Contacts of the helix formed by residues 122 - 138 (chain A) in PDB entry 7V3X
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 ASP 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A PHE* 1.3 78.1 + - - +
123A LEU* 1.3 71.5 + - - +
125A ALA* 3.9 4.5 - - - +
126A LEU* 3.2 23.7 + - - +
150A VAL* 5.7 2.6 - - - +
163A GLU* 5.6 2.3 - - - +
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Residues in contact with LEU 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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121A PHE 4.7 1.1 - - - +
122A ASP* 1.3 85.0 + - - +
124A SER* 1.3 52.8 + - - +
126A LEU* 3.1 12.4 + - - +
127A ILE* 2.9 39.8 + - + +
163A GLU* 3.2 32.5 - - + +
166A ARG* 6.2 1.6 - - + -
167A LEU* 5.7 2.9 - - + +
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Residues in contact with SER 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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121A PHE* 3.3 25.5 + - - +
123A LEU* 1.3 74.6 - - - +
125A ALA* 1.3 64.5 + - - -
127A ILE* 3.3 11.3 + - - +
128A GLU* 3.1 36.0 + - - +
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Residues in contact with ALA 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 PHE 3.2 21.1 + - - +
122A ASP* 3.8 7.2 + - - +
123A LEU 3.4 0.2 - - - -
124A SER* 1.3 79.0 + - - +
126A LEU* 1.3 61.5 + - - +
128A GLU* 3.5 16.0 + - - +
129A ARG* 3.2 33.7 + - - +
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Residues in contact with LEU 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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74A VAL* 4.3 6.3 - - + -
76A PHE* 3.4 43.1 - - + -
106A LEU* 5.9 2.2 - - + -
108A ALA* 3.5 18.6 - - + -
122A ASP 3.2 14.5 + - - +
123A LEU* 3.1 15.3 + - - +
125A ALA* 1.3 72.6 - - - +
127A ILE* 1.3 67.0 + - - +
129A ARG* 3.0 15.3 + - + +
130A ILE* 2.8 48.8 + - + +
144A ILE* 5.4 1.8 - - + -
167A LEU* 4.6 17.3 - - + -
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Residues in contact with ILE 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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123A LEU* 2.9 28.1 + - + +
124A SER* 3.3 10.5 + - - +
126A LEU* 1.3 70.2 - - - +
128A GLU* 1.3 53.2 + - + +
130A ILE* 3.1 10.5 + - + +
131A ASN* 2.7 36.4 + - + +
166A ARG 4.7 1.1 - - - +
167A LEU* 3.2 42.0 - - + +
170A ARG* 3.7 35.0 - - + -
171A LEU* 5.2 3.4 - - + -
174A ILE* 4.8 15.7 - - + +
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Residues in contact with GLU 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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124A SER* 3.1 24.3 + - - +
125A ALA* 3.5 15.6 - - - +
127A ILE* 1.3 76.9 - - + +
129A ARG* 1.3 52.7 + - + +
131A ASN* 3.4 7.6 + - - +
132A TYR* 2.7 35.3 + - - +
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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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104A PHE* 5.3 0.3 - - - -
106A LEU* 3.3 37.9 - - + +
107A ASP 3.0 28.2 + - - +
108A ALA* 4.2 14.8 - - - +
125A ALA* 3.2 22.4 + - - +
126A LEU* 3.0 13.4 + - + +
128A GLU* 1.3 73.0 - - + +
130A ILE* 1.3 64.4 + - - +
132A TYR* 3.4 12.4 - - - +
133A ALA* 3.2 22.0 + - - +
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Residues in contact with ILE 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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72A VAL* 5.2 3.1 - - + +
74A VAL* 4.0 18.4 - - + -
106A LEU* 4.1 10.3 - - + -
126A LEU* 2.8 45.6 + - + +
127A ILE* 3.4 11.0 - - + +
129A ARG* 1.3 75.2 - - - +
131A ASN* 1.3 51.8 + - - +
133A ALA* 3.0 8.2 + - - +
134A ILE* 2.9 57.9 + - + +
142A VAL* 4.4 11.9 - - + -
144A ILE* 4.2 20.4 - - + -
167A LEU* 4.5 7.4 - - + -
171A LEU* 4.1 16.2 - - + -
174A ILE* 5.9 1.3 - - + -
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Residues in contact with ASN 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 ILE* 2.7 23.6 + - + +
128A GLU* 3.6 7.1 - - - +
130A ILE* 1.3 72.7 - - - +
132A TYR* 1.3 61.2 + - - +
134A ILE* 4.3 7.4 - - - -
135A GLN* 2.4 62.5 + - - +
174A ILE* 3.4 36.5 - - + +
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Residues in contact with TYR 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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104A PHE* 6.1 3.8 - + - -
128A GLU 2.7 21.7 + - - +
129A ARG* 3.4 13.0 - - - +
130A ILE 3.1 0.2 - - - -
131A ASN* 1.3 73.4 - - - +
133A ALA* 1.3 55.7 + - + +
135A GLN* 3.5 3.2 + - - +
136A LYS* 2.8 63.1 + - + +
137A TYR* 6.1 0.7 - + - -
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Residues in contact with ALA 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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72A VAL* 4.0 16.2 - - + -
104A PHE* 3.4 38.6 - - + -
106A LEU* 5.1 0.2 - - + -
129A ARG 3.2 7.2 + - - +
130A ILE* 3.0 8.1 + - - +
132A TYR* 1.3 77.3 - - + +
134A ILE* 1.3 56.7 + - - +
136A LYS* 4.1 2.0 - - - -
137A TYR* 2.7 48.7 + - + +
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Residues in contact with ILE 134 (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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72A VAL* 4.7 3.6 - - + -
130A ILE* 2.9 42.6 + - + +
131A ASN* 3.9 4.5 - - - +
133A ALA* 1.3 75.0 - - - +
135A GLN* 1.3 62.5 + - - +
138A ARG* 2.8 31.0 + - - -
139A ALA* 3.0 35.0 + - + +
142A VAL* 4.1 23.1 - - + -
171A LEU* 4.9 1.3 - - + -
174A ILE* 3.4 36.8 - - + +
175A GLY 6.4 0.2 - - - -
176A ALA* 4.1 9.9 - - + -
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Residues in contact with GLN 135 (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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131A ASN* 2.4 57.4 + - - +
132A TYR* 3.9 3.4 - - - +
134A ILE* 1.3 89.5 - - - +
136A LYS* 1.3 66.0 + - - +
138A ARG* 3.8 7.2 + - - +
174A ILE* 4.6 7.6 - - - +
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Residues in contact with LYS 136 (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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132A TYR* 2.8 52.9 + - + +
133A ALA* 3.8 4.5 - - - +
135A GLN* 1.3 74.6 - - - +
137A TYR* 1.3 101.7 + - + +
138A ARG* 3.9 0.7 + - - +
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Residues in contact with TYR 137 (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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70A PRO* 3.3 19.5 - - + +
71A GLY 5.6 1.1 - - - +
72A VAL* 5.0 3.8 - - + -
98A VAL 5.7 0.4 - - - -
101A GLY* 3.5 37.4 - - - +
102A LYS 5.8 1.1 - - - +
103A LEU 5.0 2.5 - - - -
104A PHE* 3.5 55.2 - + + -
132A TYR* 6.1 0.2 - + - -
133A ALA* 2.7 36.4 + - + +
136A LYS* 1.3 113.8 + - + +
138A ARG* 1.3 69.5 + - - +
139A ALA* 4.6 8.7 - - + -
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Residues in contact with ARG 138 (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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70A PRO* 3.2 20.0 - - + +
134A ILE 2.8 10.2 + - - -
135A GLN* 3.8 6.1 + - - +
136A LYS 3.5 2.9 - - - +
137A TYR* 1.3 79.1 - - - +
139A ALA* 1.3 60.2 + - - +
140A ARG* 3.8 7.7 + - - +
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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