Contacts of the helix formed by residues 94 - 112 (chain B) in PDB entry 1D0N
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 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLU* 4.0 15.0 - - - -
92B GLU 3.8 2.4 + - - -
93B CYS* 1.3 77.7 - - - +
95B GLN* 1.3 67.2 + - - +
96B ASP* 3.7 2.4 + - - +
97B GLU* 2.8 49.6 + - - -
98B SER* 2.7 36.6 + - - -
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Residues in contact with GLN 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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94B SER* 1.3 80.7 - - - +
96B ASP* 1.3 96.9 + - - +
98B SER* 2.9 8.6 + - - -
99B GLY* 2.8 25.3 + - - -
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B SER* 3.3 3.1 - - - +
95B GLN* 1.3 100.7 + - - +
97B GLU* 1.3 57.1 + - + +
99B GLY* 3.6 1.4 - - - -
100B ALA* 2.8 34.1 + - - +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLU* 4.0 9.9 - - - +
245A GLN* 4.4 5.4 + - - -
46B VAL* 4.0 16.6 - - + +
48B LYS* 5.7 6.1 - - - +
65B GLY 2.9 25.6 - - - +
66B ASP* 4.5 5.0 - - - +
67B ALA* 3.5 17.2 - - + +
93B CYS* 4.0 7.2 - - - -
94B SER* 2.8 32.6 + - - +
96B ASP* 1.3 79.5 - - + +
98B SER* 1.3 61.8 + - - +
100B ALA* 3.4 8.1 + - - +
101B ALA 3.1 17.5 + - - -
145B VAL* 5.7 7.4 - - + -
146B ALA* 4.9 7.6 + - - +
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 4.2 1.8 - - - -
87B TYR* 4.6 1.6 - - - -
89B LEU* 3.2 39.7 - - - +
93B CYS* 4.0 5.3 - - - -
94B SER 2.7 24.5 + - - -
95B GLN* 2.9 18.9 + - - -
97B GLU* 1.3 75.3 - - - +
99B GLY* 1.3 63.3 + - - +
101B ALA* 3.4 3.3 + - - +
102B ALA* 3.2 21.5 + - - +
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLN 2.8 19.3 + - - -
96B ASP* 3.2 2.2 + - - -
98B SER* 1.3 75.9 + - - +
100B ALA* 1.3 64.9 + - - +
102B ALA* 3.2 7.1 + - - +
103B ILE* 2.9 32.6 + - - +
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 3.8 15.3 - - + -
49B PHE* 3.6 36.5 - - + +
96B ASP 2.8 17.0 + - - +
97B GLU* 3.6 7.2 - - - +
98B SER 3.3 0.2 - - - -
99B GLY* 1.3 76.2 - - - +
101B ALA* 1.3 57.3 + - - +
103B ILE* 3.2 7.3 + - - +
104B PHE* 2.9 35.2 + - + -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 3.9 17.7 - - + +
67B ALA* 3.8 19.3 - - + -
68B TYR 4.5 1.8 - - - +
69B VAL* 4.1 5.9 - - + +
87B TYR* 4.1 21.8 - - + -
89B LEU* 4.7 0.2 - - + -
97B GLU 3.1 11.7 + - - +
98B SER 3.6 8.5 - - - +
99B GLY 3.2 0.4 - - - -
100B ALA* 1.3 79.7 - - - +
102B ALA* 1.3 56.5 + - - +
104B PHE* 3.3 3.7 + - - +
105B THR* 3.0 31.7 + - - -
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Residues in contact with ALA 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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87B TYR* 4.0 28.2 - - + +
98B SER 3.2 11.0 + - - +
99B GLY* 3.2 9.6 + - - +
101B ALA* 1.3 75.1 - - - +
103B ILE* 1.3 67.3 + - + +
105B THR* 3.3 5.8 + - - -
106B VAL* 3.1 29.8 + - - +
332B LEU* 3.9 11.1 - - + +
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Residues in contact with ILE 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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49B PHE* 3.9 32.3 - - + -
99B GLY* 2.9 26.0 + - - +
100B ALA* 3.2 8.7 + - - +
102B ALA* 1.3 77.4 - - + +
104B PHE* 1.3 57.9 + - + +
106B VAL* 3.3 8.0 + - - +
107B GLN* 3.0 57.8 + - - +
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Residues in contact with PHE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU 6.0 0.4 - - - -
29B HIS* 3.8 24.0 - + + -
32B PHE* 4.1 13.4 - + - -
46B VAL* 4.5 7.9 - - + -
49B PHE* 3.5 53.6 - + - -
50B ASP* 3.9 7.6 - - - -
51B LEU* 3.6 45.3 - - + -
69B VAL* 4.3 7.9 - - + -
100B ALA 2.9 23.3 + - - +
101B ALA 3.7 4.7 - - - +
103B ILE* 1.3 77.3 - - - +
105B THR* 1.3 56.0 + - - +
107B GLN* 4.6 12.6 - - - +
108B LEU* 2.8 32.6 + - - +
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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
----------------------------------------------------------
69B VAL* 4.5 3.8 - - - +
85B LEU* 3.6 32.3 - - + +
87B TYR* 3.4 35.4 - - + +
101B ALA 3.0 18.4 + - - -
102B ALA* 3.6 5.4 - - - -
103B ILE 3.2 0.2 - - - -
104B PHE* 1.3 77.2 - - - +
106B VAL* 1.3 56.6 + - - +
108B LEU 3.3 0.2 + - - -
109B ASP* 2.9 24.3 + - - +
118B GLN* 3.2 38.5 + - + +
332B LEU* 4.4 5.4 - - + -
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ALA 3.1 15.1 + - - +
103B ILE* 3.6 9.4 - - - +
105B THR* 1.3 77.5 - - - +
107B GLN* 1.3 62.6 + - + +
109B ASP* 3.3 5.9 + - - +
110B ASP* 3.0 24.8 + - - +
118B GLN* 3.7 9.4 - - - +
328B ARG 5.3 1.6 - - - +
329B LYS* 4.0 52.9 - - + +
332B LEU* 3.4 24.7 - - + +
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Residues in contact with GLN 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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28B GLU* 5.6 7.8 - - + +
32B PHE* 3.5 22.1 - - + -
49B PHE* 6.0 0.3 - - - -
103B ILE* 3.0 41.2 + - - +
104B PHE* 4.2 14.2 - - - +
106B VAL* 1.3 78.7 - - + +
108B LEU* 1.3 60.3 + - - +
110B ASP* 3.4 10.8 + - + +
111B TYR* 3.1 20.8 + - - +
329B LYS* 5.7 6.1 - - - -
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Residues in contact with LEU 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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32B PHE* 3.8 39.0 - - + -
35B ALA* 4.1 16.4 - - + -
44B TRP* 4.4 23.3 - - + -
51B LEU* 5.6 2.2 - - + -
69B VAL* 4.4 7.6 - - + -
71B LEU* 4.6 7.6 - - + -
85B LEU* 3.9 28.3 - - + -
104B PHE 2.8 19.5 + - - +
105B THR* 3.8 3.4 - - - +
107B GLN* 1.3 74.7 - - - +
109B ASP* 1.3 65.7 + - - +
111B TYR* 3.3 10.4 + - + -
112B LEU* 3.0 35.9 + - + +
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Residues in contact with ASP 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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85B LEU* 3.9 9.6 - - + +
105B THR 2.9 6.2 + - - +
106B VAL 3.4 6.0 - - - +
108B LEU* 1.3 77.9 - - - +
110B ASP* 1.3 57.5 + - - +
112B LEU* 2.9 13.7 + - - -
114B GLY* 2.8 52.0 + - - -
116B ALA* 3.3 27.3 + - - +
118B GLN* 3.3 33.3 + - - +
319B LYS* 3.7 19.5 + - - -
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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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106B VAL 3.0 13.2 + - - +
107B GLN* 3.5 14.3 - - + +
108B LEU 3.2 0.2 - - - -
109B ASP* 1.3 78.8 + - - +
111B TYR* 1.3 62.0 + - - +
113B ASN* 3.0 16.5 + - - +
114B GLY* 4.2 4.6 + - - +
329B LYS* 3.5 32.7 + - - +
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Residues in contact with TYR 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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27B VAL* 4.5 15.9 - - - -
28B GLU* 5.4 6.3 - - + -
32B PHE* 2.9 52.7 + + + -
33B LEU* 3.5 25.8 + - + +
35B ALA 5.0 3.4 - - - -
37B LYS* 5.1 7.2 - - - -
107B GLN 3.1 13.6 + - - +
108B LEU* 3.6 11.4 - - + +
109B ASP 3.2 0.2 - - - -
110B ASP* 1.3 75.6 - - - +
112B LEU* 1.3 75.9 + - + +
113B ASN* 3.0 14.4 + - - +
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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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35B ALA 4.4 14.8 - - - +
36B GLY 5.1 0.2 - - - +
71B LEU* 4.4 13.0 - - + -
83B TYR* 3.7 55.9 - - + +
85B LEU* 4.7 1.6 - - + -
108B LEU* 3.0 37.0 + - + +
109B ASP* 2.9 6.7 + - - +
111B TYR* 1.3 89.2 - - + +
113B ASN* 1.3 69.4 + - - +
114B GLY 3.0 3.1 + - - -
115B ARG* 2.9 30.2 + - - +
116B ALA* 4.6 9.9 - - + -
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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