Contacts of the helix formed by residues 107 - 120 (chain A) in PDB entry 5J1T
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 GLY 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A LEU* 4.6 2.2 - - - -
105A GLY 3.7 0.2 - - - -
106A THR* 1.3 79.6 - - - +
108A LYS* 1.4 58.9 + - - +
110A PHE* 3.7 6.1 - - - -
111A VAL* 2.8 35.5 + - - +
269A PHE* 3.5 7.6 - - - -
401A ATP 3.1 35.2 + - - -
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Residues in contact with LYS 108 (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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100A LEU* 3.6 19.6 - - + +
101A HIS 4.0 0.7 - - - +
102A GLY 3.1 17.3 + - - +
103A TRP 3.0 19.6 + - - -
107A GLY* 1.4 73.8 - - - +
109A ASN* 1.3 64.9 + - - +
111A VAL* 3.8 2.3 - - - +
112A SER* 2.9 28.0 + - - -
206A LEU* 4.2 19.3 - - + -
207A SER* 3.3 34.5 - - - +
269A PHE* 3.7 30.1 - - + -
401A ATP 2.7 55.2 + - - +
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Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LYS* 1.3 77.5 - - - +
110A PHE* 1.3 63.4 + - - +
112A SER* 3.2 5.2 + - - -
113A LYS* 3.0 33.3 + - - +
124A LEU* 5.5 3.3 - - - +
131A LEU* 4.9 10.5 - - - +
168A ILE* 5.8 0.2 - - - +
170A ASP* 3.1 25.8 + - - +
206A LEU* 3.5 17.7 - - - +
401A ATP 2.9 21.5 + - - +
402A MG 2.0 32.1 - - - -
385B GLU* 3.8 21.7 + - - +
386B ASN* 5.0 4.8 - - - +
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Residues in contact with PHE 110 (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 ASN* 3.3 38.6 - - + -
69A LEU* 3.8 20.0 - - + -
107A GLY* 3.5 7.6 - - - +
109A ASN* 1.3 80.2 - - - +
111A VAL* 1.3 59.9 + - - +
113A LYS* 3.3 18.5 + - + +
114A ILE* 3.2 40.5 + - + +
401A ATP 2.9 69.6 + + - +
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Residues in contact with VAL 111 (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 LEU* 4.9 7.4 - - + -
69A LEU* 3.5 39.3 - - + -
75A ALA* 5.5 0.7 - - + -
79A ILE* 4.2 18.8 - - + -
100A LEU* 4.1 12.8 - - + -
107A GLY 2.8 23.9 + - - +
108A LYS 3.8 2.9 - - - +
110A PHE* 1.3 70.4 - - - +
112A SER* 1.3 61.1 + - - +
114A ILE* 3.0 11.6 + - + +
115A ILE* 2.9 48.0 + - + +
269A PHE* 3.9 13.7 - - + -
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Residues in contact with SER 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 4.1 2.1 - - - +
108A LYS 2.9 14.7 + - - -
109A ASN* 3.2 12.5 + - - -
111A VAL* 1.3 74.7 - - - +
113A LYS* 1.3 57.7 + - - +
115A ILE* 3.4 12.4 + - - +
116A ALA* 3.0 28.9 + - - +
124A LEU* 4.4 5.2 - - - +
168A ILE* 4.4 23.0 - - - +
204A ILE* 4.0 10.8 - - - +
206A LEU* 3.4 24.1 - - - +
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Residues in contact with LYS 113 (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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109A ASN* 3.0 29.0 + - - +
110A PHE* 3.5 15.9 - - + +
112A SER* 1.3 73.9 - - - +
114A ILE* 1.3 61.3 + - + +
116A ALA* 3.3 1.1 + - - +
117A GLU* 2.8 50.0 + - + +
124A LEU* 3.4 41.3 - - + -
401A ATP 4.4 11.9 + - - -
385B GLU* 2.7 38.2 + - - -
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Residues in contact with ILE 114 (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 LEU* 4.0 8.7 - - + -
64A ASP* 3.6 40.6 - - + +
65A LEU* 4.0 30.3 - - + -
68A ASN* 4.6 3.8 - - + -
69A LEU* 4.8 4.5 - - + -
110A PHE* 3.2 41.0 + - + +
111A VAL* 3.0 11.7 + - - +
113A LYS* 1.3 76.1 - - + +
115A ILE* 1.3 64.2 + - + +
117A GLU* 3.4 13.1 + - - +
118A ASN* 2.9 35.1 + - - +
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Residues in contact with ILE 115 (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 LEU* 4.8 6.1 - - + -
65A LEU* 6.1 0.2 - - + -
79A ILE* 3.8 34.8 - - + -
83A VAL* 4.2 16.8 - - + -
98A LEU* 4.4 3.4 - - + -
100A LEU* 5.2 3.1 - - + -
111A VAL* 2.9 35.0 + - + +
112A SER* 3.6 8.3 - - - +
114A ILE* 1.3 78.8 - - + +
116A ALA* 1.3 64.1 + - - +
118A ASN* 3.1 13.4 + - - +
119A ILE* 3.2 33.4 + - + +
166A ILE* 5.2 1.8 - - + -
202A MET* 4.2 17.3 - - - -
204A ILE* 4.3 20.0 - - + -
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Residues in contact with ALA 116 (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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112A SER 3.0 17.6 + - - +
113A LYS 3.7 2.9 - - - +
115A ILE* 1.3 78.6 - - - +
117A GLU* 1.3 59.2 + - - +
119A ILE* 3.2 1.7 + - - +
120A TYR* 2.9 33.6 + - - +
123A GLY* 3.7 24.9 - - - +
124A LEU* 3.9 13.7 - - + +
129A VAL* 4.2 16.2 - - + -
166A ILE* 4.8 8.5 - - + -
168A ILE* 5.3 1.6 - - + -
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Residues in contact with GLU 117 (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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54A ARG 4.7 4.9 + - - -
64A ASP* 4.0 10.8 - - - +
113A LYS* 2.8 43.9 + - + +
114A ILE* 3.8 16.1 - - - +
116A ALA* 1.3 71.5 - - - +
118A ASN* 1.3 64.8 + - - +
119A ILE 3.5 0.3 + - - -
120A TYR 3.6 12.4 + - - +
121A GLU* 5.2 0.7 - - - -
122A GLY 5.5 0.2 - - - -
123A GLY* 3.7 19.9 - - - +
124A LEU 5.4 0.2 - - - +
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Residues in contact with ASN 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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54A ARG 4.4 4.5 + - - -
55A SER 4.4 1.9 - - - -
56A LEU* 3.5 39.6 + - + +
60A ALA* 3.7 12.0 - - - +
61A LEU* 3.5 35.1 + - + +
64A ASP* 2.9 27.4 + - - +
114A ILE* 2.9 34.6 + - - +
115A ILE 3.1 4.0 + - - +
117A GLU* 1.3 79.6 - - - +
119A ILE* 1.3 60.4 + - - +
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Residues in contact with ILE 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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54A ARG* 3.7 21.9 - - - +
56A LEU* 4.5 16.9 + - + -
83A VAL* 4.1 4.5 - - + -
87A ILE* 4.0 28.5 - - + -
115A ILE* 3.2 24.2 + - + +
116A ALA 3.2 3.8 + - - +
118A ASN* 1.3 82.1 - - + +
120A TYR* 1.3 91.7 + - + +
164A ARG* 5.7 1.1 - - + +
166A ILE* 3.7 20.6 - - + -
202A MET* 3.8 20.9 - - + -
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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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54A ARG* 4.5 2.5 - - - +
116A ALA 2.9 13.8 + - - +
117A GLU* 3.6 10.6 - - - +
119A ILE* 1.3 107.6 - - + +
121A GLU* 1.3 66.2 + - - +
122A GLY 3.3 0.2 + - - -
123A GLY 3.0 15.1 + - - -
126A SER* 3.4 27.4 - - - +
128A TYR* 3.7 27.4 - + + -
129A VAL* 3.7 19.5 - - + -
162A CYS* 3.8 8.2 - - - -
164A ARG* 2.7 44.6 + - - +
166A ILE* 4.0 10.8 - - + -
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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