Contacts of the strand formed by residues 64 - 70 (chain D) in PDB entry 3D87
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 GLY 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D LEU* 4.2 0.7 - - - -
41D ASP* 3.4 11.4 - - - -
63D ALA* 1.3 81.5 - - - +
65D GLN* 1.3 57.3 + - - -
66D TYR* 4.1 1.6 - - - -
79D LEU* 2.8 13.6 - - - +
80D LEU* 2.5 39.6 + - - +
196D LEU* 3.0 20.8 - - - +
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Residues in contact with GLN 65 (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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7D ASP* 4.6 3.1 - - - +
8D VAL* 5.3 1.4 - - - +
39D THR 3.7 0.2 - - - +
40D LEU* 3.6 2.0 - - - +
41D ASP* 2.2 63.4 + - - +
64D GLY* 1.3 71.6 - - - -
66D TYR* 1.3 69.3 + - - +
67D THR* 3.8 5.6 + - - +
77D HIS* 3.5 28.3 + - + +
78D SER 3.3 3.3 + - - +
79D LEU* 3.2 38.3 + - + +
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Residues in contact with TYR 66 (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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26D LEU* 3.0 34.5 - - + -
38D TRP* 4.1 9.4 - + + -
39D THR 3.5 8.7 - - - -
40D LEU* 3.1 32.8 - - + +
47D LEU* 3.9 20.4 - - + +
53D LEU* 4.8 5.4 - - + -
55D ILE* 3.7 30.9 - - + +
62D ASP* 2.4 36.2 + - - -
63D ALA 4.1 7.6 - - - -
65D GLN* 1.3 76.9 - - - +
67D THR* 1.3 62.2 + - - +
77D HIS* 3.0 27.8 - - - +
78D SER* 2.6 19.8 + - - +
80D LEU* 4.3 14.6 - - + -
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Residues in contact with THR 67 (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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38D TRP* 3.2 29.6 - - - -
39D THR* 3.0 18.4 + - - -
41D ASP 3.8 16.4 + - - -
65D GLN* 3.9 4.5 + - - +
66D TYR* 1.3 79.4 + - - +
68D CYS* 1.3 68.2 + - - +
69D HIS* 3.3 12.3 - - + -
74D VAL* 3.4 34.8 - - + -
76D SER 3.4 11.4 - - - +
77D HIS* 3.9 12.4 + - + +
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Residues in contact with CYS 68 (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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28D CYS* 3.0 46.9 - - + -
36D ILE* 4.9 0.4 - - + -
37D THR 3.6 4.3 - - - -
38D TRP* 4.0 13.9 - - - -
67D THR* 1.3 74.4 - - - +
69D HIS* 1.3 72.8 + - - +
74D VAL* 3.3 14.4 - - - -
75D LEU* 3.4 3.3 + - + -
76D SER* 2.9 53.6 + - - +
77D HIS* 4.0 3.1 - - - -
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Residues in contact with HIS 69 (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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35D GLY 3.3 0.2 - - - +
36D ILE* 2.8 37.5 - - - +
37D THR* 2.8 37.7 + - - +
38D TRP* 4.0 0.9 - - - -
39D THR* 3.4 39.3 + - + +
67D THR* 3.3 28.3 + - + +
68D CYS* 1.3 76.6 + - - +
70D LYS* 1.3 52.5 + - - +
71D GLY 5.5 0.4 - - - +
72D GLY 5.7 1.3 - - - +
73D GLU 2.8 23.4 + - - +
74D VAL* 3.3 24.6 - - + +
75D LEU* 3.1 6.7 - - - -
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Residues in contact with LYS 70 (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 THR* 5.1 0.2 + - - -
32D GLU* 2.8 48.1 + - + +
34D ASP* 3.3 26.9 - - - +
35D GLY* 3.6 6.7 - - - +
36D ILE* 4.9 4.0 - - + +
69D HIS* 1.3 73.2 - - - +
71D GLY* 1.3 71.4 + - - +
72D GLY 3.8 0.7 - - - -
73D GLU* 2.9 23.1 + - + +
75D LEU* 2.7 33.0 - - + +
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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