Contacts of the helix formed by residues 94 - 112 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A GLY 4.8 1.8 + - - -
92A GLU 3.9 2.4 + - - -
93A CYS* 1.3 82.3 - - - +
95A GLN* 1.3 62.0 + - - +
96A ASP* 3.4 13.3 + - - +
97A GLU* 3.5 20.7 + - - +
98A SER* 2.9 19.9 + - - -
241B GLU* 4.0 20.6 + - - -
245B GLN* 5.7 1.4 - - - +
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Residues in contact with GLN 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A SER* 1.3 79.0 - - - +
96A ASP* 1.3 74.8 + - - +
97A GLU 3.3 1.6 - - - -
98A SER* 3.4 7.2 + - - +
99A GLY* 2.9 26.8 + - - -
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A SER* 3.4 5.9 + - - +
95A GLN* 1.3 96.0 + - - +
97A GLU* 1.3 63.5 + - + +
99A GLY* 3.9 0.3 - - - -
100A ALA* 3.0 26.9 + - - +
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 3.8 30.4 - - - +
48A LYS* 3.9 23.0 + - - +
49A PHE 4.6 2.4 + - - -
65A GLY 5.2 7.4 - - - +
66A ASP* 5.6 2.7 - - - +
67A ALA* 3.6 14.5 - - + +
93A CYS* 4.1 14.6 - - - -
94A SER* 3.5 17.6 + - - +
96A ASP* 1.3 79.3 - - + +
98A SER* 1.3 59.6 + - - +
99A GLY 3.1 1.3 - - - -
100A ALA* 3.3 5.2 + - - +
101A ALA* 3.0 25.6 + - - +
145A VAL* 4.8 12.6 - - - +
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Residues in contact with SER 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA* 4.2 2.0 - - - -
87A TYR* 4.5 3.8 - - - -
89A LEU* 3.3 35.2 - - - -
93A CYS* 4.0 5.5 - - - -
94A SER 2.9 23.9 + - - -
95A GLN* 3.4 10.4 + - - +
97A GLU* 1.3 75.6 - - - +
99A GLY* 1.3 66.7 + - - +
101A ALA* 3.3 4.5 + - - +
102A ALA* 3.0 23.2 + - - +
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLN* 2.9 26.3 + - - -
96A ASP* 3.9 1.1 - - - -
98A SER* 1.3 75.8 + - - +
100A ALA* 1.3 65.0 + - - +
101A ALA 3.1 0.2 + - - -
102A ALA* 3.1 7.1 + - - +
103A ILE* 2.9 33.9 + - - +
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 3.5 20.4 - - + -
49A PHE* 3.8 26.2 - - + +
96A ASP 3.0 18.1 + - - +
97A GLU* 3.5 9.0 - - - +
99A GLY* 1.3 76.2 - - - +
101A ALA* 1.3 62.0 + - - +
103A ILE* 3.4 12.9 + - - +
104A PHE* 3.0 31.1 + - - -
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 4.1 14.3 - - + +
67A ALA* 3.9 18.6 - - + -
68A TYR 4.7 2.9 - - - +
69A VAL* 4.3 4.4 - - + +
87A TYR* 3.9 23.1 - - + -
89A LEU* 4.7 0.4 - - + -
97A GLU 3.0 13.6 + - - +
98A SER* 3.4 9.4 - - - +
99A GLY 3.1 0.2 - - - -
100A ALA* 1.3 74.1 - - - +
102A ALA* 1.3 65.7 + - - +
104A PHE* 3.2 3.9 + - - +
105A THR* 3.0 26.9 + - - -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TYR* 3.9 22.6 - - + +
98A SER 3.0 15.6 + - - +
99A GLY* 3.1 6.0 + - - +
101A ALA* 1.3 75.4 - - - +
103A ILE* 1.3 63.9 + - + +
105A THR* 3.4 4.5 + - - -
106A VAL* 3.2 29.1 + - - +
332A LEU* 3.9 15.6 - - + +
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 4.2 27.4 - - + -
99A GLY* 2.9 23.8 + - - +
100A ALA* 3.5 11.7 - - - +
102A ALA* 1.3 79.0 - - + +
104A PHE* 1.3 57.2 + - + +
106A VAL* 3.5 5.3 + - - +
107A GLN* 3.1 60.1 + - + +
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 4.2 16.8 - + + -
32A PHE* 4.3 14.1 - + + -
46A VAL* 4.2 10.3 - - + -
49A PHE* 3.7 45.5 - + - -
50A ASP* 3.9 14.1 - - - -
51A LEU* 3.5 46.0 - - + -
69A VAL* 4.2 12.8 - - + -
100A ALA 3.0 24.7 + - - +
101A ALA 3.2 4.7 + - - +
103A ILE* 1.3 74.6 - - + +
105A THR* 1.3 61.1 + - - +
107A GLN* 4.6 9.9 - - - +
108A LEU* 2.8 37.4 + - + +
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 4.6 4.9 - - - +
85A LEU* 3.3 37.0 - - + +
86A HIS 4.9 0.2 - - - -
87A TYR* 3.4 31.7 + - + +
101A ALA 3.0 14.4 + - - -
102A ALA 3.7 8.1 - - - -
104A PHE* 1.3 76.1 - - - +
106A VAL* 1.3 57.9 + - - +
109A ASP 2.9 23.9 + - - -
118A GLN* 3.2 34.5 + - + +
332A LEU* 4.3 9.0 - - + -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ALA 3.2 14.2 + - - +
103A ILE* 3.6 8.7 - - - +
105A THR* 1.3 77.7 - - - +
107A GLN* 1.3 64.5 + - + +
109A ASP* 3.3 6.1 + - - +
110A ASP* 3.1 24.6 + - - +
118A GLN* 3.9 9.6 - - - +
329A LYS* 3.9 51.7 + - + +
332A LEU* 3.8 22.9 - - + +
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 3.6 16.8 - - + -
49A PHE* 5.6 1.7 - - - -
103A ILE* 3.1 38.5 + - + +
104A PHE* 4.2 11.0 - - - +
106A VAL* 1.3 81.1 - - + +
108A LEU* 1.3 60.6 + - - +
110A ASP* 3.5 8.8 - - - +
111A TYR* 3.0 26.0 + - - +
329A LYS* 5.9 3.8 - - - +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 3.9 27.1 - - + -
35A ALA* 4.3 18.2 - - + -
44A TRP* 4.6 15.3 - - + -
51A LEU* 5.4 4.3 - - + -
69A VAL* 4.3 15.0 - - + -
71A LEU* 4.9 3.1 - - + -
85A LEU* 4.0 24.2 - - + -
104A PHE 2.8 19.7 + - - +
105A THR 3.8 3.4 - - - +
107A GLN* 1.3 74.1 - - - +
109A ASP* 1.3 66.6 + - - +
111A TYR* 3.2 10.0 + - + +
112A LEU* 3.1 42.9 + - + +
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Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 3.8 11.4 - - + +
105A THR 2.9 8.1 + - - +
106A VAL 3.5 4.9 - - - +
107A GLN 3.3 0.2 - - - -
108A LEU* 1.3 79.1 - - - +
110A ASP* 1.3 54.2 + - - +
112A LEU* 3.1 11.6 + - - +
113A ASN 3.3 0.3 + - - -
114A GLY* 2.6 45.4 + - - -
116A ALA* 3.0 35.5 + - - +
118A GLN* 3.3 32.8 + - - +
319A LYS* 3.9 15.8 + - - -
328A ARG* 5.7 2.1 - - - -
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Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL 3.1 13.2 + - - +
107A GLN* 3.5 12.8 - - - +
108A LEU 3.2 0.2 - - - -
109A ASP* 1.3 79.1 + - - +
111A TYR* 1.3 57.3 + - - +
113A ASN* 2.9 21.7 + - - +
114A GLY* 4.0 6.4 + - - +
329A LYS* 3.2 30.5 + - - +
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Residues in contact with TYR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.6 34.0 + - + -
32A PHE* 3.3 50.3 - + + -
33A LEU* 3.2 26.8 - - + +
35A ALA 5.1 0.9 - - - -
37A LYS* 4.3 15.3 + - - -
107A GLN 3.0 14.1 + - - +
108A LEU* 3.2 9.8 + - + +
110A ASP* 1.3 77.3 - - - +
112A LEU* 1.3 75.3 + - + +
113A ASN* 3.1 9.3 + - - +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA 4.1 19.1 - - - +
71A LEU* 4.1 20.9 - - + -
83A TYR* 4.2 43.2 - - + +
85A LEU* 5.1 2.2 - - + -
108A LEU* 3.1 38.5 + - + +
109A ASP* 3.4 10.1 - - - +
110A ASP 3.1 0.6 - - - -
111A TYR* 1.3 89.9 - - + +
113A ASN* 1.3 71.5 + - - +
115A ARG* 3.2 23.2 - - + +
116A ALA* 5.0 4.5 - - + -
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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