Contacts of the helix formed by residues 123 - 138 (chain A) in PDB entry 2J3W
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A PHE* 3.8 21.6 - - - -
121A ILE* 3.8 4.4 + - - +
122A ARG* 1.3 76.4 - - - +
124A SER* 1.3 65.6 + - - +
125A ALA* 3.3 11.1 + - - +
126A PHE* 2.8 40.2 + - - +
127A ASP* 3.0 21.9 + - - -
117E GLU* 5.3 8.9 + - - -
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A SER* 1.3 71.6 + - - +
125A ALA* 1.3 57.3 + - - +
127A ASP* 3.4 9.9 + - - +
128A ARG* 2.9 65.4 + - - +
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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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123A SER* 3.1 8.6 + - - +
124A SER* 1.3 80.0 - - - +
126A PHE* 1.3 60.2 + - - +
128A ARG* 3.4 27.6 - - - +
129A LYS* 3.1 46.4 + - - +
117E GLU* 6.1 0.7 - - - +
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Residues in contact with PHE 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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9A ILE* 4.6 9.9 - - + -
18A PHE* 3.5 36.8 - + - -
102A VAL* 4.6 4.5 - - + -
105A LEU* 3.6 45.0 - - + +
106A TYR* 4.2 8.5 - - - -
109A PHE* 4.1 21.8 - + + -
121A ILE* 3.6 32.8 - - + -
123A SER* 2.8 28.8 + - - +
125A ALA* 1.3 74.3 - - - +
127A ASP* 1.3 64.9 + - - +
129A LYS* 3.3 5.1 + - - +
130A VAL* 3.1 41.8 + - + +
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Residues in contact with ASP 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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18A PHE* 2.8 34.6 - - + -
20A MET* 4.3 7.8 - - - +
121A ILE 5.0 3.5 - - - +
122A ARG* 5.8 1.9 + - - -
123A SER 3.0 21.8 + - - +
124A SER* 3.7 9.2 - - - +
126A PHE* 1.3 77.0 - - - +
128A ARG* 1.3 64.2 + - + +
130A VAL* 3.3 2.4 + - - +
131A GLN* 3.0 25.5 + - - +
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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 SER* 2.9 48.7 + - - +
125A ALA* 3.4 33.1 - - - +
126A PHE 3.3 0.2 - - - -
127A ASP* 1.3 77.8 - - + +
129A LYS* 1.3 62.7 + - + +
131A GLN* 3.5 6.8 + - - +
132A PHE* 3.1 21.7 + - - +
35D GLU* 5.5 1.0 - - - +
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Residues in contact with LYS 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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105A LEU* 3.3 39.7 - - + +
108A LYS* 6.2 1.8 - - - +
125A ALA* 3.1 30.7 + - - +
126A PHE* 3.3 1.1 + - - +
128A ARG* 1.3 75.3 - - + +
130A VAL* 1.3 61.7 + - - +
132A PHE* 3.2 10.0 + - + +
133A LEU* 2.9 32.6 + - + +
35D GLU* 5.8 4.5 - - - +
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Residues in contact with VAL 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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7A PHE* 4.5 2.5 - - + -
18A PHE* 3.7 30.1 - - + -
20A MET* 3.0 22.8 - - + +
98A PHE* 3.8 21.3 - - + -
102A VAL* 4.3 12.1 - - + -
105A LEU* 3.7 16.8 - - + -
126A PHE* 3.1 28.4 + - + +
127A ASP 3.8 2.2 - - - +
129A LYS* 1.3 72.6 - - - +
131A GLN* 1.3 62.1 + - - +
133A LEU* 3.0 9.2 + - - +
134A GLY* 2.8 25.1 + - - -
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Residues in contact with GLN 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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20A MET* 3.0 40.7 - - - +
21A GLU 4.7 3.8 + - - +
22A PHE* 3.8 20.0 - - + -
127A ASP* 3.0 16.4 + - - +
128A ARG* 3.6 8.3 - - - +
130A VAL* 1.3 73.9 - - - +
132A PHE* 1.3 62.9 + - - +
134A GLY* 3.1 2.8 + - - -
135A LYS* 3.1 40.9 + - + +
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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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128A ARG 3.1 13.6 + - - +
129A LYS* 3.4 13.0 - - - +
130A VAL 3.2 0.2 - - - -
131A GLN* 1.3 78.0 - - - +
133A LEU* 1.3 67.2 + - + +
135A LYS* 3.3 10.9 + - + +
136A LYS* 2.9 41.6 + - + +
32D LYS 3.6 16.2 - - - -
33D ASP 3.5 25.4 - - - -
34D TYR 4.1 1.3 - - - -
35D GLU* 3.3 53.6 - - + +
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Residues in contact with LEU 133 (chain A).
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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98A PHE* 3.6 15.2 - - + -
101A ASP* 3.7 31.9 - - + +
102A VAL* 3.6 38.4 - - + +
105A LEU* 4.3 10.3 - - + -
129A LYS* 2.9 21.2 + - + +
130A VAL* 3.0 11.4 + - - +
132A PHE* 1.3 90.7 - - + +
134A GLY* 1.3 64.6 + - - +
136A LYS* 4.3 5.4 - - + +
137A HIS* 2.9 34.9 + - + +
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Residues in contact with GLY 134 (chain A).
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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22A PHE* 3.8 17.5 - - - -
98A PHE* 3.5 17.0 - - - -
130A VAL 2.8 10.9 + - - -
131A GLN 3.1 4.2 + - - -
133A LEU* 1.3 76.6 - - - +
135A LYS* 1.3 57.6 + - - +
138A LEU* 2.7 33.1 + - - -
139A LEU* 3.1 12.6 + - - -
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Residues in contact with LYS 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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22A PHE* 4.7 1.1 - - + -
131A GLN* 3.1 31.1 + - + +
132A PHE* 3.5 14.1 - - + +
134A GLY* 1.3 76.7 - - - +
136A LYS* 1.3 61.7 + - - +
139A LEU* 3.3 50.5 - - + +
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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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101A ASP* 4.0 11.0 + - - +
132A PHE* 2.9 33.4 + - + +
133A LEU* 3.8 8.0 - - + +
134A GLY 3.3 0.2 - - - -
135A LYS* 1.3 80.2 - - - +
137A HIS* 1.3 87.5 + - + +
29D GLN* 5.8 1.3 - - - +
32D LYS* 3.3 35.9 - - + +
33D ASP* 2.9 34.3 + - - +
43F ARG* 5.9 0.6 - - - +
53F ARG* 5.6 5.5 - - - +
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Residues in contact with HIS 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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91A GLN* 3.1 19.2 - - - +
94A GLY* 3.6 24.8 - - - +
97A ASN* 3.2 33.3 + - + +
98A PHE* 3.8 21.3 - - + -
101A ASP* 2.7 30.4 + - - -
133A LEU* 2.9 31.7 + - + +
135A LYS 4.8 0.4 - - - -
136A LYS* 1.3 108.6 + - + +
138A LEU* 1.3 60.4 + - - +
139A LEU 5.3 1.1 - - - -
140A SER* 5.6 0.7 - - - -
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Residues in contact with LEU 138 (chain A).
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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5A PHE* 3.8 36.9 - - + -
22A PHE* 3.8 34.3 - - + -
85A MET* 3.8 21.3 - - + -
91A GLN* 3.2 24.8 + - - +
95A ILE* 4.3 17.0 - - + +
98A PHE* 3.7 39.0 - - + -
134A GLY* 2.7 18.3 + - - +
137A HIS* 1.3 72.4 - - - +
139A LEU* 1.3 67.4 + - + +
140A SER* 3.1 5.0 + - - -
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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