Contacts of the helix formed by residues 119 - 130 (chain A) in PDB entry 1JQD
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A VAL* 3.7 1.8 - - - -
90A PRO* 3.9 17.7 - - + -
118A GLU* 1.3 76.4 - - - +
120A SER* 1.3 60.0 + - - +
121A SER* 3.5 8.2 + - - -
122A GLU* 2.8 42.0 + - - +
123A TYR* 2.9 28.6 + - - +
400A SAH 3.4 28.7 - - + +
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Residues in contact with SER 120 (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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59A ILE* 3.7 27.8 - - - -
88A VAL* 4.1 9.0 - - - -
119A THR* 1.3 72.6 - - - +
121A SER* 1.3 59.0 + - - +
123A TYR* 3.6 3.6 - - - +
124A GLN* 2.8 31.0 + - - +
141A MET* 4.9 1.1 - - - -
144A MET* 4.8 0.2 - - - -
148A VAL* 3.7 22.0 - - - +
154A THR* 4.5 5.2 + - - +
158A PHE* 3.8 22.3 - - - -
400A SAH 2.9 19.5 + - - -
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR* 3.1 9.3 - - - -
120A SER* 1.3 81.4 + - - +
122A GLU* 1.3 65.4 + - - +
124A GLN* 3.2 13.6 + - - +
125A SER* 3.1 23.6 + - - -
148A VAL* 6.2 3.4 - - - -
154A THR* 6.0 2.5 - - - -
400A SAH 5.3 1.3 + - - -
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Residues in contact with GLU 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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90A PRO* 5.2 0.5 - - - +
117A LYS 4.8 0.2 - - - +
118A GLU* 3.2 22.3 - - + +
119A THR* 2.8 45.6 + - - +
121A SER* 1.3 74.7 - - - +
123A TYR* 1.3 66.5 + - - +
125A SER* 3.1 9.1 + - - -
126A ARG* 3.0 27.6 + - + +
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Residues in contact with TYR 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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57A LEU* 4.1 15.7 - - + +
86A GLU* 5.0 1.5 + - - -
88A VAL* 3.7 25.8 - - + -
116A HIS* 4.5 15.3 - + - -
118A GLU* 3.2 28.4 - - - +
119A THR 2.9 16.9 + - - +
120A SER 3.6 3.6 - - - +
122A GLU* 1.3 78.2 - - - +
124A GLN* 1.3 58.8 + - - +
126A ARG* 3.3 5.9 + - - +
127A MET* 2.9 73.3 + - + +
134A GLN* 4.0 3.1 + - - -
136A TRP* 3.8 28.1 + - - -
157A PHE* 4.7 0.9 - + - -
158A PHE* 4.0 30.7 - + - -
161A LEU* 4.5 7.2 - - + +
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Residues in contact with GLN 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 SER 2.8 19.0 + - - +
121A SER* 3.4 13.1 + - - +
122A GLU 3.2 0.2 - - - -
123A TYR* 1.3 77.3 - - - +
125A SER* 1.3 59.1 + - - +
127A MET* 3.2 3.5 + - - +
128A LEU* 2.9 41.6 + - + +
153A ALA* 4.1 14.6 + - - +
154A THR* 4.4 15.4 + - - -
157A PHE* 3.3 60.3 - - + +
158A PHE* 5.1 1.6 - - - -
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Residues in contact with SER 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 3.1 13.0 + - - -
122A GLU* 3.1 18.4 + - - -
124A GLN* 1.3 78.9 - - - +
126A ARG* 1.3 61.1 + - - +
128A LEU* 3.1 17.9 + - - +
129A GLU* 3.1 14.6 + - - +
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Residues in contact with ARG 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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116A HIS* 4.4 15.0 + - - -
118A GLU* 2.7 45.6 + - - -
122A GLU* 3.0 16.4 + - + +
123A TYR* 3.5 6.9 - - - +
125A SER* 1.3 77.6 + - - +
127A MET* 1.3 93.2 + - - +
129A GLU* 3.2 19.0 + - - +
130A LYS* 3.7 15.3 + - - +
209B ASP* 3.9 41.0 + - - +
210B ASN* 4.6 15.3 - - - +
212B GLY* 5.9 1.2 - - - -
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Residues in contact with MET 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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123A TYR* 2.9 60.3 + - + +
124A GLN 3.7 4.5 - - - +
126A ARG* 1.3 119.6 - - + +
128A LEU* 1.3 60.7 + - - +
129A GLU 3.2 0.2 - - - -
130A LYS* 3.4 34.0 - - + +
132A GLU 4.9 1.2 - - - +
133A LEU* 3.6 18.8 - - + +
134A GLN* 3.7 22.2 - - - +
157A PHE* 4.2 13.7 - - + -
161A LEU* 5.7 1.8 - - + -
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Residues in contact with LEU 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 GLN* 2.9 39.4 + - + +
125A SER* 3.1 9.6 + - - +
127A MET* 1.3 75.2 - - - +
129A GLU* 1.3 60.2 + - - +
130A LYS 3.2 11.0 - - - +
133A LEU* 3.8 29.2 - - + -
157A PHE* 4.1 11.9 - - + -
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Residues in contact with GLU 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 SER 3.1 10.3 + - - +
126A ARG* 3.2 13.9 + - - +
128A LEU* 1.3 74.4 - - - +
130A LYS* 1.3 67.4 + - + +
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Residues in contact with LYS 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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126A ARG* 4.0 13.9 - - - +
127A MET* 3.4 32.3 - - + +
128A LEU* 3.2 12.4 - - - +
129A GLU* 1.3 86.0 - - + +
131A LYS* 1.3 63.2 + - - +
132A GLU 3.6 12.1 - - - +
212B GLY* 3.3 32.3 + - - -
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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