Contacts of the helix formed by residues 107 - 116 (chain A) in PDB entry 5JRE
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A TYR* 2.7 33.9 + - - -
101A LYS* 4.4 1.6 - - - +
106A VAL* 1.3 77.9 - - - +
108A THR* 1.3 64.2 + - - +
109A TRP* 2.9 9.7 + - - +
110A VAL* 2.7 35.6 + - - +
111A TYR* 3.1 19.5 + - - +
70B PRO* 5.6 0.5 - - - +
71B MET* 3.6 20.9 - - + +
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Residues in contact with THR 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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101A LYS* 3.1 32.1 + - - +
107A ASP* 1.3 74.6 - - - +
109A TRP* 1.3 56.2 + - - +
111A TYR* 3.5 3.2 - - - +
112A LEU* 3.1 39.6 + - + +
8B LEU* 3.8 22.9 - - + -
11B GLU* 3.9 10.8 - - + +
12B TYR* 4.1 25.6 - - + +
15B LEU* 3.8 15.8 - - + +
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Residues in contact with TRP 109 (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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73A TYR* 4.3 0.9 - + - +
77A PHE* 3.7 27.0 - + - -
107A ASP* 2.9 9.3 + - - +
108A THR* 1.3 75.5 - - - +
110A VAL* 1.3 65.7 + - - +
111A TYR 3.3 0.2 + - - -
112A LEU* 3.3 5.1 + - + +
113A PHE* 3.2 48.4 + + - -
159A ASN* 3.9 24.7 - - + -
162A LEU* 5.0 1.8 - - + -
12B TYR* 3.7 27.1 - + - -
15B LEU* 4.0 22.4 - - + +
16B GLU* 3.5 27.4 - - - -
19B LYS* 4.8 6.5 - - + -
71B MET* 4.0 31.3 + - + +
72B PHE* 3.8 31.6 - + - -
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Residues in contact with VAL 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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73A TYR* 3.6 10.5 - - + +
77A PHE* 3.3 37.2 - - + +
80A LEU* 4.1 34.1 - - + +
81A GLN* 4.5 4.2 - - - +
84A VAL* 3.9 12.3 - - + +
106A VAL* 3.6 30.5 - - + -
107A ASP* 2.7 20.0 + - - +
109A TRP* 1.3 73.5 - - - +
111A TYR* 1.3 58.4 + - - +
113A PHE* 3.5 2.6 + - - +
114A GLY* 3.0 26.7 + - - -
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Residues in contact with TYR 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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84A VAL* 3.9 13.0 - - + +
98A ILE* 3.9 7.6 - - - +
99A PRO 2.7 29.6 + - - -
100A SER* 3.7 2.9 - - - -
101A LYS* 3.5 35.4 - - + -
104A LEU* 4.3 9.2 - - + -
106A VAL* 4.0 4.7 - - + -
107A ASP 3.1 18.0 + - - +
108A THR 3.5 4.9 - - - +
109A TRP 3.2 0.2 - - - -
110A VAL* 1.3 81.1 - - - +
112A LEU* 1.3 62.9 + - + +
114A GLY* 3.3 1.2 + - - -
115A ILE* 2.8 57.2 + - + +
2B LEU* 4.1 5.6 - - + +
3B PRO* 3.9 16.8 + - - +
8B LEU* 4.0 38.8 - - + -
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Residues in contact with LEU 112 (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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108A THR* 3.1 28.4 + - + +
109A TRP* 3.3 4.4 + - - +
111A TYR* 1.3 79.4 - - + +
113A PHE* 1.3 60.1 - - - +
115A ILE* 3.8 4.1 - - + +
116A GLY* 2.9 27.0 + - - -
152A LEU* 4.6 14.6 - - + +
155A ILE* 4.0 24.5 - - + -
157A LEU* 4.6 7.2 - - + -
162A LEU* 3.9 21.2 - - + +
2B LEU* 4.9 2.0 - - + -
8B LEU* 4.0 16.4 - - + -
12B TYR* 3.4 46.2 - - + -
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Residues in contact with PHE 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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77A PHE* 3.7 29.8 - + + -
81A GLN* 3.5 15.1 + - - -
109A TRP* 3.2 55.2 + + - +
110A VAL 3.8 3.6 - - - +
112A LEU* 1.3 78.7 - - - +
114A GLY* 1.3 60.9 + - - +
116A GLY 3.5 5.4 + - - -
117A ASP* 3.4 18.7 - - - +
159A ASN* 3.6 23.3 - - - -
161A ASP* 3.8 27.1 - - + -
162A LEU* 3.6 25.4 - - + -
165A LYS* 3.7 21.3 - - - +
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Residues in contact with GLY 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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81A GLN* 3.6 28.0 - - - +
84A VAL* 4.0 10.8 - - - -
85A GLU* 3.8 5.3 - - - +
110A VAL 3.0 15.1 + - - -
111A TYR 3.7 2.2 - - - -
113A PHE* 1.3 74.5 - - - +
115A ILE* 1.3 63.6 + - - +
117A ASP* 3.1 19.2 + - - +
118A ILE* 3.7 9.2 + - - +
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Residues in contact with ILE 115 (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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84A VAL* 4.0 4.7 - - + +
88A ALA* 4.1 17.9 - - + -
98A ILE* 3.6 29.8 - - + -
99A PRO* 5.0 0.7 - - + +
111A TYR* 2.8 54.7 + - + +
112A LEU* 3.9 6.1 - - + +
114A GLY* 1.3 66.7 - - - +
116A GLY* 1.3 59.2 + - - +
117A ASP 3.0 9.9 + - - -
118A ILE* 3.2 25.5 + - + +
119A ALA 4.8 0.2 + - - -
148A LEU* 4.0 19.0 - - + +
152A LEU* 4.6 7.4 - - + -
2B LEU* 3.6 25.4 - - + -
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Residues in contact with GLY 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 LEU 2.9 18.0 + - - -
114A GLY 3.2 0.8 - - - -
115A ILE* 1.3 77.4 - - - +
117A ASP* 1.3 63.8 + - - +
118A ILE 3.7 0.2 - - - -
119A ALA 5.0 0.6 + - - -
152A LEU* 5.0 13.0 - - - +
162A LEU* 6.0 0.2 - - - -
165A LYS* 3.7 35.2 - - - +
168A TYR* 3.7 14.7 - - - -
169A VAL* 4.4 5.7 - - - +
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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