Contacts of the helix formed by residues 96 - 110 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D VAL* 1.3 76.8 - - - +
97D GLN* 1.3 66.9 + - - +
98D GLY* 3.0 6.1 + - - +
99D THR* 2.6 41.0 + - - -
100D LEU* 3.2 8.4 + - - +
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Residues in contact with GLN 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TRP* 3.3 17.0 + - + +
95D VAL 3.9 0.8 + - - -
96D ASP* 1.3 72.7 - - - +
98D GLY* 1.3 57.1 + - - +
100D LEU* 3.5 8.1 + - - +
101D PHE* 2.9 31.1 + - - +
126D MET* 5.6 9.4 - - + +
138D THR* 2.7 50.0 + - - +
139D PHE* 3.2 25.1 - - + -
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Residues in contact with GLY 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C VAL* 5.9 9.0 - - - -
96D ASP* 3.0 9.5 + - - -
97D GLN* 1.3 78.6 - - - +
99D THR* 1.3 56.6 + - - +
101D PHE* 3.2 7.7 + - - +
102D GLU* 2.9 36.5 + - - +
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Residues in contact with THR 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 3.8 18.6 - - + +
57D LYS* 5.0 8.7 - - + -
95D VAL* 3.4 29.3 - - + +
96D ASP* 2.6 30.8 + - - -
98D GLY* 1.3 72.0 - - - +
100D LEU* 1.3 51.9 + - - +
102D GLU* 2.9 9.8 + - - +
103D LEU* 2.7 43.8 + - + +
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TRP* 3.9 4.7 - - + -
93D LEU* 4.4 17.7 - - + +
95D VAL* 3.6 11.6 - - + +
96D ASP 3.2 9.1 + - - +
97D GLN* 3.7 11.4 - - - +
99D THR* 1.3 79.1 - - - +
101D PHE* 1.3 63.4 + - - +
103D LEU* 3.6 4.7 - - + +
104D ILE* 3.0 29.9 + - + +
119D THR* 4.2 27.6 - - + -
122D THR* 4.1 16.2 - - + -
123D VAL* 3.6 27.8 - - + -
126D MET* 3.4 34.1 - - + -
139D PHE* 5.7 0.2 - - + -
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Residues in contact with PHE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C VAL* 4.8 15.0 - - + -
108C SER 3.7 4.5 - - - -
109C TRP* 3.0 81.8 - + + +
111C SER* 3.8 18.2 - - - -
112C LEU* 4.3 16.9 - - + +
97D GLN 2.9 13.1 + - - +
98D GLY* 3.4 6.5 - - - +
99D THR 3.2 0.2 - - - -
100D LEU* 1.3 75.9 - - - +
102D GLU* 1.3 75.8 + - - +
104D ILE* 3.6 2.3 + - - +
105D LEU* 3.1 51.0 + - + +
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Residues in contact with GLU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C VAL* 5.9 2.6 - - - +
51D ASN* 5.7 0.7 - - - +
54D ILE* 3.3 29.1 - - + +
98D GLY* 2.9 27.4 + - - +
99D THR* 2.9 7.8 + - - +
101D PHE* 1.3 87.2 - - - +
103D LEU* 1.3 51.1 + - - +
105D LEU* 3.1 17.3 + - - +
106D ALA* 2.8 34.7 + - - +
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 3.5 27.6 - - + -
57D LYS* 3.8 26.7 - - + -
58D VAL* 4.1 13.5 - - + +
92D PHE* 4.4 9.2 - - + -
93D LEU* 3.7 29.4 - - + -
95D VAL* 5.1 2.5 - - + -
99D THR* 2.7 32.2 + - + +
100D LEU* 3.3 10.5 + - + +
102D GLU* 1.3 69.8 - - - +
104D ILE* 1.3 57.5 + - - +
106D ALA* 3.5 0.3 - - - +
107D ALA* 2.6 39.3 + - - +
115D LEU* 4.2 8.5 - - + +
119D THR* 4.3 10.8 - - + -
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TRP* 3.8 16.8 - - + -
112C LEU* 4.9 11.0 - - + -
116C LEU* 4.8 17.3 - - + -
120C ILE* 4.5 10.3 - - + -
100D LEU* 3.0 18.4 + - + +
101D PHE* 4.0 4.9 - - - +
103D LEU* 1.3 75.0 - - - +
105D LEU* 1.3 59.2 + - - +
107D ALA* 3.8 3.0 - - - +
108D ASN* 3.0 26.0 + - - +
116D LEU* 4.5 14.2 - - + +
119D THR* 3.3 36.3 - - - +
120D CYS* 4.4 6.5 - - - +
123D VAL* 3.5 31.4 - - + -
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C LEU* 3.6 28.7 - - + -
113C PRO* 4.6 6.3 - - + -
116C LEU* 4.1 9.9 - - + -
49D ASN 5.9 1.6 - - - +
101D PHE* 3.1 42.3 + - + +
102D GLU* 3.1 18.8 + - - +
103D LEU 3.0 0.6 - - - -
104D ILE* 1.3 76.2 - - - +
106D ALA* 1.3 56.4 + - - +
108D ASN* 3.2 4.7 + - - +
109D TYR* 2.6 38.7 + - - +
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Residues in contact with ALA 106 (chain D).
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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49D ASN 5.3 2.2 + - - +
50D VAL* 4.1 19.1 - - + -
54D ILE* 3.4 33.7 - - + -
58D VAL* 4.0 12.8 - - + -
102D GLU 2.8 12.3 + - - +
103D LEU 3.5 2.7 - - - +
105D LEU* 1.3 72.4 - - - +
107D ALA* 1.3 55.1 + - - +
109D TYR* 3.0 5.9 + - - -
110D LEU* 2.6 41.4 + - + +
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Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D VAL* 5.1 1.3 - - - +
103D LEU 2.6 21.9 + - - +
104D ILE* 3.8 6.5 - - - +
106D ALA* 1.3 73.5 - - - +
108D ASN* 1.3 56.1 + - - +
110D LEU* 3.7 0.4 - - - -
111D ASP 2.9 6.2 + - - -
112D ILE* 2.8 40.1 + - - +
115D LEU* 3.2 30.9 - - + +
116D LEU* 3.8 23.4 - - - +
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Residues in contact with ASN 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PRO* 5.3 3.2 - - - +
116C LEU* 3.3 44.0 - - + +
104D ILE 3.0 20.0 + - - +
105D LEU* 3.6 5.3 + - - +
107D ALA* 1.3 75.4 - - - +
109D TYR* 1.3 63.8 + - - +
111D ASP* 2.8 23.8 + - - +
116D LEU* 3.9 18.2 - - + +
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Residues in contact with TYR 109 (chain D).
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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26D THR* 2.5 37.8 + - + -
30D MET* 4.2 10.2 - - + +
46D PRO 4.1 2.1 + - - -
47D LEU* 3.9 12.0 - - + +
48D PRO* 3.7 21.1 - - - +
49D ASN* 3.0 49.1 + - + +
50D VAL* 3.3 32.1 - - + -
105D LEU 2.6 22.9 + - - +
106D ALA* 3.5 2.5 - - - +
108D ASN* 1.3 76.5 - - - +
110D LEU* 1.3 63.8 + - + +
111D ASP 3.3 0.2 + - - -
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D SER* 2.3 31.4 + - - +
25D VAL 3.3 0.2 + - - -
26D THR* 3.2 15.8 + - + -
27D ILE* 3.8 21.1 - - + -
47D LEU* 3.8 24.9 - - + -
50D VAL* 4.1 13.5 - - + -
55D LEU* 5.1 3.4 - - + -
58D VAL* 3.6 37.7 - - + -
106D ALA 2.6 21.4 + - - +
109D TYR* 1.3 98.2 - - + +
111D ASP* 1.3 66.8 + - - +
112D ILE* 3.9 10.5 - - + -
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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