Contacts of the helix formed by residues 119 - 129 (chain B) in PDB entry 1JQE
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 THR 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B VAL* 3.7 2.7 - - - -
90B PRO* 3.7 19.3 - - + -
118B GLU* 1.3 77.8 - - - +
120B SER* 1.3 65.7 + - - +
121B SER* 3.7 7.3 + - - -
122B GLU* 3.0 36.8 + - - +
123B TYR* 2.9 22.2 + - - +
401B SAH 3.4 30.3 - - + +
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Residues in contact with SER 120 (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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59B ILE* 3.6 26.2 - - - -
88B VAL* 3.9 9.4 - - - -
119B THR* 1.3 71.9 - - - +
121B SER* 1.3 59.8 + - - +
123B TYR* 3.2 3.7 + - - +
124B GLN* 2.8 31.4 + - - +
144B MET* 4.8 0.7 - - - -
148B VAL* 3.8 19.6 - - - +
154B THR* 4.2 10.3 + - - -
158B PHE* 4.0 21.2 - - - -
401B SAH 2.9 19.7 + - - -
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B THR* 3.1 9.0 + - - -
120B SER* 1.3 84.2 + - - +
122B GLU* 1.3 57.8 + - - +
124B GLN* 3.3 12.1 + - - +
125B SER* 2.9 28.8 + - - -
148B VAL* 6.3 2.5 - - - -
149B LYS* 6.1 6.3 - - - -
154B THR* 5.9 1.8 - - - -
401B SAH 5.9 1.1 - - - -
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Residues in contact with GLU 122 (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 LYS 4.6 0.3 - - - +
118B GLU* 3.0 34.5 - - + +
119B THR* 3.0 33.0 + - - +
121B SER* 1.3 74.1 - - - +
123B TYR* 1.3 60.9 + - - +
125B SER* 3.3 7.3 + - - -
126B ARG* 2.8 31.7 + - - +
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Residues in contact with TYR 123 (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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57B LEU* 3.9 24.2 - - + +
86B GLU* 4.6 1.3 + - - -
88B VAL* 3.7 22.4 - - + -
116B HIS* 3.9 16.4 - + - -
118B GLU* 3.3 25.9 + - - -
119B THR 2.9 13.4 + - - +
120B SER* 3.4 7.4 - - - +
122B GLU* 1.3 76.9 - - - +
124B GLN* 1.3 58.0 + - - +
126B ARG* 3.3 20.4 + - - +
127B MET* 2.9 57.6 + - + +
134B GLN* 3.8 11.2 + - - -
136B TRP* 3.5 30.7 + - - -
157B PHE* 4.6 0.2 - + - -
158B PHE* 3.8 20.4 - + - -
161B LEU* 4.6 6.9 - - + +
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Residues in contact with GLN 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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120B SER 2.8 17.4 + - - +
121B SER* 3.4 11.1 - - - +
123B TYR* 1.3 78.3 - - - +
125B SER* 1.3 62.2 + - - +
127B MET* 3.2 3.3 + - - +
128B LEU* 3.1 38.4 + - + +
153B ALA* 4.0 20.4 + - - +
154B THR* 4.2 10.9 + - - -
157B PHE* 3.3 62.9 - - + +
158B PHE* 4.7 1.7 - - - -
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Residues in contact with SER 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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121B SER 2.9 17.0 + - - -
122B GLU* 3.5 8.3 - - - -
124B GLN* 1.3 75.9 - - - +
126B ARG* 1.3 64.0 + - - +
128B LEU* 3.3 22.6 + - - +
129B GLU* 3.6 19.0 + - - +
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Residues in contact with ARG 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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116B HIS* 3.4 27.0 + - - -
118B GLU* 2.9 34.0 + - - -
122B GLU 2.8 16.6 + - - +
123B TYR* 3.5 21.0 - - - +
125B SER* 1.3 77.2 + - - +
127B MET* 1.3 79.6 + - + +
129B GLU* 3.2 26.1 - - + +
130B LYS 4.5 0.7 + - - -
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Residues in contact with MET 127 (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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123B TYR* 2.9 47.0 + - + +
124B GLN 3.2 5.1 + - - +
126B ARG* 1.3 120.4 - - + +
128B LEU* 1.3 62.2 + - - +
129B GLU 3.3 0.3 + - - -
130B LYS 4.0 6.1 + - - -
131B LYS 4.4 1.6 + - - -
132B GLU 4.0 17.4 - - - +
133B LEU* 5.5 0.9 - - - -
134B GLN* 3.6 32.8 - - - +
157B PHE* 4.0 15.9 - - + -
161B LEU* 5.5 3.6 - - + -
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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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124B GLN* 3.1 29.0 + - + +
125B SER* 3.3 14.1 + - - +
127B MET* 1.3 75.5 - - - +
129B GLU* 1.3 69.7 + - - +
131B LYS* 3.2 12.8 + - - -
157B PHE* 4.3 20.6 - - + -
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Residues in contact with GLU 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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125B SER* 3.6 15.6 + - - +
126B ARG* 3.2 24.9 - - + +
128B LEU* 1.3 78.5 - - - +
130B LYS* 1.3 61.2 + - - +
131B LYS* 2.8 8.8 + - - -
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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