Contacts of the helix formed by residues 101 - 115 (chain B) in PDB entry 1C3Q
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B GLY 4.0 0.8 + - - -
99B GLY 5.0 0.9 - - - -
100B ALA* 1.3 86.1 - - + +
102B PRO* 1.3 75.9 - - - +
103B PHE 3.9 2.5 + - - -
104B ARG* 2.9 28.0 + - - +
105B THR* 3.3 15.3 + - - -
51C GLU* 2.9 39.1 + - + +
54C ASP* 4.7 14.8 - - + -
55C MET* 4.1 23.3 - - + +
58C ILE* 6.5 0.4 - - + -
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Residues in contact with PRO 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B THR* 1.3 86.7 - - + +
103B PHE* 1.3 64.6 + - + +
105B THR* 3.2 7.5 + - - +
106B GLU* 3.0 26.8 + - - +
50C GLU 5.9 1.6 - - - +
54C ASP* 4.1 19.5 - - + +
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 3.5 32.1 - - + -
70B SER 4.0 3.6 - - - -
71B LYS* 3.8 30.3 - - + -
74B VAL* 4.9 1.8 - - + -
101B THR* 4.2 5.8 - - - +
102B PRO* 1.3 82.2 - - + +
104B ARG* 1.3 54.0 + - - +
106B GLU* 4.0 4.2 - - + +
107B SER* 2.7 50.8 + - - -
48C ALA* 3.9 12.6 - - + -
50C GLU* 3.8 48.9 - - + +
51C GLU* 4.2 14.4 - - + -
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Residues in contact with ARG 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 3.6 12.0 + - + +
67B GLY* 2.9 32.6 + - - -
68B THR* 4.4 1.4 - - - +
69B LEU* 4.0 22.9 - - + +
96B VAL* 3.5 26.6 + - - +
97B GLY* 3.7 30.8 - - - +
98B ALA* 4.2 2.8 - - - +
100B ALA* 5.1 2.0 - - - -
101B THR* 2.9 22.8 + - - +
102B PRO 3.1 0.8 - - - -
103B PHE* 1.3 76.4 - - - +
105B THR* 1.3 64.8 + - - +
107B SER* 3.4 0.3 + - - -
108B ALA* 3.1 23.2 + - - +
303B TZE 5.1 2.2 - - - -
44C VAL* 5.8 0.2 - - - +
45C MET 3.7 14.8 + - - -
46C ALA* 3.9 5.5 - - - +
51C GLU* 2.7 36.2 + - - +
55C MET* 4.5 10.0 - - - +
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Residues in contact with THR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA* 4.4 8.1 - - - +
99B GLY* 2.8 27.9 + - - +
101B THR 3.3 7.7 + - - -
102B PRO* 3.2 10.0 + - - +
104B ARG* 1.3 77.4 - - - +
106B GLU* 1.3 64.1 + - - +
108B ALA* 3.5 3.5 + - - +
109B ARG* 3.1 40.4 + - - +
129B HIS* 3.6 28.3 - - + +
130B THR* 4.5 3.3 - - - +
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PRO 3.0 17.0 + - - +
103B PHE* 4.1 5.4 - - + +
105B THR* 1.3 76.8 - - - +
107B SER* 1.3 59.3 + - - +
109B ARG* 3.2 18.2 + - - +
110B ASP* 2.8 41.4 + - - +
113B ARG* 2.4 33.9 + - - +
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 5.0 3.8 - - - -
69B LEU* 3.4 27.7 - - - +
74B VAL* 3.9 18.0 - - - +
103B PHE* 2.7 37.7 + - - -
104B ARG 3.8 3.1 - - - -
105B THR 3.3 0.2 - - - -
106B GLU* 1.3 73.8 - - - +
108B ALA* 1.3 67.1 + - - +
110B ASP* 3.3 10.3 + - - +
111B ILE* 3.2 28.9 + - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 4.2 15.4 - - + +
93B LEU* 4.4 7.0 - - + +
95B PRO* 4.3 11.2 - - + -
98B ALA* 4.6 1.8 - - + -
104B ARG 3.1 16.6 + - - +
105B THR 3.6 5.6 - - - +
107B SER* 1.3 76.2 - - - +
109B ARG* 1.3 63.8 + - - +
111B ILE* 3.3 11.4 + - - +
112B ILE* 3.1 28.4 + - - +
130B THR* 4.0 22.4 - - + +
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Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B THR* 3.1 23.8 + - - +
106B GLU* 3.5 22.3 + - - +
108B ALA* 1.3 77.7 - - - +
110B ASP* 1.3 58.8 + - - +
112B ILE* 3.2 9.8 + - + +
113B ARG* 2.9 54.3 + - + +
129B HIS 3.2 22.9 + - - -
130B THR* 2.8 29.9 + - + +
131B VAL 4.2 1.9 + - - -
132B GLY* 3.9 15.2 - - - -
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B VAL* 5.1 5.0 - - + +
78B ILE* 4.3 15.7 - - + -
106B GLU* 2.8 30.9 + - - +
107B SER* 3.6 9.4 - - - +
108B ALA 3.3 0.4 - - - -
109B ARG* 1.3 72.4 - - - +
111B ILE* 1.3 63.0 + - - +
113B ARG* 2.7 35.3 + - - +
114B GLU* 3.0 30.9 + - + +
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 4.0 22.0 - - + -
66B ILE* 4.1 15.0 - - + -
74B VAL* 4.4 7.0 - - + -
77B MET* 3.9 31.2 - - + -
78B ILE* 4.2 23.1 - - + -
93B LEU* 4.1 21.8 - - + -
107B SER 3.2 15.8 + - - +
108B ALA* 3.5 7.4 - - - +
110B ASP* 1.3 77.6 - - - +
112B ILE* 1.3 54.5 + - - +
115B VAL* 2.7 43.8 + - + +
117B LEU* 4.5 10.8 - - + -
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 4.1 11.4 - - + -
108B ALA 3.1 14.9 + - - +
109B ARG* 3.6 9.0 - - + +
111B ILE* 1.3 76.2 - - - +
113B ARG* 1.3 62.6 + - + +
114B GLU 3.5 0.2 + - - -
115B VAL 3.6 15.9 + - - +
117B LEU* 3.9 22.9 - - + -
120B ILE* 4.5 4.5 - - + -
130B THR* 3.5 32.5 - - + -
161B LEU* 4.0 42.4 - - + +
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLU* 2.4 34.2 + - - -
109B ARG* 2.9 37.0 + - + +
110B ASP* 2.7 32.1 + - - +
111B ILE 3.2 0.2 - - - -
112B ILE* 1.3 79.7 - - + +
114B GLU* 1.3 69.7 + - + +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 3.6 31.4 - - + -
82B LYS* 3.0 42.9 + - - +
85B ASN* 4.3 3.3 + - - -
110B ASP* 3.0 18.0 + - + +
111B ILE 4.2 1.1 - - - +
113B ARG* 1.3 91.0 - - + +
115B VAL* 1.3 58.8 + - + +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 5.1 0.7 - - + -
77B MET 4.8 0.9 - - - +
78B ILE* 4.1 23.1 - - + +
81B GLY* 3.7 33.2 - - - +
85B ASN* 3.5 12.8 - - - +
91B VAL* 4.0 15.9 - - + -
111B ILE* 2.7 33.2 + - + +
112B ILE* 3.6 13.0 - - - +
113B ARG 3.7 0.8 - - - -
114B GLU* 1.3 83.8 - - + +
116B ARG* 1.3 73.1 - - - +
117B LEU* 3.3 13.5 + - + +
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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