Contacts of the strand formed by residues 97 - 109 (chain D) in PDB entry 3DOY
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 LYS 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D PRO* 3.8 8.9 - - - +
83D PHE* 4.1 6.3 - - + -
87D TRP* 3.2 42.0 - - + -
93D ILE* 3.8 16.8 - - - +
94D ALA 3.4 13.6 + - - +
95D LYS 3.2 2.2 + - - -
96D THR* 1.3 98.5 - - - +
98D ILE* 1.3 65.8 + - - +
131D MET* 4.8 5.2 - - - -
155D ILE* 3.9 23.8 - - + -
156D ALA 3.2 16.2 - - - +
157D GLU* 2.8 33.0 + - - +
158D ARG* 3.0 20.5 + - - +
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Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C PHE* 4.3 24.2 - - + -
62C LYS* 4.5 12.8 - - + -
64C ILE* 4.1 18.6 - - + -
22D PRO* 4.0 13.7 - - + -
97D LYS* 1.3 80.5 - - - +
99D VAL* 1.3 67.5 + - - +
100D TYR* 3.5 35.2 - - + +
155D ILE* 3.4 7.2 - - - +
156D ALA* 2.9 36.6 + - + +
157D GLU 5.4 0.7 - - - +
158D ARG* 3.8 35.9 - - + +
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C HIS* 5.6 0.3 + - - -
59C PHE* 4.0 22.2 - - - -
21D LEU* 5.4 4.0 - - + -
22D PRO* 4.6 7.4 - - + +
23D HIS* 4.7 19.5 + - + -
75D ALA 5.8 1.3 - - - +
79D GLY* 4.9 20.2 - - - +
98D ILE* 1.3 84.0 - - - +
100D TYR* 1.3 69.3 + - - +
101D PHE 4.3 0.7 + - - -
153D ALA* 3.6 26.0 - - + -
154D MET 3.2 13.5 - - - +
155D ILE* 4.6 15.0 - - + +
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Residues in contact with TYR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LYS* 4.7 6.9 - - - -
64C ILE* 3.2 33.2 - - + +
112C PRO* 3.7 37.7 - - + +
98D ILE* 3.5 24.7 - - + +
99D VAL* 1.3 76.5 - - - +
101D PHE* 1.3 69.1 + - - +
102D MET* 3.4 3.3 + - + +
153D ALA* 3.3 4.6 - - - -
154D MET* 2.7 54.3 + - + -
156D ALA* 4.3 20.9 - - + -
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Residues in contact with PHE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C VAL* 3.7 15.0 - - + -
109C PHE* 3.6 34.4 - + + +
1003C CL 3.8 26.3 - - + +
71D VAL* 4.0 7.4 - - + -
72D GLU* 3.4 23.6 - - - -
75D ALA* 3.2 33.0 - - + -
99D VAL 4.2 0.4 - - - -
100D TYR* 1.3 78.9 - - - +
102D MET* 1.3 60.5 + - - +
103D THR 3.9 6.3 - - - -
104D ILE* 3.5 38.1 - - + -
151D LEU* 3.6 27.6 - - + -
152D LYS 4.1 4.5 - - - -
153D ALA* 4.7 3.4 - - + +
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Residues in contact with MET 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LYS* 3.5 0.5 - - - +
109C PHE* 3.0 32.6 + - - +
100D TYR* 4.1 8.3 - - + +
101D PHE* 1.3 77.1 - - - +
103D THR* 1.3 68.1 + - + +
132D ILE* 4.4 20.0 - - + -
152D LYS* 2.8 59.3 + - + +
153D ALA 4.3 3.1 - - - +
154D MET* 3.8 34.3 - - + +
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Residues in contact with THR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C VAL 3.0 15.9 - - - +
108C LYS* 4.0 17.7 - - + -
109C PHE* 4.3 1.5 - - - -
101D PHE* 3.9 1.0 - - - -
102D MET* 1.3 86.2 - - + +
104D ILE* 1.3 71.9 + - - +
105D ASP* 5.0 5.6 + - - +
151D LEU* 3.2 6.4 - - - +
152D LYS* 3.0 60.2 + - - +
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C VAL* 4.4 9.0 - - + -
71C VAL* 5.2 4.3 - - + -
104C ILE* 5.3 2.5 - - + -
106C LYS 3.8 0.3 + - - -
107C VAL* 2.9 46.9 + - + +
109C PHE* 4.0 24.0 - - + -
71D VAL* 4.1 19.7 - - + -
101D PHE* 3.5 33.0 - - + -
103D THR* 1.3 81.0 - - - +
105D ASP* 1.3 68.8 + - - +
107D VAL* 3.4 27.4 - - + -
149D ALA* 5.0 0.4 - - + -
150D GLU 3.3 11.0 - - - +
151D LEU* 4.8 0.7 - - + -
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Residues in contact with ASP 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ILE 4.5 0.2 - - - -
105C ASP* 3.5 16.7 - - - +
106C LYS* 3.5 33.0 + - - +
107C VAL 4.0 2.8 + - - +
108C LYS* 5.2 3.5 + - - -
103D THR* 5.0 5.0 - - - +
104D ILE* 1.3 85.2 + - - +
106D LYS* 1.3 86.8 + - + +
107D VAL* 3.2 6.1 + - - +
150D GLU* 2.9 39.8 + - + +
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Residues in contact with LYS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ILE 3.8 0.2 + - - -
105C ASP* 3.1 30.6 + - - +
106C LYS* 6.0 2.9 - - - +
105D ASP* 1.3 88.2 + - + +
107D VAL* 1.3 62.1 + - - +
108D LYS* 3.7 22.3 + - + +
148D GLU* 3.8 4.2 - - - +
149D ALA* 3.7 11.1 + - - -
150D GLU* 4.2 24.8 + - + -
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Residues in contact with VAL 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C THR* 3.1 22.9 - - - +
104C ILE* 3.1 52.4 + - + +
105C ASP* 4.5 0.4 + - - +
71D VAL* 4.6 7.6 - - + -
104D ILE* 3.4 34.1 - - + -
105D ASP 3.6 7.6 - - - +
106D LYS* 1.3 73.9 - - - +
108D LYS* 1.3 59.2 + - - +
109D PHE* 4.1 15.5 - - + -
148D GLU 3.1 11.9 - - - +
149D ALA* 3.8 9.6 - - + -
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Residues in contact with LYS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C MET 3.5 3.6 - - - -
103C THR* 3.8 24.2 - - + +
105C ASP* 5.1 5.9 + - - -
106D LYS* 3.7 21.5 + - + +
107D VAL* 1.3 73.1 + - - +
109D PHE* 1.3 63.1 + - - +
110D ARG* 3.8 20.9 - - + +
147D ALA* 3.1 9.2 - - - +
148D GLU* 3.0 59.9 + - - +
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Residues in contact with PHE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PHE* 3.3 33.5 - - + +
102C MET* 2.9 24.8 + - - +
104C ILE* 3.7 32.8 - - + -
67D GLY* 3.3 46.7 - - - -
68D VAL* 4.1 1.1 - - + -
70D ILE* 4.9 5.8 - - + -
71D VAL* 4.3 12.8 - - + -
107D VAL* 4.1 13.5 - - + -
108D LYS* 1.3 78.1 - - - +
110D ARG* 1.3 61.4 + - - +
111D ILE 3.8 2.2 - - - +
146D VAL 3.8 3.8 - - - +
147D ALA* 4.0 14.8 - - + -
148D GLU 5.7 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