Contacts of the strand formed by residues 81 - 90 (chain D) in PDB entry 1RD3
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 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D VAL 3.7 0.2 - - - +
67D ARG* 3.2 5.2 - - - -
68D ILE* 2.7 41.5 + - + +
78D ASN* 4.7 20.8 - - - +
79D ILE 3.6 13.7 - - - +
80D GLU* 1.3 95.9 + - - +
82D ILE* 1.3 68.1 + - - +
83D SER* 6.2 0.2 - - - -
112D VAL* 4.2 18.4 - - + -
113D ALA* 5.4 9.6 - - + +
118D ILE* 4.0 22.2 - - + -
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Residues in contact with ILE 82 (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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65D LEU* 3.7 26.5 - - + -
66D VAL 3.2 10.1 - - - +
67D ARG* 3.6 37.9 - - + +
76D TYR* 5.2 13.9 - - + +
80D GLU* 5.0 4.9 - - + +
81D LYS* 1.3 80.6 - - - +
83D SER* 1.3 70.9 + - - +
84D MET* 5.2 4.5 - - - -
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Residues in contact with SER 83 (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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65D LEU* 3.9 1.6 - - - -
66D VAL* 3.0 41.3 + - - +
68D ILE* 5.1 4.3 - - - -
81D LYS* 5.4 0.7 - - - -
82D ILE* 1.3 80.7 - - - +
84D MET* 1.3 76.2 + - - +
85D LEU* 4.8 0.3 - - - +
108D LEU* 3.4 36.0 - - - +
109D LYS 4.4 0.7 + - - -
110D LYS 4.0 8.3 + - - -
112D VAL* 5.9 2.7 - - - -
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Residues in contact with MET 84 (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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36D LYS* 3.3 42.8 - - - +
61D GLU 5.4 0.7 - - - +
64D LEU 4.8 2.9 - - - +
65D LEU* 4.6 19.1 - - + -
82D ILE* 5.2 4.3 - - - -
83D SER* 1.3 85.2 + - - +
85D LEU* 1.3 63.8 + - - +
108D LEU* 3.6 2.3 - - - -
109D LYS* 3.0 54.1 + - + +
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Residues in contact with LEU 85 (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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33D LEU* 4.8 2.9 - - + -
61D GLU* 3.5 34.0 + - + +
62D ASN* 5.8 1.2 + - - -
64D LEU* 3.5 41.4 + - + +
65D LEU* 4.7 1.8 - - - +
66D VAL* 4.4 12.6 - - + -
83D SER 4.8 1.3 - - - +
84D MET* 1.3 78.5 - - - +
86D GLU* 1.3 63.0 + - - +
87D LYS 4.8 1.8 - - - +
88D ILE* 4.5 9.9 - - + -
106D MET* 3.9 37.2 - - + -
107D LYS 3.8 3.8 - - - +
108D LEU* 3.8 26.0 - - + -
109D LYS* 3.9 14.6 + - - +
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Residues in contact with GLU 86 (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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61D GLU* 3.6 11.2 - - - +
85D LEU* 1.3 73.2 - - - +
87D LYS* 1.3 67.8 + - + +
89D TYR* 5.5 0.7 + - - -
107D LYS* 2.7 57.1 + - + +
108D LEU 4.0 1.3 - - - +
109D LYS* 3.7 36.5 - - + +
245D PHE 4.9 1.0 - - - +
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Residues in contact with LYS 87 (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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61D GLU* 3.1 24.7 + - - +
85D LEU* 3.7 1.2 - - - +
86D GLU* 1.3 91.6 - - + +
88D ILE* 1.3 69.8 + - - +
89D TYR* 3.3 42.4 - - + +
106D MET* 3.4 5.4 - - - +
107D LYS* 3.0 29.3 + - + +
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Residues in contact with ILE 88 (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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59D LEU* 3.7 27.4 - - + -
60D PHE 3.9 14.1 - - + -
61D GLU* 3.5 40.7 + - + +
64D LEU* 3.7 30.5 - - + -
85D LEU* 4.5 5.4 - - + -
87D LYS* 1.3 87.1 - - - +
89D TYR* 1.3 68.8 + - - +
90D ILE* 4.0 16.9 + - + -
105D LEU 3.7 2.5 - - - +
106D MET* 4.5 12.1 - - + -
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Residues in contact with TYR 89 (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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51D TRP* 3.6 31.6 - + - -
86D GLU* 5.5 0.5 + - - -
87D LYS* 3.3 44.6 - - + +
88D ILE* 1.3 76.5 - - - +
90D ILE* 1.3 63.0 + - - +
91D HIS 4.1 0.2 - - - -
104D ALA* 3.2 4.7 - - - -
105D LEU* 2.8 46.7 + - + +
107D LYS* 4.4 3.4 - - + +
237D TRP* 3.6 10.8 - - + -
241D VAL* 3.6 20.4 - - + -
245D PHE* 3.0 62.0 - + + +
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Residues in contact with ILE 90 (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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56D ALA* 3.8 22.2 - - + +
59D LEU* 4.0 25.8 - - + -
60D LEU* 3.8 36.1 - - + +
88D ILE* 4.0 18.0 + - + +
89D TYR* 1.3 74.9 - - - +
91D HIS* 1.3 79.9 + - - +
92D PRO* 3.1 6.2 - - - +
94D TYR* 3.9 14.8 - - + -
103D ILE 4.1 2.7 - - - -
104D ALA* 4.1 3.1 - - + -
237D TRP* 4.0 2.1 - - - -
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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