Contacts of the helix formed by residues 117 - 129 (chain A) in PDB entry 1JTF
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 ASP 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ARG* 3.8 11.9 + - - -
115A PHE 4.8 1.6 - - - +
116A VAL* 1.3 74.6 - - - +
118A GLU* 1.3 68.6 + - - +
119A GLU* 3.5 18.3 + - - +
120A TYR* 2.7 38.0 + - - +
121A LEU* 3.1 27.5 + - - +
159A LEU* 4.8 3.8 - - - -
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Residues in contact with GLU 118 (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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117A ASP* 1.3 75.7 - - - +
119A GLU* 1.3 61.5 + - - +
121A LEU* 3.4 19.6 - - - +
122A ARG* 3.1 38.1 + - - +
159A LEU* 4.8 3.8 - - + +
162A VAL* 3.2 31.7 - - + +
166A ILE* 3.4 16.9 - - + +
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Residues in contact with GLU 119 (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 ARG* 6.3 0.4 - - - -
117A ASP* 3.2 16.6 + - - +
118A GLU* 1.3 75.1 - - - +
120A TYR* 1.3 67.3 + - - +
122A ARG* 3.0 27.2 + - - +
123A SER* 3.3 6.5 + - - +
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Residues in contact with TYR 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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92A MET* 4.1 9.2 - - - +
94A ILE* 4.0 13.6 - - + +
112A VAL* 3.3 22.5 - - - +
114A ARG* 3.4 47.8 - - + +
116A VAL* 3.6 33.4 - - + -
117A ASP* 2.7 27.7 + - - +
119A GLU* 1.3 71.3 - - - +
121A LEU* 1.3 69.6 + - - +
123A SER* 2.6 30.5 + - - -
124A ILE* 2.9 38.8 + - + +
127A GLN* 4.4 3.8 + - - -
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Residues in contact with LEU 121 (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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67A ILE* 4.1 9.9 - - + -
116A VAL* 4.3 10.8 - - + -
117A ASP 3.1 15.2 + - - +
118A GLU* 3.4 8.7 - - - +
120A TYR* 1.3 77.9 - - - +
122A ARG* 1.3 56.4 + - - +
124A ILE* 4.0 10.5 - - + -
125A LYS* 3.0 28.8 + - - +
159A LEU* 3.9 14.4 - - + -
162A VAL* 3.6 30.3 - - + -
163A MET* 4.0 18.2 - - + -
166A ILE* 3.7 14.1 - - + +
167A LEU* 3.2 40.8 - - + +
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Residues in contact with ARG 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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118A GLU* 3.1 42.0 + - - +
119A GLU* 3.2 14.4 - - - +
120A TYR 2.8 4.2 + - - -
121A LEU* 1.3 72.7 - - - +
123A SER* 1.3 58.3 + - - +
125A LYS* 3.4 2.9 + - - +
126A LYS* 3.1 33.8 + - + +
165A SER 5.7 0.2 + - - -
166A ILE* 3.4 41.2 - - + +
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Residues in contact with SER 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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119A GLU* 3.3 4.2 + - - -
120A TYR* 2.6 42.3 + - - -
122A ARG* 1.3 71.2 - - - +
124A ILE* 1.3 59.0 + - - +
125A LYS 3.0 1.6 - - - -
126A LYS* 3.0 26.3 + - - +
127A GLN* 2.8 34.7 + - - +
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Residues in contact with ILE 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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65A VAL* 3.9 28.7 - - + -
67A ILE* 5.3 0.2 - - + -
92A MET* 4.0 6.7 - - + -
94A ILE* 4.0 12.1 - - + -
120A TYR* 2.9 51.2 + - + +
121A LEU* 3.5 19.3 - - + +
123A SER* 1.3 75.4 - - - +
125A LYS* 1.3 59.6 + - - +
127A GLN* 3.4 22.1 - - - +
128A LEU* 3.0 43.8 + - + +
167A LEU* 3.9 19.1 - - + -
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Residues in contact with LYS 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 LEU 3.0 19.9 + - - +
122A ARG* 3.6 7.0 - - - +
123A SER 3.0 0.2 - - - -
124A ILE* 1.3 78.0 - - - +
126A LYS* 1.3 63.5 + - + +
128A LEU* 4.1 1.9 - - + +
129A HIS* 3.3 31.5 + - - +
131A SER 4.6 7.5 + - - -
133A ILE* 4.0 17.5 - - + +
166A ILE* 3.5 24.9 - - + +
167A LEU* 3.1 35.2 + - + +
168A ASN* 4.2 12.7 + - - +
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Residues in contact with LYS 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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122A ARG* 3.1 15.7 + - + +
123A SER* 3.0 30.9 + - - +
125A LYS* 1.3 78.0 - - + +
127A GLN* 1.3 60.1 - - - +
129A HIS* 3.3 21.4 + - - +
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Residues in contact with GLN 127 (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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92A MET* 3.4 23.8 - - + +
120A TYR* 4.4 4.4 + - - -
123A SER* 2.8 21.0 + - - +
124A ILE* 3.4 30.7 - - - +
126A LYS* 1.3 72.9 - - - +
128A LEU* 1.3 70.6 + - + +
129A HIS 4.0 4.2 - - - +
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Residues in contact with LEU 128 (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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63A THR* 4.1 23.8 - - + +
65A VAL* 3.9 16.8 - - + -
90A LYS* 4.2 12.9 + - - +
92A MET* 3.8 27.4 - - + -
124A ILE* 3.0 34.0 + - + +
125A LYS* 4.1 3.6 - - + +
126A LYS 3.4 0.2 - - - -
127A GLN* 1.3 81.3 - - + +
129A HIS* 1.3 68.4 + - - +
131A SER* 3.1 24.9 + - - +
133A ILE* 3.8 32.8 - - + -
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Residues in contact with HIS 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 LYS* 3.3 23.1 + - - +
126A LYS* 3.3 20.5 + - - +
127A GLN 4.0 5.4 - - - +
128A LEU* 1.3 81.6 - - - +
130A PRO* 1.3 91.2 - - + +
131A SER 3.7 2.2 - - - +
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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