Contacts of the helix formed by residues 122 - 134 (chain B) in PDB entry 2X7N
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B GLU 5.3 0.7 - - - +
99B GLU* 5.7 2.1 - - - +
120B ASP 3.6 2.7 + - - +
121B ILE* 1.3 78.7 - - - +
123B ARG* 1.3 63.2 + - - +
124B GLU* 3.3 15.2 + - - +
125B THR* 2.5 44.5 + - - +
126B GLU* 3.0 21.4 + - - +
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Residues in contact with ARG 123 (chain B).
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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121B ILE 4.0 0.6 + - - -
122B ASP* 1.3 70.4 - - - +
124B GLU* 1.3 69.8 + - - +
126B GLU* 3.0 11.8 + - - +
127B GLU* 3.0 55.7 + - + +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ASP* 3.3 11.4 + - - +
123B ARG* 1.3 82.7 - - - +
125B THR* 1.3 63.6 + - - +
127B GLU* 3.3 14.9 + - - +
128B LEU* 3.2 21.3 + - + +
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 4.0 27.1 - - + -
98B GLU 4.3 10.0 + - - -
99B GLU* 4.6 8.5 - - + +
121B ILE* 3.4 23.8 - - + -
122B ASP* 2.5 37.6 + - - +
124B GLU* 1.3 76.7 - - - +
126B GLU* 1.3 64.4 + - - +
128B LEU* 3.2 9.3 + - + +
129B ILE* 3.0 32.8 + - + +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL* 4.3 0.2 - - - -
121B ILE* 4.0 10.3 - - + +
122B ASP 3.0 17.0 + - - +
123B ARG* 3.0 10.7 + - - +
125B THR* 1.3 76.9 - - - +
127B GLU* 1.3 62.1 + - + +
129B ILE* 3.7 11.8 + - - +
130B SER* 3.2 21.5 + - - -
137B VAL* 3.4 43.5 - - + +
138B PHE* 4.1 0.2 - - - -
139B ARG* 3.6 42.1 + - - +
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Residues in contact with GLU 127 (chain B).
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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123B ARG* 3.0 54.2 + - + +
124B GLU* 3.6 12.6 - - - +
125B THR 3.1 0.2 - - - -
126B GLU* 1.3 77.0 - - + +
128B LEU* 1.3 60.4 + - - +
130B SER* 3.4 6.6 + - - -
131B ASP* 2.8 31.3 + - - +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 5.5 0.2 - - + -
93B LYS* 5.5 2.0 - - - +
95B GLN* 4.4 19.7 - - + +
96B ARG 4.5 16.4 - - - +
97B VAL* 4.6 20.0 - - + -
98B GLU 5.7 1.1 - - - +
124B GLU* 3.2 14.8 + - + +
125B THR* 3.4 12.8 - - + +
127B GLU* 1.3 77.1 - - - +
129B ILE* 1.3 57.1 + - + +
131B ASP* 3.3 11.9 + - + +
132B VAL* 2.8 45.5 + - + +
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 4.1 22.2 - - + -
97B VAL* 5.3 5.4 - - + -
108B ILE* 3.7 20.0 - - + -
115B ALA* 4.9 2.2 - - + -
117B VAL* 3.6 20.9 - - + -
121B ILE* 3.5 31.9 - - + -
125B THR* 3.0 19.4 + - + +
126B GLU* 3.8 6.3 - - - +
128B LEU* 1.3 73.5 - - + +
130B SER* 1.3 66.1 + - - +
133B LEU* 2.9 53.3 + - + +
137B VAL* 4.1 13.2 - - + -
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Residues in contact with SER 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLU* 3.2 11.3 + - - -
127B GLU* 3.6 7.2 - - - -
129B ILE* 1.3 79.5 - - - +
131B ASP* 1.3 53.8 + - - +
134B GLY* 2.7 34.5 + - - -
135B VAL* 2.8 27.4 + - - +
136B GLU* 4.9 0.5 - - - -
137B VAL* 3.4 19.0 - - - +
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LYS* 4.6 13.2 + - - -
127B GLU 2.8 18.5 + - - +
128B LEU* 3.4 13.1 - - + +
130B SER* 1.3 76.2 + - - +
132B VAL* 1.3 66.1 + - + +
134B GLY* 3.1 12.5 + - - -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ARG* 4.3 6.1 - - - +
69B GLY* 4.1 15.5 + - - -
70B LEU 4.5 1.3 - - - +
71B LEU* 3.9 22.9 - - + -
93B LYS* 3.7 56.0 - - + +
95B GLN* 3.6 31.6 - - + -
128B LEU* 2.8 28.3 + - + +
129B ILE 4.3 0.4 - - - +
131B ASP* 1.3 74.7 - - + +
133B LEU* 1.3 62.3 + - + +
134B GLY 3.5 0.3 + - - -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLY* 3.8 11.7 - - - -
66B ASN* 3.3 24.6 + - - +
68B ARG* 3.0 20.0 + - - +
69B GLY* 3.4 32.8 - - - +
71B LEU* 4.0 24.0 - - + -
108B ILE* 4.6 5.2 - - + -
110B CYS* 4.0 28.5 - - + -
115B ALA* 4.7 3.4 - - + -
129B ILE* 2.9 40.4 + - + +
132B VAL* 1.3 73.8 - - + +
134B GLY* 1.3 64.6 + - - +
135B VAL* 3.3 7.6 + - + -
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ARG* 3.3 26.1 + - - -
112B ASP 4.5 0.2 - - - +
130B SER 2.7 14.5 + - - -
131B ASP* 3.1 10.9 + - - -
132B VAL 3.2 0.6 + - - -
133B LEU* 1.3 79.4 - - - +
135B VAL* 1.3 54.9 + - - +
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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