Contacts of the strand formed by residues 68 - 75 (chain R) in PDB entry 4DOH
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 THR 68 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66R LYS* 4.0 18.8 + - - +
67R VAL* 1.3 76.7 - - - +
69R TYR* 1.3 73.1 + - - +
89R ASN* 3.0 22.0 + - - +
90R ILE 2.8 46.7 - - - +
91R ASN* 4.7 5.5 + - - +
114R ALA* 3.3 1.0 - - - -
115R ILE* 3.0 53.6 + - - +
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Residues in contact with TYR 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R PRO* 4.2 7.6 - - + -
56R TRP* 3.4 39.5 - + + -
58R PRO* 3.4 13.7 - - - +
59R PRO* 3.2 27.6 - - + +
67R VAL* 3.5 21.5 - - + +
68R THR* 1.3 88.3 - - - +
70R THR* 1.3 62.2 + - - +
87R CYS 3.2 8.8 - - - +
89R ASN* 3.2 2.9 + - - -
90R ILE* 3.1 35.0 + - + +
91R ASN 4.5 6.1 - - - -
92R ARG 2.8 27.6 - - - -
93R THR* 3.6 10.0 - - + +
112R VAL* 4.0 4.7 - - + -
113R ARG 3.3 13.5 - - - +
114R ALA* 3.8 19.1 - - + -
115R ILE* 5.0 0.9 - - - +
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Residues in contact with THR 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69R TYR* 1.3 72.4 - - - +
71R VAL* 1.3 61.2 + - - +
72R GLN* 6.4 0.4 - - - -
87R CYS 3.4 2.0 - - - -
88R ARG* 3.4 26.7 - - + -
89R ASN* 2.8 38.1 - - + +
112R VAL* 3.1 4.1 - - - +
113R ARG* 2.9 56.4 + - - +
115R ILE* 3.9 9.3 - - + +
123R TRP* 4.1 7.6 - - - -
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Residues in contact with VAL 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R LEU* 4.0 16.8 - - + -
56R TRP* 4.4 6.1 - - + -
69R TYR 5.0 0.2 - - - +
70R THR* 1.3 79.4 - - - +
72R GLN* 1.3 73.6 + - - +
73R TYR 4.9 0.4 - - - +
83R ASN* 4.6 0.2 - - - -
84R LYS* 3.7 29.2 + - + +
87R CYS* 3.3 31.7 + - + +
90R ILE* 4.9 2.7 - - + -
95R CYS* 4.1 21.8 - - + -
97R LEU* 4.7 9.6 - - + -
111R ARG 3.1 12.6 - - - +
112R VAL* 4.0 14.6 - - + -
123R TRP* 5.1 0.2 - - - -
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Residues in contact with GLN 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70R THR* 6.4 0.2 - - - -
71R VAL* 1.3 80.8 - - - +
73R TYR* 1.3 61.2 + - - +
81R TRP* 3.5 22.0 - - + +
82R LEU 3.2 14.5 - - - +
83R ASN* 3.1 23.5 + - - +
84R LYS 5.1 0.2 - - - +
110R ALA* 3.3 4.7 - - - +
111R ARG* 2.7 79.4 + - + +
123R TRP* 3.4 21.6 - - + -
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Residues in contact with TYR 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72R GLN* 1.3 74.3 - - - +
74R PHE* 1.3 59.4 + - - +
75R ILE* 4.5 16.2 - - + -
81R TRP* 3.5 5.2 - - - -
82R LEU* 3.0 73.1 + - + +
83R ASN 3.7 16.8 - - - -
84R LYS* 4.8 3.6 - - + -
97R LEU* 4.4 24.5 - - + -
100R GLU* 3.4 53.5 - - + +
101R THR* 5.3 3.1 - - + -
108R TYR* 4.9 4.3 - + - -
109R TYR 3.6 9.6 - - - +
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Residues in contact with PHE 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ILE* 3.3 47.1 - - + -
61A ASP* 4.2 5.2 - - + -
73R TYR* 1.3 73.4 - - - +
75R ILE* 1.3 92.3 + - - +
76R TYR* 3.7 2.0 - - - -
78R GLN* 3.0 31.6 - - + -
79R LYS 3.4 24.0 - - - -
80R LYS 4.1 4.0 - - - -
81R TRP* 3.2 57.0 - + + -
108R TYR* 3.4 7.6 - - - +
109R TYR* 2.8 35.9 + + + +
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Residues in contact with ILE 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73R TYR* 4.5 17.5 - - + -
74R PHE* 1.3 83.1 - - - +
76R TYR* 1.3 67.1 - - - +
77R GLY 3.2 0.2 + - - -
78R GLN* 2.9 50.1 + - + +
80R LYS 5.0 3.4 + - - -
82R LEU* 5.0 10.3 - - + -
100R GLU 5.2 0.9 - - - +
106R HIS* 3.9 35.7 - - + +
107R GLN 3.8 8.1 - - - +
108R TYR* 3.8 21.3 - - + -
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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