Contacts of the helix formed by residues 101 - 119 (chain A) in PDB entry 2Q8I
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A SER* 3.7 15.7 - - - +
99A PRO 2.7 8.9 + - - +
100A GLU* 1.3 79.9 - - - +
102A PRO* 1.4 72.2 - - - +
103A GLN* 3.3 20.2 + - - +
104A VAL* 2.9 35.6 + - + +
105A LEU* 3.4 7.9 + - - +
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Residues in contact with PRO 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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99A PRO 5.2 0.2 - - - +
100A GLU 3.9 6.7 - - - +
101A ASP* 1.4 87.8 - - - +
103A GLN* 1.3 57.8 + - + +
105A LEU* 3.3 14.1 + - + +
106A ASP* 2.9 28.3 + - - +
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Residues in contact with GLN 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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101A ASP* 3.0 17.0 + - - +
102A PRO* 1.3 78.0 - - + +
104A VAL* 1.3 58.0 + - + +
106A ASP* 3.5 15.6 + - - +
107A ASN* 2.7 65.9 + - - +
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Residues in contact with VAL 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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46A TYR* 3.3 33.4 - - + +
94A TYR* 3.8 10.1 - - + -
97A LYS* 3.8 24.2 - - + +
98A SER 3.4 26.0 - - - +
101A ASP* 2.9 27.3 + - + +
103A GLN* 1.3 74.9 - - + +
105A LEU* 1.3 53.8 + - + +
107A ASN* 3.7 6.4 - - - +
108A PHE* 2.8 36.6 + - - +
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Residues in contact with LEU 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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42A GLU* 3.8 42.3 - - + +
43A LYS* 4.8 13.2 - - + +
46A TYR* 3.7 42.4 - - + -
99A PRO* 3.4 31.9 - - + +
101A ASP 3.4 7.0 + - - +
102A PRO* 3.3 10.7 + - + +
104A VAL* 1.3 76.9 - - - +
106A ASP* 1.3 65.0 + - - +
108A PHE* 3.4 5.1 + - - +
109A LEU* 3.2 22.2 + - - +
168A HIS* 5.4 1.0 + - - -
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Residues in contact with ASP 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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102A PRO 2.9 14.7 + - - +
103A GLN* 3.1 24.7 + - - +
105A LEU* 1.3 79.4 - - - +
107A ASN* 1.3 64.0 + - - +
109A LEU* 3.3 22.2 + - - +
110A GLN* 3.4 25.2 + - - +
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Residues in contact with ASN 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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94A TYR* 3.4 19.1 - - + +
103A GLN* 2.7 47.6 + - - +
104A VAL* 3.9 4.9 + - - +
106A ASP* 1.3 72.8 - - - +
108A PHE* 1.3 66.4 + - - +
110A GLN* 3.3 11.5 + - - +
111A VAL* 3.0 25.2 + - + +
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Residues in contact with PHE 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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46A TYR* 3.4 43.3 - + + -
49A LEU* 4.2 13.7 - - + -
50A ARG* 4.0 30.5 - - + -
91A LEU* 3.9 21.1 - - + -
94A TYR* 3.7 26.9 + + + -
104A VAL 2.8 22.5 + - - +
105A LEU 3.7 5.4 - - - +
106A ASP 3.2 0.2 - - - -
107A ASN* 1.3 72.6 - - - +
109A LEU* 1.3 65.0 + - - +
111A VAL* 2.9 14.4 + - + +
112A LEU* 2.9 48.5 + - + +
168A HIS* 4.2 12.1 - - - -
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Residues in contact with LEU 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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42A GLU* 5.0 4.5 - - - +
105A LEU 3.2 10.4 + - - +
106A ASP* 3.4 15.5 - - - +
108A PHE* 1.3 79.5 - - - +
110A GLN* 1.3 78.6 + - - +
112A LEU* 3.1 20.5 + - - +
113A ILE* 3.1 24.0 + - + +
168A HIS* 3.7 31.4 - - + +
169A THR* 4.0 13.9 - - + -
172A PHE* 4.3 7.4 - - + +
173A GLY* 3.7 37.9 - - - +
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Residues in contact with GLN 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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106A ASP* 3.4 30.6 + - - +
107A ASN* 3.3 11.5 + - - +
109A LEU* 1.3 90.4 - - - +
111A VAL* 1.3 65.9 + - + +
113A ILE* 3.3 21.6 + - - +
114A LYS* 2.9 25.6 + - - +
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Residues in contact with VAL 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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90A GLU* 4.3 24.5 - - + +
91A LEU* 4.2 22.9 - - + -
94A TYR* 3.1 28.0 - - + +
107A ASN* 3.0 16.7 + - + +
108A PHE* 2.9 13.3 + - + +
110A GLN* 1.3 77.2 - - + +
112A LEU* 1.3 62.0 + - - +
114A LYS* 3.1 14.6 + - - +
115A VAL* 3.0 34.3 + - + +
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Residues in contact with LEU 112 (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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49A LEU* 4.2 5.8 - - + -
53A LEU* 3.6 29.4 - - + -
91A LEU* 4.0 10.5 - - + -
108A PHE* 2.9 39.7 + - + +
109A LEU* 3.1 7.6 + - - +
111A VAL* 1.3 75.5 - - - +
113A ILE* 1.3 55.9 + - - +
115A VAL* 3.2 6.4 + - + +
116A ARG* 2.9 30.7 + - - +
165A ILE* 3.9 25.6 - - + +
168A HIS* 3.5 42.6 - - + -
169A THR* 4.4 7.4 - - + -
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Residues in contact with ILE 113 (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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109A LEU* 3.1 22.3 + - + +
110A GLN* 3.4 32.8 - - - +
111A VAL 3.2 0.2 - - - -
112A LEU* 1.3 74.7 - - - +
114A LYS* 1.3 59.7 + - - +
116A ARG* 3.2 29.5 + - - +
117A ASN* 2.9 45.7 + - - +
169A THR* 4.2 13.2 - - + -
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Residues in contact with LYS 114 (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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90A GLU* 3.2 32.8 + - - +
110A GLN 2.9 17.1 + - - +
111A VAL* 3.1 13.9 + - - +
113A ILE* 1.3 79.0 - - - +
115A VAL* 1.3 56.8 + - + +
117A ASN* 3.6 8.0 + - - +
118A ARG* 3.0 39.4 + - - +
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Residues in contact with VAL 115 (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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53A LEU* 5.9 0.2 - - + -
57A LEU* 6.1 0.9 - - + -
87A SER* 3.5 25.1 - - - +
90A GLU* 4.3 5.2 - - - +
91A LEU* 4.9 13.5 - - + -
111A VAL* 3.0 31.7 + - + +
112A LEU* 4.0 3.6 - - + +
114A LYS* 1.3 73.2 - - - +
116A ARG* 1.3 70.1 + - - +
118A ARG* 3.6 16.4 - - - +
119A HIS* 2.9 43.3 + - + +
165A ILE* 3.7 24.0 - - + -
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Residues in contact with ARG 116 (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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112A LEU 2.9 13.8 + - - +
113A ILE* 3.5 36.6 + - - +
115A VAL* 1.3 78.5 - - - +
117A ASN* 1.3 68.9 + - - +
119A HIS* 3.1 11.5 + - - -
120A ASN* 3.1 11.8 + - - +
162A ARG* 3.1 53.6 + - + +
165A ILE* 3.8 26.3 - - + +
166A ASN* 3.1 28.0 + - - -
169A THR* 3.1 23.4 + - - +
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Residues in contact with ASN 117 (chain A).
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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113A ILE* 2.9 37.8 + - - +
114A LYS* 3.8 7.8 - - - +
116A ARG* 1.3 79.6 + - - +
118A ARG* 1.3 62.4 + - - +
120A ASN* 3.1 37.6 + - - +
121A ASP* 4.7 1.2 + - - +
162A ARG* 5.9 0.2 + - - -
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Residues in contact with ARG 118 (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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83A TRP* 3.6 60.4 - - + -
86A GLN* 3.4 34.3 + - - +
87A SER* 2.8 26.8 + - - +
90A GLU* 2.7 41.3 + - - -
114A LYS* 3.0 34.9 + - - +
115A VAL* 3.2 16.8 + - - +
117A ASN* 1.3 76.4 - - - +
119A HIS* 1.3 60.7 + - + +
120A ASN 3.3 0.9 + - - -
121A ASP* 4.4 3.3 + - - +
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Residues in contact with HIS 119 (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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57A LEU* 4.0 18.6 - - + -
83A TRP* 3.9 5.7 + - + -
84A TYR* 3.5 30.8 - + - -
87A SER* 3.1 34.9 + - - -
115A VAL* 2.9 29.0 + - + +
116A ARG* 3.1 5.8 + - - +
118A ARG* 1.3 86.7 - - + +
120A ASN* 1.3 62.7 + - - +
121A ASP 3.3 2.0 - - - -
122A VAL* 3.1 29.8 + - + +
158A ARG* 3.4 17.3 + - + +
161A PHE* 4.3 15.2 - + + +
162A ARG* 4.2 8.5 - - - +
165A ILE* 5.7 1.0 - - - +
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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