Contacts of the helix formed by residues 117 - 130 (chain A) in PDB entry 2JIF
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLU* 4.6 3.2 + - - -
61A GLU* 2.6 26.6 + - - +
106A GLU* 3.7 6.8 - - - +
116A ALA* 1.3 80.8 - - - +
118A PHE* 1.3 64.6 + - - +
119A LEU 3.5 0.7 + - - -
120A SER* 3.2 31.4 + - - -
121A THR* 3.5 3.8 + - - -
358A GLU* 3.2 13.9 - - - -
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Residues in contact with PHE 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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106A GLU* 3.6 33.1 + - - +
117A SER* 1.3 74.2 - - - +
119A LEU* 1.3 62.4 + - - +
121A THR* 3.0 14.5 + - + -
122A VAL* 3.1 30.6 + - + -
144A THR* 4.6 15.5 - - + -
292A GLU* 3.8 42.6 - - + -
295A ILE* 3.9 20.2 - - + -
296A GLY 5.0 1.6 - - - -
354A ALA* 3.8 26.2 - - + -
357A LEU* 3.9 26.2 - - + -
358A GLU* 3.1 14.9 + - + +
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Residues in contact with LEU 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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57A PHE* 4.1 7.0 - - + -
61A GLU* 3.6 27.1 - - - +
118A PHE* 1.3 76.8 - - - +
120A SER* 1.3 51.3 + - - +
122A VAL* 3.2 10.6 + - + +
123A LEU* 2.8 48.7 + - + +
351A TYR* 4.1 29.4 - - + +
354A ALA* 3.8 24.2 - - + -
355A ARG* 3.6 40.6 - - + +
358A GLU* 2.9 21.1 + - - +
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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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60A GLU* 4.8 1.4 - - - +
61A GLU* 3.2 20.9 + - - +
64A ILE* 3.7 24.2 - - - +
105A ILE* 4.1 3.6 - - - -
116A ALA* 3.8 18.1 - - - +
117A SER* 3.2 26.7 + - - -
119A LEU* 1.3 74.0 - - - +
121A THR* 1.3 58.5 + - - +
123A LEU* 3.2 7.5 + - - +
124A VAL* 2.8 35.2 + - - +
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Residues in contact with THR 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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105A ILE* 3.4 31.9 - - + +
106A GLU* 2.9 26.1 + - - +
117A SER 3.5 0.6 + - - -
118A PHE* 3.0 13.5 + - + -
120A SER* 1.3 76.3 - - - +
122A VAL* 1.3 65.2 + - + +
124A VAL* 3.2 2.1 + - - +
125A ILE* 2.9 34.8 + - + +
143A ASN* 3.9 16.9 + - + -
144A THR* 3.7 29.8 - - + -
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Residues in contact with VAL 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 PHE* 3.1 39.3 + - + +
119A LEU* 3.2 22.6 + - + +
121A THR* 1.3 76.7 - - + +
123A LEU* 1.3 57.9 + - - +
125A ILE* 3.3 3.3 + - - -
126A GLU* 3.0 25.5 + - - +
295A ILE* 3.8 20.0 - - + +
296A GLY* 5.1 1.8 - - - +
299A ALA* 3.5 24.2 - - + +
350A THR* 3.9 16.6 - - + -
351A TYR* 4.3 11.7 - - + -
354A ALA* 4.1 5.8 - - + -
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Residues in contact with LEU 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 PHE* 3.7 42.4 - - + -
61A GLU* 4.0 29.8 - - + +
64A ILE* 6.2 0.4 - - + -
65A LYS* 4.7 22.5 - - + +
119A LEU* 2.8 29.3 + - + +
120A SER* 3.7 5.6 - - - +
122A VAL* 1.3 69.8 - - - +
124A VAL* 1.3 61.2 + - + +
126A GLU* 3.8 7.8 - - - +
127A GLU* 2.9 32.9 + - - +
351A TYR* 3.5 35.4 - - + +
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Residues in contact with VAL 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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64A ILE* 3.4 30.1 - - + +
65A LYS* 6.1 0.2 - - - +
68A VAL* 3.6 18.3 - - + +
102A LEU* 3.9 19.3 - - + -
105A ILE* 3.8 16.4 - - + -
120A SER 2.8 21.2 + - - +
121A THR 3.2 4.5 + - - +
123A LEU* 1.3 77.2 - - + +
125A ILE* 1.3 57.3 + - - +
127A GLU* 3.8 2.5 - - - +
128A LEU* 3.0 37.9 + - + +
139A CYS* 3.8 25.8 - - - -
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Residues in contact with ILE 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 THR* 2.9 38.7 + - + +
122A VAL* 3.7 5.8 - - - +
124A VAL* 1.3 77.4 - - - +
126A GLU* 1.3 61.4 + - - +
128A LEU* 3.4 4.7 + - - -
129A ALA* 3.0 23.4 + - - +
136A ALA* 3.6 15.6 - - + +
139A CYS* 4.7 7.4 - - - -
140A GLU* 3.5 42.6 - - + +
144A THR* 4.0 1.8 - - + -
296A GLY* 3.4 31.9 - - - +
299A ALA* 4.1 1.3 - - + -
300A GLN* 3.6 20.0 - - + +
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Residues in contact with GLU 126 (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 LYS* 5.5 3.8 - - - -
122A VAL* 3.0 15.9 + - + +
123A LEU* 3.8 11.2 - - - +
125A ILE* 1.3 76.7 - - - +
127A GLU* 1.3 66.0 + - - +
129A ALA 3.3 0.3 + - - -
130A LYS* 3.1 35.4 + - - +
299A ALA* 3.4 18.8 + - + +
302A LEU* 3.7 9.9 - - + -
303A GLY* 3.4 26.9 - - - +
347A ARG* 2.9 36.0 + - - -
351A TYR* 2.5 31.6 + - - -
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Residues in contact with GLU 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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65A LYS* 3.4 32.2 - - + +
68A VAL* 3.9 9.4 - - + -
69A LYS* 3.3 54.1 - - - +
72A ALA* 4.5 2.4 - - - +
123A LEU 2.9 18.3 + - - +
124A VAL 3.8 3.1 - - - +
126A GLU* 1.3 79.6 - - - +
128A LEU* 1.3 61.3 + - - +
130A LYS* 3.3 50.0 + - - +
131A VAL* 4.0 8.5 + - - +
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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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68A VAL* 3.8 18.4 - - + -
71A PHE* 4.3 11.7 - - + -
72A ALA* 4.4 5.6 - - + +
76A ILE* 3.5 31.8 - - + +
97A LEU* 4.0 11.7 - - + -
102A LEU* 4.8 0.4 - - + -
124A VAL* 3.0 26.1 + - + +
125A ILE* 3.8 3.4 - - - +
127A GLU* 1.3 77.2 - - - +
129A ALA* 1.3 51.3 + - - +
131A VAL* 3.0 8.8 + - - +
132A ASP* 2.8 33.7 + - - +
135A VAL* 4.2 10.6 - - + +
136A ALA* 4.0 11.9 - - + +
139A CYS* 3.6 37.5 - - + -
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Residues in contact with ALA 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 ILE 3.0 17.8 + - - +
126A GLU 3.8 2.9 - - - +
128A LEU* 1.3 71.9 - - - +
130A LYS* 1.3 64.2 + - - +
131A VAL 3.0 3.4 + - - -
132A ASP 3.6 11.3 + - - -
133A ALA* 3.9 6.8 + - - -
136A ALA* 3.5 18.6 - - + +
300A GLN* 3.3 34.3 - - + +
304A LEU* 3.3 21.9 - - + +
403A TYR* 4.0 2.9 - - - -
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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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65A LYS* 4.5 11.3 - - - +
126A GLU* 3.1 39.0 + - - +
127A GLU* 3.3 45.6 + - - +
129A ALA* 1.3 76.4 - - - +
131A VAL* 1.3 58.6 + - + +
303A GLY 3.1 22.9 + - - +
306A GLN* 4.1 19.9 - - + +
307A GLY* 3.7 15.4 - - - +
310A ASP* 4.8 8.4 + - - +
347A ARG* 5.2 0.8 - - - +
403A TYR* 2.7 27.5 + - - -
1435A EDO 4.4 0.7 + - - -
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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