Contacts of the helix formed by residues 96 - 110 (chain N) in PDB entry 1FQV
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 96 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95N VAL* 1.3 77.2 - - - +
97N GLN* 1.3 65.1 + - - +
98N GLY* 3.0 6.5 + - - +
99N THR* 2.6 40.7 + - - -
100N LEU* 3.1 8.3 + - - +
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Residues in contact with GLN 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M TRP* 3.1 26.1 + - + +
95N VAL 3.8 0.4 + - - -
96N ASP* 1.3 72.5 - - - +
98N GLY* 1.3 63.3 + - - +
100N LEU* 3.8 6.9 - - + +
101N PHE* 2.9 18.9 + - - +
126N MET* 5.3 11.4 - - + +
138N THR* 2.8 49.2 + - - +
139N PHE* 3.1 27.2 - - + -
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Residues in contact with GLY 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M VAL* 5.7 11.2 - - - -
96N ASP* 3.0 8.9 + - - +
97N GLN* 1.3 78.2 - - - +
99N THR* 1.3 56.7 + - - +
101N PHE* 2.9 9.7 + - - +
102N GLU* 2.8 36.6 + - - +
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Residues in contact with THR 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N ILE* 3.9 17.8 - - + +
57N LYS* 5.3 7.4 - - + -
95N VAL* 3.5 29.0 - - + +
96N ASP* 2.6 28.8 + - - -
98N GLY* 1.3 71.4 - - - -
100N LEU* 1.3 57.6 + - - +
102N GLU* 3.1 10.2 + - - +
103N LEU* 2.8 37.6 + - + +
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Residues in contact with LEU 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M TRP* 4.1 5.6 - - + -
93N LEU* 4.5 16.8 - - + +
95N VAL* 3.7 11.1 - - + +
96N ASP 3.1 9.2 + - - +
97N GLN* 3.8 9.4 - - - +
99N THR* 1.3 78.8 - - - +
101N PHE* 1.3 58.5 + - - +
103N LEU* 3.2 3.9 + - - +
104N ILE* 2.9 35.2 + - + +
119N THR* 4.2 34.1 - - + +
122N THR* 3.9 15.0 - - + -
123N VAL* 3.7 26.2 - - + -
126N MET* 3.4 33.9 - - + -
139N PHE* 5.8 0.2 - - + -
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Residues in contact with PHE 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M VAL* 5.1 12.1 - - + -
108M SER 3.6 5.6 - - - -
109M TRP* 3.2 71.3 - + + +
111M SER* 3.6 19.7 - - - -
112M LEU* 4.2 19.9 - - + +
97N GLN 2.9 15.1 + - - +
98N GLY* 3.2 11.2 - - - +
100N LEU* 1.3 74.1 - - - +
102N GLU* 1.3 76.1 + - - +
104N ILE* 3.6 2.6 + - - +
105N LEU* 3.2 47.7 + - + +
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Residues in contact with GLU 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N ASN* 5.9 0.2 - - - +
54N ILE* 3.4 27.2 - - + +
98N GLY* 2.8 23.4 + - - +
99N THR* 3.3 9.2 - - - +
101N PHE* 1.3 86.6 - - - +
103N LEU* 1.3 56.7 + - - +
105N LEU* 3.3 17.1 + - - +
106N ALA* 2.8 29.1 + - - +
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Residues in contact with LEU 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N ILE* 3.6 23.1 - - + +
57N LYS* 3.9 27.4 - - + -
58N VAL* 4.3 10.8 - - + +
92N PHE* 4.7 8.5 - - + -
93N LEU* 3.9 26.9 - - + -
95N VAL* 4.8 3.8 - - + -
99N THR* 2.8 33.8 + - + +
100N LEU* 3.2 10.5 + - - +
102N GLU* 1.3 74.2 - - - +
104N ILE* 1.3 62.2 + - - +
105N LEU 3.0 1.6 - - - -
106N ALA* 3.1 2.3 + - - +
107N ALA* 2.7 34.6 + - - +
115N LEU* 4.1 7.9 - - + +
119N THR* 4.2 11.4 - - + -
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Residues in contact with ILE 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M TRP* 3.6 18.2 - - + -
112M LEU* 5.1 7.0 - - + -
116M LEU* 4.7 19.1 - - + -
120M ILE* 4.4 9.9 - - + -
100N LEU* 2.9 14.3 + - + +
101N PHE 4.1 4.3 - - - +
102N GLU 3.5 0.2 - - - -
103N LEU* 1.3 75.6 - - - +
105N LEU* 1.3 57.6 + - - +
107N ALA* 3.7 3.1 - - - +
108N ASN* 2.9 30.2 + - - +
116N LEU* 4.1 20.1 - - + +
119N THR* 3.4 30.3 - - - +
120N CYS* 4.1 7.9 - - - +
123N VAL* 3.4 33.4 - - + -
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Residues in contact with LEU 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112M LEU* 3.6 26.9 - - + -
113M PRO* 4.3 8.3 - - + -
116M LEU* 3.9 10.8 - - + -
49N ASN 6.0 1.3 - - - +
101N PHE* 3.2 41.6 + - + +
102N GLU* 3.3 18.6 + - - +
103N LEU 3.0 0.6 - - - -
104N ILE* 1.3 74.8 - - - +
106N ALA* 1.3 56.7 + - - +
108N ASN* 3.0 5.3 + - - +
109N TYR* 2.6 39.2 + - - +
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Residues in contact with ALA 106 (chain N).
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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49N ASN 5.3 2.5 - - - -
50N VAL* 4.2 18.6 - - + -
54N ILE* 3.5 25.1 - - + -
58N VAL* 4.1 13.0 - - + -
102N GLU 2.8 18.5 + - - +
103N LEU* 3.5 3.4 - - - +
105N LEU* 1.3 75.6 - - - +
107N ALA* 1.3 55.6 + - - +
109N TYR* 4.3 5.4 - - - -
110N LEU* 2.7 40.8 + - + +
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Residues in contact with ALA 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N VAL* 5.2 1.1 - - - +
103N LEU 2.7 15.5 + - - +
104N ILE* 3.7 6.1 - - - +
106N ALA* 1.3 73.3 - - - +
108N ASN* 1.3 56.6 + - - +
110N LEU 3.7 0.2 - - - -
111N ASP* 2.9 6.4 + - - -
112N ILE* 2.9 39.2 + - - +
115N LEU* 3.1 36.2 - - + +
116N LEU* 3.8 24.8 - - - +
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Residues in contact with ASN 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M PRO* 5.4 3.4 - - - +
115M GLU* 6.3 0.2 - - - +
116M LEU* 3.0 44.6 - - + +
104N ILE 2.9 19.7 + - - +
105N LEU* 3.0 5.6 + - - +
107N ALA* 1.3 74.2 - - - +
109N TYR* 1.3 63.6 + - - +
111N ASP* 2.8 22.5 + - - +
116N LEU* 3.8 18.2 - - + +
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Residues in contact with TYR 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N THR* 2.4 41.2 + - + -
30N MET* 4.1 15.2 - - + +
47N LEU* 3.9 9.7 - - + +
48N PRO* 3.7 23.4 - - - +
49N ASN* 3.2 46.4 + - + +
50N VAL* 3.3 31.2 - - + -
105N LEU* 2.6 21.7 + - + +
106N ALA* 3.5 2.5 - - - +
108N ASN* 1.3 76.6 - - - +
110N LEU* 1.3 65.7 + - + +
111N ASP* 3.1 2.6 + - - +
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Residues in contact with LEU 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N SER* 2.5 30.6 + - - +
25N VAL 3.1 8.1 + - - -
26N THR* 3.1 9.5 + - + -
27N ILE* 3.8 19.5 - - + -
47N LEU* 3.8 22.4 - - + -
50N VAL* 4.1 14.6 - - + -
55N LEU* 5.1 5.4 - - + -
58N VAL* 3.7 35.7 - - + -
106N ALA 2.7 21.1 + - - +
109N TYR* 1.3 97.1 - - + +
111N ASP* 1.3 67.7 + - - +
112N ILE* 4.0 8.3 - - + -
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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