Contacts of the helix formed by residues 101 - 115 (chain A) in PDB entry 1ESQ
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 THR 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLY 4.1 0.6 + - - -
99A GLY 4.7 1.1 - - - -
100A ALA* 1.3 83.3 - - - +
102A PRO* 1.3 75.0 - - - +
103A PHE 4.2 0.9 - - - -
104A ARG* 3.1 22.9 + - - +
105A THR* 3.3 14.0 + - - -
51B GLU* 2.8 38.3 + - - +
54B ASP* 4.0 7.9 - - + -
55B MET* 3.9 41.7 - - + +
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Residues in contact with PRO 102 (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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100A ALA 4.8 0.4 - - - +
101A THR* 1.3 86.0 - - - +
103A PHE* 1.3 55.9 + - - +
105A THR* 3.3 7.7 + - - +
106A GLU* 2.9 50.8 + - + +
54B ASP* 3.9 24.5 - - + +
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Residues in contact with PHE 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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69A LEU* 3.6 37.0 - - + -
70A SER 4.3 2.9 - - - -
71A LYS* 4.0 27.6 - - + -
74A VAL* 5.1 1.8 - - + -
101A THR* 3.2 0.4 - - - +
102A PRO* 1.3 81.3 - - - +
104A ARG* 1.3 56.4 + - - +
106A GLU* 3.5 15.0 + - + +
107A SER* 2.8 46.0 + - - -
48B ALA* 4.0 14.6 - - + -
50B GLU* 3.4 49.8 + - + +
51B GLU* 4.0 17.0 - - + -
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Residues in contact with ARG 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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66A ILE* 3.6 18.8 + - + +
67A GLY* 2.7 36.8 + - - -
68A THR* 4.3 0.8 - - - +
69A LEU* 3.9 18.1 - - + +
96A VAL* 3.5 19.3 + - - +
97A GLY* 3.5 36.6 - - - +
98A ALA* 4.3 1.3 - - - -
100A ALA* 4.7 0.7 - - - -
101A THR* 3.1 16.9 + - - +
103A PHE* 1.3 74.1 - - - +
105A THR* 1.3 61.4 + - - +
108A ALA* 2.9 30.7 + - - +
320A TZP 4.7 3.4 - - - -
44B VAL* 5.0 1.8 - - - +
45B MET 3.2 17.2 + - - -
46B ALA* 3.8 4.9 - - - +
51B GLU* 2.6 36.6 + - - +
55B MET* 3.8 16.0 - - - +
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Residues in contact with THR 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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98A ALA* 4.5 3.6 - - - +
99A GLY* 2.9 34.4 + - - +
101A THR 3.3 5.7 + - - -
102A PRO* 3.3 11.7 + - - +
104A ARG* 1.3 79.3 - - - +
106A GLU* 1.3 65.2 + - + +
108A ALA* 3.2 5.4 + - - +
109A ARG* 3.1 63.7 + - - +
129A HIS* 4.0 10.2 - - - +
130A THR* 5.1 1.1 - - - -
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Residues in contact with GLU 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 41.6 + - + +
103A PHE* 3.7 16.9 - - + +
105A THR* 1.3 77.4 - - + +
107A SER* 1.3 53.3 + - - +
109A ARG* 3.2 10.4 + - - +
110A ASP* 2.8 40.2 + - - +
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Residues in contact with SER 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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66A ILE* 4.9 5.4 - - - -
69A LEU* 3.3 26.9 - - - +
74A VAL* 3.8 22.1 - - - +
103A PHE* 2.8 34.1 + - - -
104A ARG 3.8 2.5 - - - -
106A GLU* 1.3 74.8 - - - +
108A ALA* 1.3 66.6 + - - +
110A ASP* 3.5 7.7 - - - +
111A ILE* 3.1 31.2 + - - +
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Residues in contact with ALA 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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66A ILE* 4.4 7.4 - - + +
93A LEU* 4.1 7.4 - - + +
95A PRO* 4.4 11.7 - - + -
98A ALA* 4.4 8.3 - - + -
104A ARG 2.9 19.5 + - - +
105A THR 3.5 4.9 - - - +
107A SER* 1.3 76.9 - - - +
109A ARG* 1.3 63.8 + - - +
111A ILE* 3.4 8.0 + - - +
112A ILE* 3.1 28.3 + - - +
130A THR* 4.0 25.4 - - + +
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Residues in contact with ARG 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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105A THR* 3.1 33.6 + - - +
106A GLU* 3.4 10.1 - - - +
108A ALA* 1.3 72.9 - - - +
110A ASP* 1.3 57.7 + - - +
112A ILE* 2.7 33.0 + - + +
113A ARG* 2.9 30.0 + - - +
129A HIS 3.0 23.0 + - - -
130A THR* 3.1 26.6 + - + +
132A GLY 3.6 24.0 + - - -
133A VAL* 4.0 22.5 + - + +
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Residues in contact with ASP 110 (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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74A VAL* 5.3 4.4 - - + +
78A ILE* 3.6 22.4 - - + +
106A GLU* 2.8 22.7 + - - +
107A SER* 3.5 10.5 - - - +
109A ARG* 1.3 72.0 - - - +
111A ILE* 1.3 62.3 + - + +
113A ARG* 3.0 42.3 + - - +
114A GLU* 3.1 17.2 + - - +
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Residues in contact with ILE 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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64A LEU* 3.9 23.3 - - + -
66A ILE* 4.1 15.3 - - + -
74A VAL* 4.5 9.9 - - + -
77A MET* 3.9 31.6 - - + -
78A ILE* 4.0 24.5 - - + -
93A LEU* 4.3 22.2 - - + -
107A SER 3.1 18.2 + - - +
108A ALA* 3.6 4.7 - - - +
110A ASP* 1.3 76.7 - - - +
112A ILE* 1.3 57.4 + - - +
115A VAL* 2.8 38.9 + - + +
117A LEU* 4.8 4.3 - - + -
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Residues in contact with ILE 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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93A LEU* 3.7 21.5 - - + -
108A ALA 3.1 14.3 + - - +
109A ARG* 2.7 17.7 + - - +
111A ILE* 1.3 71.9 - - - +
113A ARG* 1.3 58.9 + - - -
115A VAL 3.6 11.8 - - - +
117A LEU* 3.8 17.0 - - + -
120A ILE* 4.2 5.8 - - + -
130A THR* 3.5 32.8 - - + -
161A LEU* 4.1 41.3 - - + +
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Residues in contact with ARG 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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106A GLU 5.6 0.2 + - - -
109A ARG* 2.9 27.6 + - - +
110A ASP* 3.0 37.7 + - - +
111A ILE 3.2 0.2 - - - -
112A ILE* 1.3 79.7 - - - +
114A GLU* 1.3 80.5 + - + +
115A VAL 3.5 0.2 - - - -
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Residues in contact with GLU 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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78A ILE* 3.6 34.3 - - + -
82A LYS* 2.9 45.8 + - - +
85A ASN* 4.8 1.4 + - - -
110A ASP* 3.1 21.6 + - - +
111A ILE 4.3 0.2 - - - +
113A ARG* 1.3 100.1 - - + +
115A VAL* 1.3 61.2 + - - +
116A ARG 4.4 0.2 + - - -
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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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64A LEU* 5.0 1.3 - - + -
77A MET 4.7 0.4 - - - +
78A ILE* 4.0 30.1 - - + +
81A GLY* 3.7 25.6 - - - +
85A ASN* 3.5 13.9 - - - +
91A VAL* 3.9 17.3 - - + -
111A ILE* 2.8 27.2 + - + +
112A ILE 3.6 13.5 - - - +
113A ARG 3.5 1.2 - - - -
114A GLU* 1.3 87.2 - - + +
116A ARG* 1.3 74.1 + - - +
117A LEU* 3.0 15.8 + - + +
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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