Contacts of the helix formed by residues 121 - 136 (chain A) in PDB entry 2JNV
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 SER 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ALA* 4.2 3.0 - - - +
119A CYS 3.6 5.0 + - - -
120A PRO* 1.3 73.4 - - - +
122A SER* 1.3 70.4 + - - +
123A LEU 3.0 2.9 + - - -
124A ILE* 3.3 17.4 + - - +
125A THR* 3.4 12.7 + - - -
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Residues in contact with SER 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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114A GLY* 3.3 31.0 + - - -
115A ALA* 4.1 6.7 - - - +
121A SER* 1.3 80.5 + - - +
123A LEU* 1.3 57.5 + - - +
125A THR* 2.9 10.3 + - - -
126A ILE* 2.7 47.0 + - - +
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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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112A LEU* 3.9 36.1 - - + +
114A GLY* 3.7 11.9 - - - +
115A ALA 4.5 0.2 - - - +
120A PRO* 4.4 24.7 - - + +
121A SER 3.0 0.8 - - - +
122A SER* 1.3 77.6 - - - +
124A ILE* 1.3 65.4 + - + +
126A ILE* 3.1 8.2 - - - +
127A LYS* 2.8 40.2 + - + +
146A PRO* 5.1 15.7 - - + -
150A LYS* 3.4 35.4 - - + +
151A GLU* 4.9 1.3 - - + -
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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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120A PRO 5.2 4.9 - - - +
121A SER* 3.3 10.4 + - - +
122A SER 3.2 0.2 - - - -
123A LEU* 1.3 88.1 - - + +
125A THR* 1.3 64.8 + - - +
127A LYS* 3.5 27.3 + - + +
128A ARG* 3.6 15.9 + - - +
150A LYS 5.2 0.4 - - - +
151A GLU* 3.8 42.4 - - + +
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Residues in contact with THR 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 SER 3.4 12.9 + - - -
122A SER* 2.9 15.4 + - - -
124A ILE* 1.3 79.6 - - - +
126A ILE* 1.3 59.5 + - + +
128A ARG* 3.1 31.5 - - - +
129A GLY* 4.1 1.9 + - - -
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Residues in contact with ILE 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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87A VAL* 5.5 0.2 - - + -
90A TYR* 5.3 12.8 - - + +
91A LEU* 3.2 47.1 - - + -
112A LEU* 3.7 16.6 - - + -
114A GLY* 3.7 18.8 - - - +
122A SER* 2.7 27.2 + - - +
123A LEU* 3.1 11.7 - - - +
125A THR* 1.3 75.2 - - + +
127A LYS* 1.3 62.4 + - - +
128A ARG 3.2 2.0 - - - -
129A GLY* 2.8 21.9 + - - +
130A ILE* 2.9 27.8 + - + +
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Residues in contact with LYS 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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112A LEU* 4.2 13.9 - - + -
123A LEU* 2.8 24.2 + - + +
124A ILE* 3.5 28.7 - - + +
125A THR 3.4 0.2 - - - -
126A ILE* 1.3 77.7 - - - +
128A ARG* 1.3 62.5 + - - +
130A ILE* 3.7 1.2 + - - +
131A GLU* 3.1 32.4 + - - +
143A ALA* 5.5 3.4 - - - +
144A VAL* 3.1 41.2 + - + +
145A GLU* 4.6 14.6 - - - +
146A PRO* 4.9 5.8 - - + -
151A GLU* 5.1 7.2 - - + -
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Residues in contact with ARG 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 ILE* 3.6 14.1 + - - +
125A THR* 3.1 28.6 - - - +
127A LYS* 1.3 81.0 - - - +
129A GLY* 1.3 58.5 + - - +
131A GLU* 3.3 13.3 - - - +
132A ARG* 2.9 29.5 + - - +
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Residues in contact with GLY 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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87A VAL* 6.0 0.2 - - - -
125A THR 4.1 1.1 + - - -
126A ILE* 2.8 12.4 + - - -
128A ARG* 1.3 82.0 - - - +
130A ILE* 1.3 64.6 + - - -
132A ARG* 3.0 7.2 + - - +
133A ARG* 2.9 29.0 + - - +
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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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83A VAL* 6.4 0.2 - - + -
84A LEU* 4.0 30.3 - - + -
87A VAL* 3.4 38.7 - - + +
110A LEU* 4.6 12.3 - - + -
112A LEU* 3.2 44.2 - - + -
126A ILE* 2.9 37.8 + - + +
127A LYS 4.3 0.4 - - - +
129A GLY* 1.3 73.1 - - - +
131A GLU* 1.3 59.2 + - - +
133A ARG* 2.8 25.6 + - + +
134A LEU* 2.8 16.6 + - + +
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Residues in contact with GLU 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 LYS* 3.1 29.3 + - + +
128A ARG* 3.3 18.5 - - - +
130A ILE* 1.3 79.6 - - - +
132A ARG* 1.3 83.2 + - - +
134A LEU* 4.5 3.1 - - - -
135A MET* 3.1 46.1 + - - +
142A ALA 5.0 1.4 - - - +
143A ALA* 4.8 7.6 - - - +
144A VAL* 3.4 37.1 + - + +
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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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128A ARG 2.9 19.3 - - - +
129A GLY* 3.0 6.4 + - - +
130A ILE 3.0 0.6 - - - -
131A GLU* 1.3 89.7 - - - +
133A ARG* 1.3 67.5 + - + +
135A MET* 4.3 4.9 - - - +
136A GLU* 3.6 31.3 + - - +
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Residues in contact with ARG 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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83A VAL* 3.1 28.7 - - + +
86A GLN* 5.0 22.4 + - + +
87A VAL* 5.8 6.3 - - + -
129A GLY* 2.9 20.3 + - - +
130A ILE* 2.8 11.3 + - + +
132A ARG* 1.3 81.7 - - + +
134A LEU* 1.3 64.5 + - - +
136A GLU* 3.2 21.2 - - - +
137A LYS* 3.7 9.8 + - - +
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Residues in contact with LEU 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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75A LEU* 3.7 21.5 - - + -
80A VAL* 4.0 17.5 - - + -
83A VAL* 3.6 22.2 - - + +
84A LEU* 4.8 2.5 - - + -
108A VAL* 5.0 6.5 - - + -
110A LEU* 4.2 20.2 - - + -
130A ILE* 2.8 15.5 + - + +
131A GLU* 4.0 5.4 - - - +
133A ARG* 1.3 74.2 - - - +
135A MET* 1.3 59.7 + - - +
136A GLU 2.9 1.6 - - - -
137A LYS* 2.7 25.8 + - - +
138A ILE* 2.8 55.1 + - + +
141A VAL* 5.6 2.7 - - + -
144A VAL* 4.8 9.6 - - + -
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Residues in contact with MET 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 GLU* 3.1 38.6 + - - +
132A ARG* 4.3 7.4 - - - +
134A LEU* 1.3 84.0 - - - +
136A GLU* 1.3 62.7 + - - +
137A LYS 3.0 1.2 + - - -
138A ILE 3.7 14.1 - - - +
139A PRO* 3.2 29.2 - - + +
141A VAL* 3.3 33.9 - - + +
142A ALA 3.4 6.1 - - - +
143A ALA* 3.3 39.5 - - - +
144A VAL* 4.6 4.5 - - + -
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Residues in contact with GLU 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 ARG* 3.6 28.6 + - - +
133A ARG* 3.2 21.7 + - - +
134A LEU 2.9 0.2 + - - -
135A MET* 1.3 78.2 - - - +
137A LYS* 1.3 74.2 + - + +
139A PRO* 5.1 0.9 - - - +
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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