Contacts of the helix formed by residues 101 - 115 (chain B) in PDB entry 3CTP
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B THR* 3.0 15.1 + - - +
99B ASP* 3.7 6.1 - - - +
100B ASP* 1.3 79.3 - - - +
102B LYS* 1.3 65.1 + - - +
103B GLU* 3.0 16.0 + - - +
104B LYS* 2.9 41.7 + - + +
105B GLU* 3.0 23.4 + - - +
126B GLN* 4.9 1.6 - - - -
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Residues in contact with LYS 102 (chain B).
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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101B ASP* 1.3 75.0 + - - +
103B GLU* 1.3 59.1 + - - +
105B GLU* 3.3 7.0 + - - +
106B LYS* 2.9 30.3 + - + +
126B GLN* 3.6 45.4 + - + +
127B CYS* 4.1 18.9 - - - -
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Residues in contact with GLU 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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101B ASP* 3.0 11.8 + - - +
102B LYS* 1.3 80.3 - - - +
104B LYS* 1.3 64.5 + - + +
106B LYS* 2.7 45.3 + - - +
107B THR* 3.0 34.7 + - - +
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Residues in contact with LYS 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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83A GLU* 5.5 7.8 - - - +
84A GLU* 4.6 12.5 + - - -
87A LYS* 4.2 20.1 - - + +
97B ASN 4.4 8.1 - - - +
98B THR* 3.4 31.4 - - - +
99B ASP* 2.7 34.1 + - + +
101B ASP* 2.9 22.2 + - + +
103B GLU* 1.3 76.3 - - + +
105B GLU* 1.3 63.5 + - - +
107B THR* 3.2 6.5 + - - -
108B TYR* 2.9 36.3 + - + -
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Residues in contact with GLU 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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66B MET* 3.9 12.2 - - - +
98B THR* 3.8 20.7 - - + +
101B ASP 3.0 13.2 + - - +
102B LYS* 3.6 7.2 - - - +
104B LYS* 1.3 78.0 - - - +
106B LYS* 1.3 58.0 + - - +
108B TYR* 3.2 1.0 + - - -
109B LEU* 2.9 29.3 + - + +
122B ALA* 4.6 1.6 - - - +
123B SER 5.5 1.3 + - - -
124B ARG 4.9 0.2 - - - +
125B SER* 2.6 28.5 + - - -
126B GLN* 2.9 27.6 + - - +
127B CYS* 3.4 16.4 - - - -
131B TYR* 2.6 27.2 + - + +
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Residues in contact with LYS 106 (chain B).
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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102B LYS* 2.9 20.0 + - + +
103B GLU* 2.7 42.8 + - - +
105B GLU* 1.3 77.7 - - - +
107B THR* 1.3 64.8 + - - +
109B LEU* 3.4 8.5 + - + +
110B GLU* 3.1 43.1 + - + +
127B CYS* 4.5 6.7 - - - -
130B GLU* 3.5 37.5 - - + +
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Residues in contact with THR 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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92A THR* 3.7 29.6 - - + -
103B GLU* 3.0 28.6 + - - +
104B LYS* 3.5 8.0 - - - -
105B GLU 3.2 0.2 - - - -
106B LYS* 1.3 78.1 - - - +
108B TYR* 1.3 61.7 + - + +
110B GLU* 3.2 11.4 + - - +
111B VAL* 2.9 30.5 + - + +
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Residues in contact with TYR 108 (chain B).
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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83A GLU* 2.5 33.1 + - - -
92A THR* 3.6 25.2 - - + +
93A LEU 3.0 40.8 + - - -
94A PHE* 4.8 4.5 - + - -
66B MET* 3.6 24.7 - - + -
96B CYS* 3.7 27.1 - - + -
97B ASN 3.7 23.3 - - - -
98B THR* 4.8 1.1 - - + -
104B LYS* 2.9 32.7 + - + +
107B THR* 1.3 76.1 - - + +
109B LEU* 1.3 62.1 + - - +
111B VAL* 3.8 9.6 - - + +
112B LEU* 2.8 35.7 + - - +
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Residues in contact with LEU 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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66B MET* 3.3 12.4 - - + +
105B GLU* 2.9 17.3 + - + +
106B LYS* 3.6 7.9 - - + +
108B TYR* 1.3 77.9 - - - +
110B GLU* 1.3 57.0 + - + +
112B LEU* 3.5 1.5 + - - +
113B GLN* 3.0 54.8 + - - +
120B ILE* 3.7 16.6 - - + -
127B CYS* 5.8 0.7 - - - -
130B GLU* 3.6 42.6 - - + +
131B TYR* 4.0 28.9 - - + +
134B ILE* 3.7 19.5 - - + -
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Residues in contact with GLU 110 (chain B).
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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106B LYS* 3.1 39.6 + - + +
107B THR* 3.5 9.9 - - - +
109B LEU* 1.3 75.2 - - + +
111B VAL* 1.3 62.4 + - + +
113B GLN* 3.3 11.4 + - - +
114B SER* 2.9 33.7 + - - +
130B GLU* 4.3 6.7 - - - +
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Residues in contact with VAL 111 (chain B).
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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62A THR* 3.6 21.8 - - - +
92A THR* 3.9 19.1 - - + +
94A PHE* 3.6 26.0 - - + -
107B THR* 2.9 30.6 + - + +
108B TYR* 3.3 10.3 + - + +
110B GLU* 1.3 77.7 - - + +
112B LEU* 1.3 63.4 + - - +
114B SER* 3.2 5.7 + - - -
115B HIS* 2.9 35.5 + - + +
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Residues in contact with LEU 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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94A PHE* 3.9 23.3 - - + -
64B GLY* 3.9 20.4 - - - -
66B MET* 3.4 27.4 - - + -
94B PHE* 4.7 3.1 - - + -
96B CYS* 4.0 20.0 - - - -
108B TYR* 2.8 23.7 + - - +
109B LEU 3.9 0.4 - - - +
111B VAL* 1.3 74.3 - - - +
113B GLN* 1.3 61.5 + - - +
115B HIS* 3.3 3.4 + - - +
116B ARG 3.1 16.1 + - - -
117B VAL* 3.4 37.8 + - + +
120B ILE* 3.9 27.1 - - + -
136B ILE* 4.7 0.2 - - - -
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Residues in contact with GLN 113 (chain B).
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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109B LEU* 3.0 50.7 + - + +
110B GLU* 3.7 9.2 - - - +
112B LEU* 1.3 76.3 - - - +
114B SER* 1.3 63.4 + - - +
116B ARG* 3.0 24.9 + - - -
120B ILE* 5.0 0.9 - - + -
130B GLU 4.9 0.4 + - - -
134B ILE* 3.3 41.4 - - + +
136B ILE* 3.7 24.5 - - + +
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Residues in contact with SER 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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110B GLU* 2.9 19.8 + - - +
111B VAL* 3.2 7.8 + - - -
113B GLN* 1.3 77.5 - - - +
115B HIS* 1.3 67.9 + - - +
116B ARG* 3.3 10.0 + - - +
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Residues in contact with HIS 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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60A SER* 3.9 19.1 + - - -
61A LYS 5.8 0.2 - - - -
62A THR* 3.9 22.5 - - - -
94A PHE* 4.0 19.5 - + + -
115A HIS* 3.4 62.0 + + + -
117A VAL* 4.8 2.4 - - - +
60B SER* 5.2 0.7 - - - -
111B VAL* 2.9 35.1 + - + +
112B LEU 3.3 5.1 + - - +
113B GLN 3.1 0.2 - - - -
114B SER* 1.3 81.7 - - - +
116B ARG* 1.3 70.9 + - - +
117B VAL* 3.2 8.6 + - + -
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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