Contacts of the helix formed by residues 105 - 116 (chain D) in PDB entry 1QDV
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 PRO 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C ARG* 3.6 32.3 - - + +
100D ARG* 5.6 0.2 - - - -
102D VAL 5.6 0.4 - - - +
103D ASN 3.5 10.5 - - - +
104D VAL* 1.3 91.1 - - + +
106D LEU* 1.3 65.5 + - - +
107D ASP* 3.4 16.8 - - - +
108D ILE* 3.2 22.7 + - + +
109D PHE* 2.9 20.4 + - - +
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Residues in contact with LEU 106 (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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100D ARG* 3.5 25.6 - - - +
104D VAL 3.4 1.4 + - - -
105D PRO* 1.3 70.3 - - - +
107D ASP* 1.3 58.1 + - - +
109D PHE 3.8 0.3 - - - -
110D SER* 2.9 49.6 + - - +
126D PHE* 4.0 13.5 - - + -
130D GLU* 3.7 32.1 - - + -
131D GLY* 5.5 4.9 - - - +
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Residues in contact with ASP 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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97C ARG* 2.5 40.3 + - - -
99C ARG* 2.9 16.6 + - - -
105D PRO* 3.4 12.6 - - - +
106D LEU* 1.3 77.7 + - - +
108D ILE* 1.3 67.9 + - - +
110D SER* 3.9 4.6 - - - -
111D GLU* 3.2 34.4 + - - +
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Residues in contact with ILE 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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90C TYR* 3.6 39.9 - - + +
97C ARG* 4.4 10.1 - - - +
99C ARG* 4.2 18.8 - - + +
81D ASN* 3.7 32.3 - - + +
84D SER* 4.1 1.8 - - - +
104D VAL* 4.0 11.0 - - + -
105D PRO* 3.6 31.4 - - + +
107D ASP* 1.3 90.1 + - - +
109D PHE* 1.3 63.0 + - - +
111D GLU* 3.2 10.4 + - - +
112D GLU* 3.1 21.6 + - + +
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Residues in contact with PHE 109 (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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84D SER* 3.5 35.7 - - - -
87D ALA* 3.6 33.4 - - + -
88D ILE* 4.3 10.3 - - + -
98D LEU* 4.1 17.3 - - + -
99D ARG 3.8 4.3 - - - -
100D ARG* 3.7 29.4 - - + -
101D PRO* 4.1 4.9 - - + -
104D VAL* 3.9 9.0 - - + -
105D PRO 2.9 17.0 + - - +
106D LEU 4.0 0.7 - - - +
108D ILE* 1.3 76.9 - - - +
110D SER* 1.3 56.0 + - - +
112D GLU* 3.1 4.1 + - + +
113D ILE* 3.0 49.7 + - + +
126D PHE* 3.7 26.9 - + - -
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Residues in contact with SER 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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106D LEU* 2.9 38.1 + - - +
107D ASP* 3.9 5.4 - - - -
109D PHE* 1.3 75.1 - - - +
111D GLU* 1.3 62.3 + - - +
113D ILE* 3.4 11.5 + - - +
114D ARG* 3.2 32.2 + - - +
123D MET* 4.7 11.2 - - - +
126D PHE* 4.1 7.6 - - - -
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Residues in contact with GLU 111 (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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90C TYR* 3.8 17.3 + - - -
94C SER* 5.7 1.4 - - - -
97C ARG* 5.0 11.5 + - - -
80D ARG* 4.3 4.2 + - - +
107D ASP* 3.2 22.1 + - - +
108D ILE* 3.2 8.8 + - - +
110D SER* 1.3 75.9 - - - +
112D GLU* 1.3 65.9 + - - +
114D ARG* 3.5 9.8 + - - +
115D PHE* 3.0 27.5 + - - +
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Residues in contact with GLU 112 (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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90C TYR* 4.8 8.3 + - - -
80D ARG* 2.9 46.5 + - - +
81D ASN* 4.0 20.1 + - + +
84D SER* 3.5 31.1 - - - +
88D ILE* 4.4 5.6 - - + -
108D ILE* 3.1 13.8 + - + +
109D PHE* 3.1 7.6 + - + +
111D GLU* 1.3 80.5 - - - +
113D ILE* 1.3 65.4 + - - +
115D PHE* 3.2 2.4 + - - +
116D TYR* 2.9 49.3 + - + -
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Residues in contact with ILE 113 (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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88D ILE* 4.3 9.4 - - + +
98D LEU* 4.0 17.7 - - + -
109D PHE* 3.0 41.8 + - + +
110D SER* 3.6 9.0 - - - +
111D GLU 3.4 0.4 - - - -
112D GLU* 1.3 75.2 - - - +
114D ARG* 1.3 64.2 + - + +
116D TYR 3.6 0.9 + - - -
117D GLU 3.2 15.4 + - - -
118D LEU* 3.4 30.7 + - + +
119D GLY 4.9 2.1 + - - +
123D MET* 3.4 45.8 - - + +
126D PHE* 3.7 20.2 - - + -
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Residues in contact with ARG 114 (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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110D SER* 3.2 20.8 + - - +
111D GLU* 3.9 7.8 - - - +
113D ILE* 1.3 75.8 - - + +
115D PHE* 1.3 66.6 - - - +
117D GLU* 3.0 20.3 + - - +
120D GLU* 5.6 9.5 + - - -
123D MET* 4.7 18.4 - - - -
127D ARG* 5.4 8.1 - - - +
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Residues in contact with PHE 115 (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 LEU* 3.5 19.6 - - + +
68D TYR* 3.4 38.6 - + - -
78D PHE* 3.5 24.9 - + - -
80D ARG* 3.3 61.0 - - - +
111D GLU 3.0 13.4 + - - +
112D GLU 3.2 4.0 + - - +
114D ARG* 1.3 78.1 - - - +
116D TYR* 1.3 74.3 + + - +
117D GLU* 3.2 14.9 + - - +
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Residues in contact with TYR 116 (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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39D ILE* 3.7 14.2 - - - +
57D THR* 3.9 4.2 - - - -
58D LEU* 3.1 26.4 + - + +
59D LEU* 4.3 21.5 + - + -
78D PHE* 4.0 17.3 - + - +
80D ARG* 3.8 16.7 - - - +
81D ASN 5.1 1.7 + - - -
84D SER* 6.0 0.9 - - - -
85D PHE* 3.7 28.1 - + - -
88D ILE* 4.0 27.8 - - + -
92D TYR* 4.6 0.6 + - - +
112D GLU* 2.9 48.7 + - + +
113D ILE 4.2 3.1 - - - +
115D PHE* 1.3 96.1 - + - +
117D GLU* 1.3 67.3 + - - +
118D LEU* 3.3 16.7 + - + +
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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