Contacts of the helix formed by residues 121 - 133 (chain A) in PDB entry 6R90
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 MET 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A THR* 4.9 0.2 - - - +
117A ARG* 3.2 41.5 - - - +
119A THR* 4.1 11.0 - - + +
120A ILE* 1.3 79.1 - - - +
122A PRO* 1.3 78.8 - - + +
123A LYS* 3.1 22.2 - - + -
124A ASP* 2.8 30.7 + - - +
125A ILE* 3.5 2.8 + - - +
48B SER* 4.6 9.0 - - - -
51B ILE* 3.2 10.2 - - - +
70I T 5.1 2.0 - - - +
71I G 3.7 29.2 - - - +
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Residues in contact with PRO 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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121A MET* 1.3 88.7 - - + +
123A LYS* 1.3 61.4 + - - +
125A ILE* 3.1 6.1 + - + +
126A GLN* 2.9 39.5 + - - +
48B SER* 5.0 2.0 - - - +
50B LEU* 4.2 38.4 - - + +
51B ILE* 3.5 13.2 - - + -
54B GLU* 4.4 20.0 - - + +
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Residues in contact with LYS 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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117A ARG* 3.4 26.1 - - - +
121A MET* 3.7 26.3 - - + +
122A PRO* 1.3 79.0 - - + +
124A ASP* 1.3 67.6 + - - +
126A GLN* 3.3 18.6 + - - +
127A LEU* 2.9 27.4 + - - +
114E HIS* 3.6 23.8 + - + +
116E LYS* 5.5 8.1 - - - +
71I G 4.6 6.5 + - - -
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Residues in contact with ASP 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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108A THR* 3.5 25.6 - - + +
111A CYS* 4.8 3.1 - - + +
112A ALA* 3.1 31.5 + - - +
117A ARG* 4.1 7.7 + - - -
121A MET* 2.8 28.6 + - - +
123A LYS* 1.3 84.8 - - - +
125A ILE* 1.3 62.9 + - - +
127A LEU* 3.1 5.7 + - - +
128A ALA* 2.9 22.9 + - - +
114E HIS* 2.8 31.4 + - - +
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Residues in contact with ILE 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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104A LEU* 4.5 11.2 - - + -
105A PHE* 4.1 11.4 - - + -
108A THR* 3.6 28.3 - - + +
121A MET 3.5 3.1 + - - +
122A PRO* 3.1 8.3 + - + +
124A ASP* 1.3 76.2 - - - +
126A GLN* 1.3 64.8 + - - +
128A ALA* 3.2 1.9 + - - +
129A ARG* 2.9 32.4 + - + +
51B ILE* 3.9 36.3 - - + -
54B GLU* 4.4 17.3 - - + +
55B THR* 4.1 11.7 - - + +
58B VAL* 4.1 24.7 - - + -
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Residues in contact with GLN 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 PRO* 2.9 30.1 + - - +
123A LYS* 3.5 16.3 - - - +
124A ASP 3.2 0.2 - - - -
125A ILE* 1.3 77.1 - - + +
127A LEU* 1.3 58.7 + - - +
129A ARG* 3.5 4.2 + - - +
130A ARG* 2.9 31.0 + - - +
54B GLU* 3.7 24.2 + - - +
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Residues in contact with LEU 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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111A CYS* 3.9 21.1 - - + -
123A LYS 2.9 14.7 + - - +
124A ASP* 3.3 8.3 - - - +
126A GLN* 1.3 76.7 - - - +
128A ALA* 1.3 64.2 + - - +
130A ARG* 3.2 5.0 + - + +
131A ILE* 2.9 46.8 + - + +
110E LEU* 4.1 28.5 - - + +
111E CYS* 4.1 18.2 - - + +
114E HIS* 3.5 38.1 - - + +
127E LEU* 5.7 0.2 - - + -
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Residues in contact with ALA 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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104A LEU* 3.9 20.0 - - + -
107A ASP* 4.6 10.8 - - + -
108A THR* 3.9 20.4 - - - +
111A CYS* 4.8 5.2 - - - -
124A ASP 2.9 15.1 + - - +
125A ILE 3.2 4.4 + - - +
127A LEU* 1.3 75.5 - - - +
129A ARG* 1.3 58.7 + - - +
131A ILE* 3.2 11.4 + - - +
132A ARG* 3.0 34.1 + - - +
131E ILE* 4.8 3.3 - - + +
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Residues in contact with ARG 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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100A TYR* 4.0 1.2 + - - +
104A LEU* 3.9 21.5 - - + -
125A ILE* 2.9 21.9 + - - +
126A GLN* 4.2 4.0 - - - +
128A ALA* 1.3 73.9 - - - +
130A ARG* 1.3 63.9 + - - +
132A ARG* 3.5 7.3 + - - +
133A GLY 3.2 3.8 + - - -
134A GLU* 2.7 74.9 + - + +
58B VAL* 3.4 50.5 + - - +
61B VAL* 4.1 28.3 - - - +
62B PHE 5.8 0.2 - - - +
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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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126A GLN 2.9 19.3 + - - +
127A LEU* 3.7 6.3 - - + +
129A ARG* 1.3 74.1 - - - +
131A ILE* 1.3 67.3 + - + +
133A GLY* 3.2 12.8 + - - -
134A GLU 5.1 2.2 - - - +
111C ASN* 4.4 17.4 - - - +
113C GLN* 4.9 7.1 + - - +
106E GLU* 4.6 8.3 + - - +
107E ASP* 4.7 2.4 - - - +
110E LEU* 3.5 41.6 - - + +
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Residues in contact with ILE 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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127A LEU* 2.9 38.5 + - + +
128A ALA* 3.6 5.6 - - - +
130A ARG* 1.3 81.1 - - + +
132A ARG* 1.3 61.5 + - - +
133A GLY* 3.2 1.2 + - - -
100C ARG* 5.1 2.6 + - - -
107E ASP* 3.6 35.1 - - + +
110E LEU* 5.9 2.0 - - + -
111E CYS* 3.3 33.9 - - - -
128E ALA* 4.8 5.8 - - - +
131E ILE* 3.6 39.7 - - + -
132E ARG* 4.6 21.7 + - + +
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Residues in contact with ARG 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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100A TYR* 4.1 28.3 + - - +
103A GLY* 4.6 15.4 + - - -
104A LEU* 4.8 16.3 - - - +
107A ASP* 3.7 27.6 + - - -
128A ALA* 3.0 19.7 + - - +
129A ARG* 3.5 7.8 + - - +
130A ARG 3.3 0.2 - - - -
131A ILE* 1.3 75.9 - - - +
133A GLY* 1.3 59.5 + - - +
134A GLU* 3.5 18.4 + - + +
96B ARG* 4.2 13.9 - - - +
100C ARG* 2.8 25.6 + - - +
131E ILE* 4.4 19.4 + - + +
132E ARG* 6.2 2.2 - - - +
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Residues in contact with GLY 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 ARG 3.2 3.2 + - - -
130A ARG* 3.2 9.4 + - - -
131A ILE 3.1 6.1 - - - -
132A ARG* 1.3 78.7 - - - +
134A GLU* 1.3 66.5 + - - +
96C LYS* 5.4 7.6 + - - +
100C ARG* 4.2 14.8 + - - -
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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