Contacts of the helix formed by residues 123 - 135 (chain A) in PDB entry 1JEQ
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 LYS 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ASP* 3.5 5.4 - - - +
64A ILE* 4.6 4.3 - - + -
65A GLN* 3.3 37.5 + - + +
68A GLN* 3.6 19.8 - - - +
119A LEU 4.0 0.6 + - - -
120A ASP* 3.1 33.1 + - - +
122A PHE* 1.3 76.0 - - - +
124A GLY* 1.3 73.9 + - - +
127A GLY* 3.2 14.2 + - - -
130A ARG* 4.7 2.9 + - - -
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Residues in contact with GLY 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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57A LEU* 6.0 0.2 - - - -
61A ASP* 3.0 27.7 + - - +
65A GLN* 5.2 0.4 - - - -
122A PHE 4.1 1.4 - - - +
123A LYS* 1.3 84.9 - - - +
125A GLN* 1.3 65.5 + - - -
126A GLN 3.4 1.1 - - - -
128A GLN* 3.1 15.6 + - - +
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Residues in contact with GLN 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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61A ASP* 4.8 0.2 + - - -
124A GLY* 1.3 71.7 - - - -
126A GLN* 1.3 65.0 + - + +
128A GLN* 2.9 32.8 + - + +
129A LYS* 3.1 41.5 + - + +
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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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123A LYS 5.3 0.4 - - - +
124A GLY 3.4 0.6 - - - -
125A GLN* 1.3 78.0 - - + +
127A GLY* 1.3 61.8 + - - +
129A LYS* 3.3 29.2 + - + +
130A ARG* 3.2 38.6 + - - +
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Residues in contact with GLY 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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121A GLN 3.1 21.8 - - - +
122A PHE* 3.3 19.2 - - - -
123A LYS 3.2 20.6 + - - -
125A GLN 3.2 0.8 - - - -
126A GLN* 1.3 77.5 - - - +
128A GLN* 1.3 64.6 + - - +
129A LYS 3.2 0.2 - - - -
130A ARG* 3.3 8.2 + - - +
131A PHE* 3.0 18.4 + - - +
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Residues in contact with GLN 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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49A PHE* 3.2 61.3 + - + +
58A THR* 3.7 20.0 + - - +
60A PHE* 4.6 5.8 - - + -
122A PHE 4.0 4.7 + - - +
124A GLY 3.1 11.6 + - - +
125A GLN* 2.9 24.8 + - - +
127A GLY* 1.3 75.1 - - - +
129A LYS* 1.3 60.6 + - + +
131A PHE* 3.2 5.9 + - - +
132A GLN* 2.8 44.3 + - - +
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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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125A GLN* 3.1 46.0 - - + +
126A GLN* 3.5 29.2 - - + +
127A GLY 3.2 0.2 - - - -
128A GLN* 1.3 78.9 - - + +
130A ARG* 1.3 63.8 + - - +
132A GLN* 3.0 9.4 + - - +
133A ASP* 2.8 37.4 + - - +
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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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120A ASP 5.5 0.8 + - - -
121A GLN* 2.5 62.1 + - + +
122A PHE* 4.2 6.9 - - + -
123A LYS 4.7 2.6 + - - -
126A GLN* 3.2 28.8 + - - +
127A GLY* 3.4 27.0 - - - +
128A GLN 3.3 0.2 - - - -
129A LYS* 1.3 80.1 - - - +
131A PHE* 1.3 60.7 + - - +
133A ASP* 3.6 8.0 + - - +
134A MET* 3.2 29.1 + - + +
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Residues in contact with PHE 131 (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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44A ALA* 3.8 19.3 - - + -
49A PHE* 3.6 30.5 - + - -
60A PHE* 3.5 21.3 - + + -
87A PHE* 3.8 41.7 - + - -
90A THR* 4.0 9.4 - - + -
122A PHE* 3.6 35.8 - + + -
127A GLY 3.0 9.9 + - - +
128A GLN 3.5 7.0 - - - +
130A ARG* 1.3 72.1 - - - +
132A GLN* 1.3 71.7 + - - +
134A MET* 3.2 3.0 + - - +
135A MET* 2.9 51.3 + - + -
137A HIS* 5.1 1.8 - - + -
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Residues in contact with GLN 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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49A PHE* 3.1 53.1 - - - +
128A GLN* 2.8 36.8 + - - +
129A LYS* 3.3 9.2 - - - +
131A PHE* 1.3 80.0 - - - +
133A ASP* 1.3 60.6 + - - +
136A GLY* 2.7 38.6 + - - -
137A HIS* 2.7 35.1 + - - +
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Residues in contact with ASP 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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92A LYS* 5.0 4.3 + - - -
129A LYS* 2.8 37.0 + - - +
130A ARG* 3.8 7.7 + - - +
132A GLN* 1.3 76.6 - - - +
134A MET* 1.3 63.0 + - - +
136A GLY 4.2 1.7 + - - -
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Residues in contact with MET 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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92A LYS* 3.1 39.2 - - + +
103A TYR* 4.6 12.6 - - + +
105A LEU* 5.3 3.8 - - - -
122A PHE* 4.1 20.0 - - + -
130A ARG* 3.2 16.1 + - + +
131A PHE* 3.2 2.9 + - - +
133A ASP* 1.3 79.3 - - - +
135A MET* 1.3 87.7 + - + +
136A GLY 4.2 0.2 + - - -
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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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87A PHE* 4.5 4.0 - - + -
90A THR* 3.5 25.9 - - + +
91A GLU 4.0 3.1 - - - -
92A LYS* 4.5 8.5 - - + +
103A TYR* 3.3 54.7 - - + -
105A LEU* 4.1 7.9 - - + -
122A PHE* 3.9 18.8 - - + -
131A PHE* 2.9 42.0 + - + +
132A GLN 3.4 1.8 - - - -
134A MET* 1.3 107.6 - - + +
136A GLY* 1.3 69.1 + - - +
137A HIS* 3.2 2.1 + - - -
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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