Contacts of the helix formed by residues 101 - 114 (chain D) in PDB entry 4Q96
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 LYS 101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1615C TYR* 4.1 2.5 - - - -
97D ASP 4.9 0.8 + - - -
98D GLU 5.0 1.0 + - - -
99D GLY 3.4 0.2 - - - -
100D CYS* 1.3 83.5 - - + +
102D LYS* 1.3 64.3 + - - +
103D PRO* 3.2 3.4 - - - -
104D LEU* 3.1 26.6 + - + +
105D GLU* 3.0 34.1 + - + +
129D MET* 2.4 43.7 + - - -
130D GLU* 4.7 1.2 - - - +
93E ALA* 4.1 9.6 - - - +
96E ALA* 4.1 12.6 - - + -
97E ASP* 3.2 36.3 + - - +
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Residues in contact with LYS 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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98D GLU* 3.3 34.1 - - - +
99D GLY* 3.3 14.6 + - - +
101D LYS* 1.3 76.4 - - - +
103D PRO* 1.4 69.5 - - + +
105D GLU* 3.2 23.7 - - + +
106D ARG* 2.9 33.8 + - - +
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Residues in contact with PRO 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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1615C TYR* 3.6 17.5 - - - +
1617C PRO* 3.6 31.9 - - + +
1619C SER* 5.0 2.5 - - - +
99D GLY 4.0 0.2 - - - +
100D CYS 3.7 4.5 - - - +
101D LYS 3.4 4.5 - - - -
102D LYS* 1.4 94.4 - - + +
104D LEU* 1.3 60.9 + - - +
106D ARG* 3.4 12.6 + - + +
107D LEU* 3.2 21.6 + - - +
57E LEU* 3.8 21.5 - - + -
61E TYR* 3.5 26.7 + - + +
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Residues in contact with LEU 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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1615C TYR* 4.4 8.1 - - - +
101D LYS* 3.1 31.6 + - + +
103D PRO* 1.3 73.4 - - - +
105D GLU* 1.3 66.5 + - - +
107D LEU* 3.2 6.9 + - + +
108D LEU* 3.1 26.5 + - - +
129D MET* 3.7 18.8 - - + -
57E LEU* 3.6 27.1 - - + -
60E LEU* 3.6 22.7 - - + -
89E PHE* 3.8 13.1 - - + +
92E VAL* 3.8 9.0 - - + -
93E ALA* 3.8 31.2 - - + +
96E ALA* 5.2 0.7 - - + -
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Residues in contact with GLU 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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101D LYS* 3.0 19.2 + - + +
102D LYS* 3.2 34.3 + - + +
104D LEU* 1.3 76.0 - - - +
106D ARG* 1.3 57.9 + - - +
108D LEU* 3.4 4.6 + - - +
109D ASN* 2.9 42.4 + - - +
129D MET* 3.9 28.1 - - + +
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Residues in contact with ARG 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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21A HIS* 3.3 54.8 + - - +
205A UNX 4.1 6.1 + - - -
1619C SER* 3.3 32.9 + - - -
102D LYS* 2.9 24.9 + - - +
103D PRO* 3.7 13.9 - - - +
105D GLU* 1.3 74.7 - - - +
107D LEU* 1.3 65.0 + - + +
109D ASN* 3.2 9.8 + - + +
110D ILE* 2.9 46.8 + - + +
61E TYR* 3.7 13.3 + - + +
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Residues in contact with LEU 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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103D PRO 3.2 15.9 + - - +
104D LEU* 3.2 9.4 + - - +
106D ARG* 1.3 75.1 - - + +
108D LEU* 1.3 59.1 + - - +
110D ILE* 3.2 10.0 + - + +
111D TRP* 3.0 41.7 + - + +
57E LEU* 5.1 1.1 - - + -
60E LEU* 3.8 38.4 - - + +
61E TYR* 4.0 31.4 - - + -
64E ASN* 3.6 40.8 - - + +
89E PHE* 4.2 17.7 - - + -
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Residues in contact with LEU 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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104D LEU 3.1 9.8 + - - +
105D GLU* 3.7 7.2 - - - +
107D LEU* 1.3 76.0 - - - +
109D ASN* 1.3 58.7 + - - +
111D TRP* 3.8 10.8 - - + -
112D GLN* 3.0 29.6 + - - +
122D ILE* 3.8 11.9 - - + +
125D LEU* 3.7 31.9 - - + +
126D LYS* 3.9 31.9 - - + +
129D MET* 3.5 37.9 - - + -
89E PHE* 3.6 25.6 - - + -
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Residues in contact with ASN 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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105D GLU* 2.9 29.0 + - - +
106D ARG* 3.6 10.0 - - + +
108D LEU* 1.3 74.9 - - - +
110D ILE* 1.3 66.0 + - + +
112D GLN* 3.7 4.6 + - - +
113D GLU* 3.1 41.0 + - - +
126D LYS* 5.4 7.3 - - - -
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Residues in contact with ILE 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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21A HIS* 6.3 0.4 - - - +
106D ARG* 2.9 36.6 + - + +
107D LEU* 3.5 12.8 - - + +
109D ASN* 1.3 77.0 - - + +
111D TRP* 1.3 59.5 + - + +
113D GLU* 3.2 8.1 + - - +
114D ARG* 2.9 51.8 + - - +
61E TYR* 6.3 1.6 - - + -
64E ASN* 4.8 11.4 - - - +
68E GLN* 3.4 28.9 - - - +
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Residues in contact with TRP 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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107D LEU* 3.0 25.8 + - + +
108D LEU* 3.8 15.3 - - + +
110D ILE* 1.3 77.5 - - + +
112D GLN* 1.3 62.1 + - - +
115D SER* 3.1 3.6 + - - -
116D VAL* 2.9 59.8 + - + +
117D TYR* 3.9 11.5 + + - +
122D ILE* 3.6 14.1 - - + -
125D LEU* 3.8 14.6 - - + -
60E LEU 4.8 3.8 - - - -
63E ALA* 5.4 1.1 - - + -
64E ASN* 3.0 47.8 + - + +
67E ILE* 4.5 10.2 - - + +
68E GLN* 4.2 4.1 - - - +
85E LEU* 3.7 32.8 - - + -
89E PHE* 3.8 33.0 - + - -
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Residues in contact with GLN 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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108D LEU 3.0 18.7 + - - +
109D ASN* 4.0 6.7 - - - +
110D ILE 3.3 0.2 - - - -
111D TRP* 1.3 77.8 - - - +
113D GLU* 1.3 68.7 + - + +
115D SER* 3.3 10.2 + - - -
117D TYR 4.8 2.7 - - - +
118D GLY 4.3 0.3 - - - -
119D GLY* 3.6 18.7 + - - +
122D ILE* 3.2 38.8 - - + +
126D LYS* 5.7 4.3 - - - -
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Residues in contact with GLU 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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109D ASN* 3.1 27.8 + - - +
110D ILE* 3.2 6.8 + - - +
112D GLN* 1.3 82.7 - - + +
114D ARG* 1.3 62.8 + - + +
115D SER* 3.1 9.2 + - - -
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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 ILE* 2.9 39.7 + - - +
113D GLU* 1.3 79.7 - - + +
115D SER* 1.3 71.2 + - - +
116D VAL* 3.2 14.0 + - + +
68E GLN* 3.0 34.4 + - - +
71E LYS* 5.4 2.1 - - - +
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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