Contacts of the helix formed by residues 102 - 116 (chain B) in PDB entry 1DT0
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 SER 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B ILE* 4.4 3.1 - - - -
97B ASN* 3.5 16.5 + - - +
100B PHE* 3.2 5.3 + - - +
101B GLY* 1.3 80.4 - - - +
103B PHE* 1.3 63.0 + - - +
104B ASP* 3.3 9.0 + - - +
105B LYS* 3.2 27.9 + - - +
106B PHE* 3.0 21.3 + - - +
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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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86B GLY 3.6 22.4 - - - -
87B GLN* 3.7 34.5 - - + +
88B PRO* 3.2 31.0 - - + -
96B ILE* 4.1 12.1 - - + -
97B ASN* 3.8 15.3 + - - +
102B SER* 1.3 74.3 - - - +
104B ASP* 1.3 66.8 + - - +
106B PHE* 3.1 14.5 + + - +
107B LYS* 3.0 55.5 + - + +
178B TRP* 5.2 1.1 - + - -
183B TRP* 3.3 32.8 - + - -
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Residues in contact with ASP 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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87B GLN* 5.2 2.8 - - - +
102B SER* 3.2 7.9 + - - +
103B PHE* 1.3 85.5 - - - +
105B LYS* 1.3 61.6 + - + +
107B LYS* 3.4 27.1 + - - +
108B GLU* 3.1 33.0 + - - +
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Residues in contact with LYS 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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100B PHE* 3.4 23.3 - - - +
101B GLY 5.3 0.4 - - - -
102B SER* 3.2 19.5 + - - +
104B ASP* 1.3 76.8 - - + +
106B PHE* 1.3 63.8 + - - +
107B LYS 3.3 0.2 - - - -
108B GLU* 3.6 31.7 - - - +
109B GLU* 3.3 30.0 + - - +
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Residues in contact with PHE 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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96B ILE* 3.8 12.6 - - + -
100B PHE* 3.5 43.5 - + + +
102B SER 3.0 11.9 + - - +
103B PHE* 3.1 20.1 + + - +
105B LYS* 1.3 76.7 - - - +
107B LYS* 1.3 64.8 + - + +
109B GLU* 3.4 2.0 + - - +
110B PHE* 2.8 38.2 + + - +
125B LEU* 3.5 44.6 - - + -
135B LEU* 4.2 9.2 - - + -
153B LEU* 4.3 2.0 - - + -
178B TRP* 3.5 33.7 - + - -
183B TRP* 3.9 16.4 - + - -
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Residues in contact with LYS 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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103B PHE* 3.0 36.7 + - + +
104B ASP* 3.6 30.4 + - - +
106B PHE* 1.3 81.7 - - + +
108B GLU* 1.3 55.2 + - - +
110B PHE* 3.7 0.7 - - - +
111B THR* 2.7 42.2 + - - -
178B TRP* 3.6 55.7 - - + +
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Residues in contact with GLU 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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104B ASP* 3.1 17.5 + - - +
105B LYS* 3.6 37.2 - - - +
107B LYS* 1.3 79.8 - - - +
109B GLU* 1.3 59.3 + - + +
111B THR* 3.4 6.6 + - - -
112B LYS* 3.0 33.6 + - + +
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Residues in contact with GLU 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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100B PHE* 3.5 30.6 - - + +
105B LYS* 3.3 18.4 + - - +
106B PHE 4.0 1.6 - - - +
107B LYS 3.3 0.4 - - - -
108B GLU* 1.3 79.0 - - + +
110B PHE* 1.3 59.6 + - - +
112B LYS* 3.6 7.0 + - + +
113B THR* 3.0 31.4 + - - -
135B LEU* 3.4 15.5 - - + +
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Residues in contact with PHE 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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106B PHE* 2.8 29.6 + + + +
107B LYS 3.7 3.1 - - - +
109B GLU* 1.3 76.9 - - - +
111B THR* 1.3 60.1 + - - +
113B THR* 3.4 5.4 + - + +
114B SER* 3.0 37.7 + - - -
123B GLY 3.9 16.2 - - - -
124B TRP* 3.7 26.5 - - - -
125B LEU* 3.8 8.7 - - + -
135B LEU* 3.7 26.2 - - + +
153B LEU* 4.0 20.4 - - + -
155B CYS* 3.8 18.8 - - + -
174B VAL* 5.1 2.2 - - + -
177B PHE* 3.7 22.0 - + - -
178B TRP* 3.3 25.6 - + + -
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Residues in contact with THR 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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107B LYS 2.7 23.2 + - - -
108B GLU* 3.5 6.3 - - - -
110B PHE* 1.3 74.2 - - - +
112B LYS* 1.3 76.8 + - - +
114B SER* 3.7 0.4 - - - -
115B VAL* 2.9 39.4 + - + +
171B PRO* 5.5 5.2 - - + +
174B VAL* 3.8 23.0 - - + +
175B GLU* 5.7 1.0 + - - +
178B TRP* 3.4 20.3 + - - -
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Residues in contact with LYS 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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108B GLU* 3.0 19.5 + - + +
109B GLU* 3.8 8.7 - - + +
111B THR* 1.3 96.6 + - + +
113B THR* 1.3 57.9 + - - +
115B VAL* 4.8 13.8 - - - +
116B GLY* 2.9 28.9 + - - -
171B PRO* 6.1 2.0 - - - +
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Residues in contact with THR 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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109B GLU 3.0 19.7 + - - -
110B PHE* 3.6 8.3 - - + +
111B THR 3.2 0.2 - - - -
112B LYS* 1.3 79.4 - - - +
114B SER* 1.3 61.6 + - - +
116B GLY 4.1 1.7 - - - -
117B THR* 3.0 21.8 + - - -
123B GLY* 4.4 5.4 - - - -
124B TRP 4.7 1.8 - - - +
135B LEU* 4.1 14.5 - - + +
136B ALA 3.5 31.9 - - - +
137B SER* 3.7 17.2 + - - -
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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 PHE* 3.0 31.4 + - - -
111B THR* 3.3 5.4 + - - -
113B THR* 1.3 75.7 - - - +
115B VAL* 1.3 66.4 + - - +
117B THR* 3.0 25.9 + - - -
123B GLY* 3.5 22.4 + - - -
155B CYS* 3.8 6.2 - - - +
157B VAL* 3.6 21.3 - - - +
170B ARG* 3.6 4.3 + - - -
174B VAL* 4.4 13.9 - - - -
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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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111B THR* 2.9 30.1 + - + +
112B LYS* 4.4 13.5 - - - +
114B SER* 1.3 73.7 - - - +
116B GLY* 1.3 58.8 + - - +
117B THR 3.1 1.1 + - - +
170B ARG* 3.0 33.2 + - + +
171B PRO* 4.0 34.5 - - + -
174B VAL* 4.0 22.4 - - + -
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Residues in contact with GLY 116 (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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112B LYS 2.9 20.1 + - - -
113B THR 4.1 3.6 - - - -
114B SER 3.2 0.2 - - - -
115B VAL* 1.3 75.8 - - - +
117B THR* 1.3 63.2 + - - +
118B PHE* 3.3 5.6 + - - +
137B SER* 5.3 0.2 - - - -
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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