Contacts of the strand formed by residues 70 - 77 (chain D) in PDB entry 1R6O
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 70 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D ILE* 3.8 21.6 - - + +
32D LEU 3.2 15.5 - - - +
33D VAL* 4.4 8.3 - - + -
64D ALA 3.7 2.1 - - - +
65D VAL* 3.6 7.6 + - - +
68D GLN* 3.2 26.6 - - + +
69D GLY* 1.3 79.2 - - - +
71D ALA* 1.3 67.0 + - - +
104D GLU* 4.3 15.8 + - - -
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Residues in contact with ALA 71 (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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31D ILE* 3.4 4.6 - - - -
32D LEU* 3.0 31.6 + - + +
61D LEU* 4.1 16.4 - - + +
64D ALA* 4.1 13.2 - - + -
65D VAL* 3.6 26.7 - - + +
68D GLN* 5.4 1.1 - - - +
70D LYS* 1.3 80.7 - - - +
72D ILE* 1.3 64.9 + - - +
73D CYS* 3.6 1.5 + - - -
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Residues in contact with ILE 72 (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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29D LYS* 3.9 40.2 - - + +
30D VAL 3.5 6.7 - - - +
31D ILE* 4.3 13.9 - - + -
53D TYR* 4.7 1.7 + - - -
61D LEU* 3.8 18.9 - - - +
71D ALA* 1.3 74.2 - - - +
73D CYS* 1.3 61.8 - - - +
74D GLY* 3.7 24.2 - - - +
75D VAL* 4.7 5.6 - - + -
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Residues in contact with CYS 73 (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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30D VAL 2.7 19.0 + - - +
31D ILE 4.4 1.8 - - - -
32D LEU* 3.8 32.8 - - - -
47D LEU* 3.8 21.1 - - + -
51D PHE* 3.6 44.5 - - + +
53D TYR* 2.6 33.4 + - - -
61D LEU* 5.3 1.6 - - - -
71D ALA* 4.0 2.7 - - - -
72D ILE* 1.3 72.8 - - - +
74D GLY* 1.3 55.1 + - - +
76D PHE* 4.8 1.0 - - - -
101D CYS* 5.6 0.7 - - - -
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Residues in contact with GLY 74 (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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29D LYS* 3.4 3.8 - - - -
30D VAL 2.8 27.6 + - - -
53D TYR* 4.8 0.4 - - - -
72D ILE* 3.5 7.6 - - - +
73D CYS* 1.3 81.8 - - - +
75D VAL* 1.3 63.6 + - - +
76D PHE* 3.5 19.2 - - - -
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Residues in contact with VAL 75 (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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27D MET* 4.1 30.7 - - + +
28D TYR 3.4 11.7 - - - +
29D LYS* 4.3 17.9 - - + -
72D ILE* 4.7 6.7 - - + -
74D GLY* 1.3 78.0 - - - +
76D PHE* 1.3 73.7 + - - +
106D ALA* 4.3 9.6 - - + -
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Residues in contact with PHE 76 (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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65B THR 6.0 1.8 - - - +
67B PRO* 4.3 17.0 - - + -
27D MET* 3.4 13.3 - - - -
28D TYR 2.7 35.1 + - - +
30D VAL* 3.5 30.3 - - + -
51D PHE* 4.2 11.4 - + + -
73D CYS 4.8 0.7 - - - -
74D GLY* 3.5 28.3 - - - -
75D VAL* 1.3 79.1 - - - +
77D THR* 1.3 68.4 + - - +
80D VAL* 3.7 26.0 - - + -
81D ALA* 3.9 4.7 - - - +
84D LYS* 3.8 32.5 - - + -
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Residues in contact with THR 77 (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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61B PHE* 3.7 23.0 - - + -
65B THR* 3.5 38.5 + - + +
26D SER 4.5 0.4 - - - -
27D MET* 3.7 21.0 - - + +
76D PHE* 1.3 77.1 - - - +
78D ALA* 1.3 59.1 + - - +
79D GLU* 3.6 8.2 + - - +
80D VAL* 3.1 29.0 + - + +
81D ALA* 2.8 27.8 + - - +
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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