Contacts of the strand formed by residues 81 - 90 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B VAL 3.9 0.2 - - - +
67B ARG* 3.2 5.5 - - - +
68B ILE* 2.7 39.1 + - + +
78B ASN* 5.0 10.1 + - - +
79B ILE 3.5 13.9 - - - +
80B GLU* 1.3 89.8 + - - +
82B ILE* 1.3 62.3 + - - +
83B SER* 6.1 0.9 - - - -
112B VAL* 4.1 21.1 - - + -
113B ALA* 5.1 14.1 - - - +
118B ILE* 3.9 19.5 - - + -
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Residues in contact with ILE 82 (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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65B LEU* 3.8 26.9 - - + -
66B VAL 3.4 8.3 - - - +
67B ARG* 3.5 39.7 - - + +
80B GLU* 5.9 0.7 - - - +
81B LYS* 1.3 76.0 - - - +
83B SER* 1.3 66.5 + - - +
84B MET* 6.1 1.6 - - - -
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Residues in contact with SER 83 (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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65B LEU* 3.8 2.9 - - - +
66B VAL* 2.7 54.7 + - - +
68B ILE* 4.9 7.4 - - - -
81B LYS* 5.5 1.1 - - - -
82B ILE* 1.3 79.3 - - - +
84B MET* 1.3 79.4 + - - +
108B LEU* 3.7 20.9 - - - +
109B LYS* 4.2 2.3 + - - +
110B LYS 4.4 5.6 + - - -
112B VAL* 5.9 3.8 - - - -
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Residues in contact with MET 84 (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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36B LYS* 4.0 31.9 - - + +
61B GLU 5.5 2.0 - - - +
62B ASN* 5.1 11.7 - - - +
64B LEU 3.9 21.3 - - - +
65B LEU* 4.6 16.4 - - - -
82B ILE* 6.1 1.3 - - - -
83B SER* 1.3 92.0 + - - +
85B LEU* 1.3 66.0 + - - +
108B LEU* 3.5 2.9 - - - -
109B LYS* 3.0 40.2 + - + +
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Residues in contact with LEU 85 (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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33B LEU* 5.0 2.0 - - + -
52B VAL* 5.8 0.2 - - + -
61B GLU* 3.7 22.7 + - + +
62B ASN* 5.2 1.0 - - - +
64B LEU* 3.5 43.6 + - + +
65B LEU 4.8 1.1 - - - +
66B VAL* 4.2 18.8 - - + -
84B MET* 1.3 84.6 - - - +
86B GLU* 1.3 63.5 + - - +
87B LYS 4.5 6.3 - - - +
88B ILE* 4.1 8.3 - - + -
106B MET* 3.8 34.5 - - + -
107B LYS 3.4 7.2 - - - +
108B LEU* 3.9 21.8 - - + -
109B LYS* 3.5 15.3 + - - -
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Residues in contact with GLU 86 (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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50B ARG* 3.7 6.2 + - - -
61B GLU* 3.4 13.1 - - - +
62B ASN* 5.6 0.5 - - - +
85B LEU* 1.3 73.4 - - - +
87B LYS* 1.3 69.8 + - + +
89B TYR* 4.7 3.1 + - - -
107B LYS* 2.8 53.1 + - + +
108B LEU 3.9 10.1 - - - +
109B LYS* 3.7 26.8 + - + +
245B PHE 5.4 0.2 - - - +
254B GOL 3.5 13.3 + - - -
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Residues in contact with LYS 87 (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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61B GLU* 3.0 38.3 + - + +
85B LEU* 3.5 1.4 - - - +
86B GLU* 1.3 91.3 - - - +
88B ILE* 1.3 71.3 + - - +
89B TYR* 3.5 39.8 - - + +
107B LYS* 3.0 30.0 + - + +
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Residues in contact with ILE 88 (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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59B LEU* 3.9 26.9 - - + -
60B PHE* 3.4 34.8 - - + +
61B GLU* 3.3 23.2 - - - +
64B LEU* 4.6 3.4 - - + -
85B LEU* 4.1 17.3 - - + -
87B LYS* 1.3 89.6 - - - +
89B TYR* 1.3 72.4 + - - +
90B ILE* 4.3 10.9 + - + -
105B LEU 3.4 7.6 - - - +
106B MET* 3.9 21.5 - - + -
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Residues in contact with TYR 89 (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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51B TRP* 3.5 36.1 - + - -
86B GLU* 4.7 2.8 + - - -
87B LYS* 3.5 43.7 - - + +
88B ILE* 1.3 78.6 - - - +
90B ILE* 1.3 62.1 + - - +
104B ALA* 3.0 5.6 - - - -
105B LEU* 2.7 42.9 + - + +
107B LYS* 4.4 5.6 - - + +
237B TRP* 3.3 13.0 - - + -
241B VAL* 3.7 21.1 - - + -
245B PHE* 3.2 54.1 - + - +
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Residues in contact with ILE 90 (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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56B ALA* 3.8 13.0 - - + +
59B LEU* 4.1 20.0 - - + -
60B LEU* 3.7 36.3 - - + +
88B ILE* 4.2 11.8 + - + -
89B TYR* 1.3 77.0 - - - +
91B HIS* 1.3 75.5 + - - +
92B PRO* 3.2 6.2 - - - +
94B TYR* 3.7 29.6 - - + -
104B ALA* 4.0 14.6 - - + -
237B TRP* 3.7 2.9 + - - -
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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