Contacts of the helix formed by residues 86 - 101 (chain B) in PDB entry 1DCT
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 PRO 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B ASP* 1.3 88.8 - - - +
87B ARG* 1.3 53.3 + - + +
89B LYS* 3.2 9.2 + - + +
90B LEU* 2.8 41.1 + - + +
18F G 4.1 3.4 - - - +
1M T 3.9 17.5 - - - +
2M C 3.0 53.8 - - - +
3M A 4.0 20.6 - - - +
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Residues in contact with ARG 87 (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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70B PRO* 3.2 35.6 - - + +
72B GLN* 3.2 32.4 - - - +
73B SER* 4.3 12.2 - - - +
74B TRP* 5.0 0.2 + - - -
79B SER* 5.0 0.6 + - - -
81B ARG* 3.1 23.8 - - - +
85B ASP* 2.5 40.8 + - - +
86B PRO* 1.3 71.2 - - + +
88B GLY* 1.3 60.6 + - - +
90B LEU* 3.4 17.8 - - - +
91B PHE* 4.1 0.9 + - - +
12G A 3.0 28.3 + - - -
13G C 4.3 2.8 + - - -
1M T 3.0 44.9 - - - +
2M C 3.9 23.3 + - - -
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Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER* 3.6 17.3 + - - -
74B TRP* 4.0 14.7 + - - -
82B GLY 3.8 10.5 - - - -
83B ILE* 4.4 4.5 - - - -
85B ASP* 3.2 10.5 + - - -
86B PRO 3.1 0.8 - - - -
87B ARG* 1.3 75.7 - - - +
89B LYS* 1.3 56.4 + - - +
90B LEU 2.9 3.1 - - - -
91B PHE* 2.8 32.1 + - - +
126B PHE* 4.4 2.8 - - - -
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 3.2 33.6 + - + +
84B ASP* 4.5 1.9 - - - +
85B ASP 3.1 23.1 + - - +
86B PRO* 3.8 6.9 - - + +
88B GLY* 1.3 74.8 - - - +
90B LEU* 1.3 61.6 + - - +
91B PHE 3.0 1.1 + - - -
92B TYR* 3.2 37.4 + - + +
93B GLU* 4.1 4.5 + - - +
18F G 4.4 25.5 + - - +
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Residues in contact with LEU 90 (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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7B PHE* 4.2 8.0 - - + -
50B ASP* 4.4 8.5 - - - +
51B ILE* 4.2 15.3 - - + -
52B SER* 4.3 12.3 - - - +
69B PRO* 5.0 0.2 - - - -
70B PRO* 3.8 14.8 - - + -
86B PRO* 2.8 23.3 + - + +
87B ARG* 3.4 15.3 - - - +
88B GLY 2.8 1.0 + - - -
89B LYS* 1.3 78.1 - - - +
91B PHE* 1.3 53.1 + - - +
93B GLU* 2.7 53.9 + - + +
94B TYR 3.6 1.7 + - - -
1M T 3.2 51.1 - - + +
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Residues in contact with PHE 91 (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 PRO* 3.1 47.2 - - + +
74B TRP* 5.3 4.9 - - - +
87B ARG 4.1 1.8 + - - +
88B GLY 2.8 16.3 + - - +
90B LEU* 1.3 77.5 - - - +
92B TYR* 1.3 56.6 + - - +
94B TYR* 2.8 31.6 + + + +
95B ILE* 3.2 6.5 + - + +
108B ALA* 4.0 22.0 - - + -
109B GLU 4.7 1.6 - - - -
110B ASN* 4.6 9.0 - - - -
114B MET* 4.5 6.1 - - + -
126B PHE* 3.1 51.6 - + + -
130B PHE* 3.7 23.8 - + - -
158B TYR* 4.0 19.1 - + - -
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Residues in contact with TYR 92 (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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83B ILE* 2.8 38.5 - - + +
89B LYS* 3.3 33.9 - - + +
90B LEU 3.0 0.6 + - - -
91B PHE* 1.3 74.0 - - - +
93B GLU* 1.3 56.7 + - - +
95B ILE* 2.9 24.7 + - + +
96B ARG* 2.6 36.2 + - - +
125B GLU* 3.7 17.5 + - + +
126B PHE* 3.5 25.5 - + - -
129B GLU* 5.1 11.7 - - + -
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Residues in contact with GLU 93 (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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7B PHE* 4.7 0.7 - - + -
51B ILE* 3.8 28.4 - - + +
52B SER* 3.8 20.4 - - - +
89B LYS 4.6 3.0 - - - +
90B LEU* 2.7 39.5 + - + +
92B TYR* 1.3 79.8 - - - +
94B TYR* 1.3 62.6 + - - +
96B ARG* 2.5 55.4 + - - +
97B ILE* 3.2 11.3 + - - +
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Residues in contact with TYR 94 (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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6B LEU* 4.0 23.2 - - + +
7B PHE* 4.3 7.1 - + + -
51B ILE* 4.6 0.4 - - - +
65B ILE* 3.0 39.8 + - + +
67B GLY* 3.7 26.7 - - - -
69B PRO* 3.8 30.5 - - + -
90B LEU 3.6 1.2 + - - -
91B PHE* 2.8 16.5 + + + +
93B GLU* 1.3 81.1 - - - +
95B ILE* 1.3 65.4 + - + +
97B ILE* 3.5 3.6 + - - +
98B LEU* 3.1 21.3 + - + +
106B PHE* 3.8 22.5 - + + -
107B LEU 3.0 24.3 + - - -
108B ALA* 3.8 13.5 - - + -
130B PHE* 4.6 8.7 - + - -
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Residues in contact with ILE 95 (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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91B PHE* 3.9 16.4 - - + +
92B TYR* 2.9 38.7 + - + +
94B TYR* 1.3 78.1 - - + +
96B ARG* 1.3 50.6 + - - +
98B LEU* 3.0 12.3 - - + +
99B LYS* 2.8 58.7 + - + +
126B PHE* 4.1 15.3 - - + -
129B GLU* 4.2 17.9 - - + -
130B PHE* 3.7 34.1 - - + -
133B ALA* 6.2 0.4 - - + -
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Residues in contact with ARG 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 4.2 5.9 + - - +
52B SER 4.5 7.7 + - - -
54B ILE 2.6 29.9 + - - -
55B SER* 4.1 1.2 - - - +
56B SER* 4.0 9.5 - - - +
92B TYR 2.6 15.0 + - - +
93B GLU* 2.5 45.8 + - - +
95B ILE* 1.3 71.1 - - - +
97B ILE* 1.3 87.4 + - - +
99B LYS* 2.9 12.3 + - + +
100B GLN* 2.9 42.8 + - - +
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Residues in contact with ILE 97 (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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4B ILE* 4.2 17.0 - - + -
6B LEU* 4.1 9.2 - - + -
51B ILE* 3.9 16.8 - - + -
56B SER* 4.4 6.7 - - - -
59B PHE* 3.3 34.5 - - + -
65B ILE* 3.8 14.8 - - + -
93B GLU 3.2 11.6 + - - +
94B TYR 3.9 3.6 - - - +
96B ARG* 1.3 98.4 - - - +
98B LEU* 1.3 54.1 + - - +
100B GLN* 2.9 7.2 + - - +
101B LYS* 2.6 53.7 + - + +
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Residues in contact with LEU 98 (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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65B ILE* 3.8 12.9 - - + +
94B TYR* 3.1 14.9 + - + +
95B ILE* 3.0 13.0 - - + +
96B ARG 3.0 0.2 - - - -
97B ILE* 1.3 77.8 - - - +
99B LYS* 1.3 58.8 + - - +
100B GLN 3.0 0.2 + - - -
102B LYS* 2.7 36.6 + - - +
103B PRO* 3.4 35.0 - - + -
106B PHE* 3.8 26.7 - - + -
130B PHE* 3.6 35.7 - - + -
133B ALA* 4.6 6.5 - - + -
135B TYR* 3.7 20.9 - - + -
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Residues in contact with LYS 99 (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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95B ILE* 2.8 35.2 + - + +
96B ARG* 2.9 12.3 + - + +
98B LEU* 1.3 73.6 - - - +
100B GLN* 1.3 68.6 + - - +
102B LYS* 3.0 33.8 + - - +
129B GLU* 3.0 36.4 + - - -
132B ASN* 5.6 7.0 - - - +
133B ALA* 4.5 16.8 - - + -
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Residues in contact with GLN 100 (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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56B SER* 3.6 34.5 + - - +
96B ARG* 2.9 35.2 + - + +
97B ILE* 2.9 6.3 + - - +
99B LYS* 1.3 89.2 - - - +
101B LYS* 1.3 66.3 + - + +
102B LYS* 3.4 1.5 - - - +
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Residues in contact with LYS 101 (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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4B ILE* 5.5 1.3 - - + -
56B SER* 3.5 31.2 + - - -
57B ASP* 4.6 3.4 + - - +
59B PHE* 3.0 28.2 + - + -
60B PRO 3.1 28.0 + - - +
61B LYS* 4.5 7.8 - - - +
62B CYS* 4.5 20.9 + - - +
65B ILE* 4.5 12.3 - - + -
97B ILE* 2.6 34.7 + - + +
98B LEU 4.4 0.2 - - - +
100B GLN* 1.3 77.5 + - + +
102B LYS* 1.3 69.9 + - - +
103B PRO* 3.4 1.7 - - + +
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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