Contacts of the strand formed by residues 68 - 72 (chain I) in PDB entry 1D3B
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 ILE 68 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I CYS* 3.5 25.6 - - - -
21I GLU 3.8 4.3 - - - +
22I THR* 4.1 0.2 - - - +
23I ASN* 3.5 9.2 + - - +
39I MET* 3.9 20.9 - - + +
41I CYS* 4.5 5.4 - - - -
63I ILE* 3.7 15.0 - - + +
64I ARG 3.4 17.3 - - - +
65I GLY* 3.1 10.4 + - - +
66I CYS 5.0 0.3 - - - -
67I LYS* 1.3 78.9 - - - +
69I ARG* 1.3 60.0 + - - +
70I PHE 3.5 29.6 - - - +
71I LEU* 4.0 19.3 - - + -
73J ARG* 3.0 33.1 - - + +
75J GLU* 6.0 0.3 - - - +
76J ASN* 3.9 1.7 + - - -
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Residues in contact with ARG 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I GLU* 2.8 47.6 + - - +
22I THR 3.5 18.4 + - - +
23I ASN* 2.9 33.0 + - - +
68I ILE* 1.3 73.9 - - - +
70I PHE* 1.3 76.9 + - + +
703I CIT 2.9 45.9 + - - +
21J LEU* 3.8 21.7 - - + +
23J ASP* 4.4 5.9 + - - -
25J ARG* 3.4 34.8 - - - +
27J PHE* 4.6 1.1 - - + -
72J LEU* 3.5 7.8 - - + +
73J ARG* 3.0 26.2 + - - +
76J ASN* 4.1 4.8 + - - +
51K ARG* 6.1 1.0 - - - +
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Residues in contact with PHE 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I THR* 5.3 2.5 - - + -
20I CYS 3.7 0.5 - - - -
21I GLU* 2.9 74.4 + - + +
68I ILE* 3.5 12.6 - - - +
69I ARG* 1.3 91.3 - - + +
71I LEU* 1.3 62.7 + - - +
72I ILE* 3.7 35.0 - - + -
27J PHE* 3.5 25.1 - + - -
47J GLU* 3.7 13.5 - - - -
65J ARG* 3.4 11.2 - - - -
67J LEU* 3.9 15.7 - - + -
70J VAL* 3.9 12.3 - - + -
71J LEU 3.2 13.7 - - - +
72J LEU* 3.9 4.5 - - + -
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Residues in contact with LEU 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I LEU* 4.1 24.9 - - + -
18I VAL* 4.2 17.3 - - + -
19I THR 3.1 13.2 - - - +
20I CYS* 4.0 19.5 - - + -
39I MET* 5.1 4.7 - - + -
41I CYS* 4.4 16.8 - - + -
43I MET* 5.8 0.2 - - - -
68I ILE* 4.0 21.5 - - + -
70I PHE* 1.3 77.7 - - - +
72I ILE* 1.3 64.0 + - - +
73I LEU* 3.9 13.2 + - + -
69J LEU 3.8 0.2 - - - +
70J VAL* 3.3 7.3 - - - +
71J LEU* 2.9 53.7 + - + -
73J ARG* 5.4 1.6 - - - -
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Residues in contact with ILE 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I VAL* 3.4 5.5 - - - +
19I THR* 2.7 51.7 + - + +
70I PHE* 3.7 29.8 - - + -
71I LEU* 1.3 74.7 - - - +
73I LEU* 1.3 66.6 + - - +
602I GOL 3.3 25.9 + - - -
65J ARG* 6.1 0.9 - - - +
67J LEU* 3.5 47.8 - - + +
68J GLY* 5.0 0.2 - - - -
69J LEU 3.5 9.6 - - - +
70J VAL* 4.5 1.8 - - + -
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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