Contacts of the helix formed by residues 85 - 99 (chain A) in PDB entry 1DSG
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 LEU 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A VAL* 4.2 10.5 - - + +
48A ARG* 3.5 35.7 - - + +
49A LEU* 3.5 30.8 - - + +
52A HIS* 3.4 40.6 - - + +
71A TYR* 3.3 19.4 + - + +
82A ASN* 2.8 36.5 + - + +
84A GLY* 1.3 79.0 - - - +
86A GLN* 1.3 58.7 + - - +
88A GLY* 2.7 20.8 + - - -
89A PHE 3.0 8.5 + - - -
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Residues in contact with GLN 86 (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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71A TYR* 3.6 8.5 + - + +
77A PHE* 3.6 37.2 + - + +
78A ASN* 4.5 15.2 - - - +
79A ASP 6.0 0.2 + - - -
82A ASN 4.4 2.6 + - - -
83A ALA* 4.1 10.9 - - - +
84A GLY* 3.2 27.8 + - - +
85A LEU* 1.3 79.0 - - + +
87A ASN* 1.3 57.7 + - - +
89A PHE* 3.1 3.0 + - - +
90A LYS* 2.9 42.5 + - - +
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Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 2.8 44.3 + - + +
42A TYR* 3.6 11.4 - - + -
45A VAL* 4.9 1.8 - - + -
84A GLY* 3.3 18.6 + - - +
85A LEU 3.0 0.6 - - - -
86A GLN* 1.3 81.1 - - - +
88A GLY* 1.3 55.9 + - - +
90A LYS* 3.8 6.8 + - - +
91A PHE* 3.2 24.1 + - - +
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Residues in contact with GLY 88 (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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45A VAL* 4.3 17.1 - - - +
46A LEU* 4.2 13.7 - - - -
49A LEU* 4.1 11.4 - - - -
85A LEU 2.7 9.7 + - - -
87A ASN* 1.3 76.9 - - - +
89A PHE* 1.3 68.0 + - - +
91A PHE* 3.2 8.3 + - - +
92A LEU* 3.1 27.0 + - - +
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Residues in contact with PHE 89 (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 LEU* 4.2 5.1 - - - +
71A TYR* 3.5 39.3 - + + +
72A ARG* 4.8 16.8 - - + -
77A PHE* 3.7 19.5 - + + -
85A LEU 3.0 4.9 + - - -
86A GLN 3.5 7.6 - - - +
88A GLY* 1.3 78.7 - - - +
90A LYS* 1.3 78.9 + - + +
92A LEU* 3.4 4.9 + - + +
93A GLU* 3.1 43.4 + - + +
108A PHE* 4.0 28.3 - + - -
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Residues in contact with LYS 90 (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 LYS* 5.1 0.7 + - - -
77A PHE* 3.5 28.7 - - - -
86A GLN* 2.9 25.6 + - - +
87A ASN* 4.0 7.0 - - - +
89A PHE* 1.3 88.0 - - + +
91A PHE* 1.3 65.6 + - - +
93A GLU* 3.2 17.8 + - - +
94A PRO* 3.1 20.3 - - - +
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Residues in contact with PHE 91 (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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26A ILE* 4.1 13.9 - - + -
29A LYS* 3.3 57.6 - - + +
30A LEU* 3.7 24.2 - - + -
42A TYR* 3.3 48.5 - + + -
46A LEU* 3.7 24.7 - - + -
87A ASN 3.2 14.5 + - - +
88A GLY* 3.2 10.5 + - - +
90A LYS* 1.3 77.6 - - - +
92A LEU* 1.3 69.9 + - + +
94A PRO* 3.1 22.9 - - - +
95A ILE* 3.7 12.1 - - + +
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Residues in contact with LEU 92 (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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26A ILE* 4.2 20.6 - - + -
46A LEU* 4.1 12.3 - - + -
49A LEU* 3.9 28.0 - - + -
88A GLY 3.1 11.2 + - - +
89A PHE* 3.9 4.7 - - + +
91A PHE* 1.3 94.5 - - + +
93A GLU* 1.3 66.0 + - - +
94A PRO 3.4 0.2 - - - -
95A ILE* 3.0 27.8 + - + +
96A HIS 3.1 9.7 + - - -
107A LEU* 4.0 29.1 - - + +
108A PHE* 4.1 23.8 - - + +
111A GLY* 4.6 6.3 - - - -
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Residues in contact with GLU 93 (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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89A PHE* 3.1 38.1 + - + +
90A LYS* 3.5 22.9 + - - +
92A LEU* 1.3 75.6 - - - +
94A PRO* 1.3 71.8 - - + +
96A HIS* 3.0 18.9 + - + +
97A LYS* 3.1 27.9 + - + +
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Residues in contact with PRO 94 (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 LYS* 3.4 23.3 - - + +
90A LYS 3.1 15.3 - - - +
91A PHE 3.1 15.0 - - - +
93A GLU* 1.3 92.3 - - + +
95A ILE* 1.3 56.1 + - + +
97A LYS* 3.3 24.8 - - + +
98A GLU* 3.0 27.9 + - - +
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Residues in contact with ILE 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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22A VAL* 4.2 9.0 - - + -
25A ALA* 4.7 14.1 - - + +
26A ILE* 4.1 19.3 - - + +
29A LYS* 4.2 13.0 - - + -
91A PHE* 3.7 32.5 - - + +
92A LEU* 3.0 26.5 + - + +
94A PRO* 1.3 77.5 - - + +
96A HIS* 1.3 60.0 + - - +
98A GLU* 2.9 10.0 + - - +
99A PHE* 2.8 46.8 + - + +
107A LEU* 4.2 19.5 - - + -
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Residues in contact with HIS 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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92A LEU 3.1 6.3 + - - +
93A GLU* 3.0 13.2 + - + +
95A ILE* 1.3 76.7 - - - +
97A LYS* 1.3 59.0 + - - +
99A PHE 2.9 3.8 - - - -
100A PRO* 2.8 41.8 + - + +
102A ILE* 2.5 46.3 + - + +
103A SER* 4.1 0.6 - - - -
104A SER* 3.5 33.3 + - - -
107A LEU* 3.6 20.1 - - + +
108A PHE* 5.8 2.4 - - - -
132A ASP* 5.3 1.3 - - - -
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Residues in contact with LYS 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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93A GLU* 3.1 31.0 + - + +
94A PRO* 3.3 23.5 - - + +
96A HIS* 1.3 78.8 - - - +
98A GLU* 1.3 60.9 + - - +
100A PRO* 3.3 15.4 - - - +
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Residues in contact with GLU 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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25A ALA* 4.8 7.7 - - - +
94A PRO 3.0 13.0 + - - +
95A ILE* 2.9 12.0 + - - +
97A LYS* 1.3 77.2 - - - +
99A PHE* 1.3 93.0 + - + +
100A PRO* 3.3 5.5 - - - +
101A TRP* 5.5 0.2 - - - -
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Residues in contact with PHE 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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21A LYS* 4.0 46.7 - - + -
22A VAL* 4.0 19.1 - - + -
25A ALA* 3.7 24.2 - - + -
95A ILE* 2.8 26.2 + - + +
96A HIS* 2.9 6.1 - - - +
98A GLU* 1.3 105.9 - - + +
100A PRO* 1.3 62.3 - - - +
101A TRP* 3.0 34.4 + + + +
102A ILE* 2.9 33.2 - - + +
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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