - +
125A LYS* 1.3 72.7 - - - +
127A ALA* 1.3 69.0 + - - +
129A GLN* 3.2 7.6 + - + +
130A ARG* 2.7 61.6 + - - +
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Residues in contact with ALA 127 (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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88A SER* 4.0 4.0 - - - +
89A GLU* 3.8 42.2 - - + +
92A ALA* 4.4 2.7 - - + -
123A ALA 3.0 19.0 + - - +
124A ILE 3.9 2.5 - - - +
126A GLU* 1.3 85.1 + - - +
128A TYR* 1.3 57.6 + - - +
130A ARG* 3.3 7.1 + - - +
131A LEU* 2.9 37.5 + - - +
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Residues in contact with TYR 128 (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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92A ALA* 3.6 35.6 - - + +
95A LEU* 4.5 0.4 - - + -
96A GLN* 3.5 27.6 - - + +
99A MET* 3.2 16.8 - - + +
124A ILE 2.8 22.8 + - - +
125A LYS 3.9 4.3 - - - +
127A ALA* 1.3 73.0 - - - +
129A GLN* 1.3 61.6 + - - +
132A PHE* 3.2 34.7 + + + +
134A ARG* 3.6 17.9 + - + +
136A LEU* 3.6 53.4 - - + -
139A ASP* 2.7 29.1 + - - -
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Residues in contact with GLN 129 (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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125A LYS 3.2 14.4 + - - +
126A GLU* 3.2 9.6 + - - +
128A TYR* 1.3 76.8 - - - +
130A ARG* 1.3 58.8 + - - +
133A ASP* 3.0 41.0 + - - +
134A ARG* 3.1 43.1 + - - +
135A SER* 3.5 16.9 - - - +
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Residues in contact with ARG 130 (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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86A HIS* 5.2 1.6 + - - -
89A GLU* 3.2 36.8 + - - +
126A GLU* 2.7 55.4 + - - +
127A ALA* 3.8 4.3 - - - +
129A GLN* 1.3 77.8 - - - +
131A LEU* 1.3 73.4 + - + +
133A ASP 4.6 1.2 + - - -
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Residues in contact with LEU 131 (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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89A GLU* 3.9 41.5 - - + +
92A ALA* 4.7 1.3 - - + -
93A ARG* 3.8 40.8 - - + +
127A ALA* 2.9 26.0 + - - +
130A ARG* 1.3 100.3 - - - +
132A PHE* 1.3 83.4 + - + +
133A ASP 3.7 0.4 - - - -
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Residues in contact with PHE 132 (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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92A ALA* 3.9 8.1 - - + -
93A ARG* 4.1 21.8 - - + -
96A GLN* 3.6 44.4 - - + -
128A TYR* 3.2 46.0 + + + +
131A LEU* 1.3 105.5 - - + +
133A ASP* 1.3 72.0 + - - +
134A ARG* 3.1 33.3 + - + +
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Residues in contact with ASP 133 (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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129A GLN* 3.0 27.2 + - - +
130A ARG 4.5 1.6 + - - -
131A LEU 3.7 1.4 - - - -
132A PHE* 1.3 79.9 - - - +
134A ARG* 1.3 60.7 + - - +
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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