Contacts of the helix formed by residues 96 - 111 (chain A) in PDB entry 3FRR
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 LEU 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LEU* 4.0 23.3 - - + -
79A LEU* 4.0 28.0 - - + -
82A ARG* 4.0 25.6 - - + +
85A LEU* 4.0 27.8 - - + -
86A ILE* 4.1 12.6 - - + -
92A LEU* 4.5 3.6 - - + -
93A ASP* 2.9 22.4 + - + +
95A GLY* 1.3 82.5 - - - +
97A ALA* 1.3 60.9 + - - +
98A GLU 3.2 2.7 - - - -
99A SER* 3.1 5.9 + - - +
100A VAL* 2.8 36.2 + - + +
128A TYR* 5.6 1.1 - - - +
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Residues in contact with ALA 97 (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 LEU* 3.8 26.9 - - + -
93A ASP 3.2 6.4 + - - +
94A SER* 3.5 18.2 + - - +
96A LEU* 1.3 76.3 - - - +
98A GLU* 1.3 57.8 + - - +
100A VAL 4.7 0.2 - - - +
101A SER* 2.9 36.1 + - - -
132A TYR* 4.9 0.9 - - - +
143A THR* 4.4 18.8 - - + +
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Residues in contact with GLU 98 (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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75A TYR* 3.3 28.7 + - + +
94A SER 4.8 1.0 + - - -
95A GLY 4.9 4.8 + - - +
96A LEU 3.2 0.6 - - - -
97A ALA* 1.3 77.1 - - - +
99A SER* 1.3 58.2 + - - +
101A SER* 4.1 0.2 - - - -
102A THR* 2.7 41.7 + - - +
143A THR* 3.7 22.6 - - - +
145A ASN* 2.8 26.9 + - + +
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Residues in contact with SER 99 (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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75A TYR* 3.3 37.9 - - - +
78A LEU* 3.2 27.9 - - - +
79A LEU* 4.0 19.5 - - - -
95A GLY 5.1 0.5 + - - -
96A LEU* 3.1 9.9 + - - +
98A GLU* 1.3 80.2 - - - +
100A VAL* 1.3 62.8 + - - +
102A THR* 3.9 1.0 - - - -
103A LEU* 3.0 32.0 + - - +
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Residues in contact with VAL 100 (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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79A LEU* 4.0 24.9 - - + -
86A ILE* 5.2 2.2 - - + -
92A LEU* 3.7 20.0 - - + -
96A LEU* 2.8 25.2 + - + +
97A ALA 4.1 1.3 - - - +
99A SER* 1.3 71.8 - - - +
101A SER* 1.3 63.1 + - - +
103A LEU* 3.3 3.1 + - - +
104A ILE* 3.1 41.2 + - + +
124A LEU* 4.1 19.6 - - + +
128A TYR* 4.1 17.9 - - + +
132A TYR* 3.9 16.6 - - + +
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Residues in contact with SER 101 (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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97A ALA 2.9 19.5 + - - -
98A GLU 4.1 1.3 - - - -
100A VAL* 1.3 73.2 - - - +
102A THR* 1.3 57.4 + - - +
104A ILE* 3.3 3.3 + - - +
105A TRP* 2.9 29.6 + - - +
132A TYR* 2.5 23.7 + - - -
136A CYS* 3.5 23.1 - - - +
141A ILE* 4.0 1.1 - - - +
143A THR* 2.8 25.7 + - - -
144A VAL* 3.7 15.6 - - - +
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Residues in contact with THR 102 (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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72A LEU* 4.1 1.1 - - + -
75A TYR* 3.5 17.8 - - + -
98A GLU 2.7 25.7 + - - -
101A SER* 1.3 74.9 - - - +
103A LEU* 1.3 58.9 + - - +
105A TRP* 3.7 0.9 - - - +
106A ALA* 2.8 29.2 + - - +
144A VAL* 3.6 12.6 - - + +
145A ASN* 2.9 28.1 + - - +
148A LEU* 3.0 46.4 - - + -
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Residues in contact with LEU 103 (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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15A LEU* 4.2 7.2 - - + -
72A LEU* 3.8 27.6 - - + +
75A TYR* 4.2 7.0 - - + -
76A CYS* 3.8 38.4 - - - +
79A LEU* 3.6 31.4 - - + -
99A SER 3.0 19.3 + - - +
100A VAL 3.8 3.6 - - - +
102A THR* 1.3 77.3 - - - +
104A ILE* 1.3 55.4 + - - +
106A ALA* 3.9 1.8 - - - +
107A ALA* 3.0 30.7 + - - +
117A LEU* 3.9 22.0 - - + +
120A VAL* 4.4 5.2 - - + -
121A ALA* 4.2 2.5 - - - +
124A LEU* 4.2 8.7 - - + -
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Residues in contact with ILE 104 (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 VAL* 3.1 24.1 + - + +
101A SER 3.7 5.8 - - - +
103A LEU* 1.3 73.3 - - - +
105A TRP* 1.3 66.1 + - - +
107A ALA* 3.8 1.7 - - - +
108A PRO* 3.3 19.8 - - - +
121A ALA* 3.9 13.5 - - + +
124A LEU* 3.9 24.2 - - + -
125A CYS* 3.9 26.2 - - - -
132A TYR* 3.8 29.4 - - + -
133A GLY* 3.6 14.4 - - - +
136A CYS* 3.6 20.4 - - + -
137A ARG* 3.7 12.7 - - + +
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Residues in contact with TRP 105 (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 SER 2.9 14.1 + - - +
102A THR 3.7 2.5 - - - +
104A ILE* 1.3 79.3 - - - +
106A ALA* 1.3 65.8 + - - +
107A ALA 3.4 0.3 + - - -
108A PRO* 3.5 3.5 - - - +
109A ARG* 2.9 70.9 + - + +
136A CYS 3.2 26.4 + - - +
137A ARG* 3.2 18.9 + - - +
138A THR 4.5 2.2 - - - -
139A ASN* 3.9 15.3 - - + +
144A VAL* 3.7 11.4 - - + -
148A LEU* 3.6 30.7 - - + -
149A MET* 3.5 43.9 - - + -
152A LEU* 3.9 23.6 - - + -
153A SER* 6.1 0.2 - - - -
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Residues in contact with ALA 106 (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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72A LEU* 3.8 34.8 - - + -
102A THR 2.8 21.7 + - - +
103A LEU* 3.9 3.4 - - - +
105A TRP* 1.3 86.7 - - + +
107A ALA* 1.3 68.6 + - - +
108A PRO 3.5 0.2 - - - -
109A ARG* 3.0 16.1 + - - +
110A LEU* 3.0 13.2 + - + +
117A LEU* 4.3 3.8 - - + -
148A LEU* 4.4 4.9 - - + -
152A LEU* 4.5 4.3 - - + -
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Residues in contact with ALA 107 (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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103A LEU 3.0 9.4 + - - +
104A ILE 3.8 0.4 - - - +
105A TRP 3.3 0.2 - - - -
106A ALA* 1.3 75.5 - - - +
108A PRO* 1.4 65.7 - - + +
110A LEU 3.1 0.9 + - - -
111A GLN* 2.7 40.3 + - - +
117A LEU* 3.5 28.0 - - + +
118A LYS* 4.3 4.9 - - - -
121A ALA* 3.4 32.8 - - + -
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Residues in contact with PRO 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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104A ILE 3.3 10.8 - - - +
105A TRP 3.5 13.2 - - - +
107A ALA* 1.4 92.8 - - + +
109A ARG* 1.3 74.4 + - + +
110A LEU 3.4 0.3 + - - -
111A GLN* 3.7 27.8 + - - +
112A SER* 4.9 1.0 + - - -
121A ALA* 5.6 0.2 - - + -
137A ARG* 3.9 24.2 - - + +
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Residues in contact with ARG 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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105A TRP* 2.9 75.5 + - + +
106A ALA 3.0 7.7 + - - +
108A PRO* 1.3 93.7 - - + +
110A LEU* 1.3 71.7 + - + +
112A SER* 5.0 4.9 + - - -
137A ARG* 3.0 25.3 + - - +
138A THR* 5.3 1.0 - - - +
152A LEU* 4.5 17.7 - - + +
154A VAL* 6.3 2.7 - - + -
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Residues in contact with LEU 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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22A LEU* 4.7 4.5 - - + -
65A LEU* 3.6 34.1 - - + -
68A ALA* 5.5 0.2 - - + -
69A MET* 4.2 19.3 - - + +
72A LEU* 3.5 28.9 - - + -
106A ALA 3.0 14.9 + - - +
109A ARG* 1.3 84.4 - - + +
111A GLN* 1.3 60.3 + - - +
112A SER* 3.1 4.5 - - - -
113A GLU* 2.9 24.9 + - + +
114A VAL* 2.9 15.3 + - + -
117A LEU* 4.1 12.1 - - + -
152A LEU* 3.9 22.2 - - + -
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Residues in contact with GLN 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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107A ALA* 2.7 21.6 + - - +
108A PRO* 3.7 27.2 - - - +
109A ARG 3.8 0.6 - - - -
110A LEU* 1.3 71.8 - - - +
112A SER* 1.3 65.8 + - - +
113A GLU 3.2 0.9 + - - -
114A VAL 3.5 12.3 - - - +
115A ALA* 3.4 23.0 + - - +
117A LEU* 5.2 0.7 - - - -
118A LYS* 3.8 49.4 - - + +
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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