Contacts of the strand formed by residues 40 - 47 (chain D) in PDB entry 3T04
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 TYR 40 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A SER* 3.5 36.3 + - - -
235A PRO* 3.7 13.9 - - + -
38D VAL* 3.4 5.3 - - - +
39D LYS* 1.3 80.9 - - + +
41D TYR* 1.3 76.3 + - - +
42D ARG* 2.8 33.5 + - - -
58D THR* 3.9 3.8 - - + -
59D VAL 3.3 15.0 - - - +
61D GLY 3.6 4.5 - - - +
84D TYR* 2.9 69.0 + + + +
86D THR 4.4 3.5 + - - -
87D PHE* 3.7 31.2 - + - -
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Residues in contact with TYR 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D TRP* 3.3 37.2 + + - -
32D TYR* 3.6 42.7 + + + +
38D VAL* 3.7 11.5 - - + +
40D TYR* 1.3 77.0 - - - +
42D ARG* 1.3 60.2 + - - +
43D ILE* 3.9 17.6 - - + +
57D PHE 4.0 0.2 - - - +
58D THR* 3.1 8.0 - - - -
59D VAL* 2.8 32.8 + - + -
60D PRO 3.7 11.9 - - - -
61D GLY* 3.5 27.6 + - - -
63D TYR 3.4 11.4 + - - -
81D VAL* 3.8 19.3 - - + -
82D TYR 3.2 5.6 - - - +
83D ALA* 3.8 20.9 - - + -
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LYS* 4.0 34.7 + - - +
144A HIS* 5.6 0.4 - - - +
145A SER 5.0 3.2 - - - +
40D TYR* 2.8 31.7 + - - -
41D TYR* 1.3 74.9 - - - +
43D ILE* 1.3 62.6 + - - +
44D THR* 4.6 7.9 - - + -
56D GLU* 3.3 36.2 + - + +
57D PHE 3.5 5.6 - - - +
58D THR* 3.7 24.1 - - + +
81D VAL* 3.7 1.4 - - - -
82D TYR* 2.9 42.8 + - + -
84D TYR* 2.9 38.9 + - + -
92D GLU* 4.9 3.0 + - - -
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Residues in contact with ILE 43 (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 ILE* 4.5 1.1 - - + -
28D TRP* 4.2 8.1 - - + -
41D TYR* 3.9 12.1 - - + +
42D ARG* 1.3 78.5 - - - +
44D THR* 1.3 65.6 + - - +
45D TYR* 4.6 0.6 - - + -
55D GLN 3.8 0.2 - - - +
56D GLU* 3.2 6.4 - - - +
57D PHE* 2.8 73.0 + - + +
59D VAL* 3.8 29.2 - - + -
66D ALA* 4.1 6.7 - - + -
68D ILE* 4.1 19.1 - - + -
79D ILE* 4.2 11.4 - - + -
80D THR 3.4 7.4 - - - +
81D VAL* 4.2 18.2 - - + -
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Residues in contact with THR 44 (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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42D ARG* 4.6 4.3 - - + -
43D ILE* 1.3 77.7 - - - +
45D TYR* 1.3 65.3 + - - +
54D VAL* 4.1 15.3 - - + +
55D GLN 3.2 7.9 - - - -
56D GLU* 3.7 24.9 - - + +
78D THR 3.8 0.7 + - - +
79D ILE* 3.3 3.1 - - - +
80D THR* 2.8 51.4 + - - -
82D TYR* 3.8 25.0 + - + +
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Residues in contact with TYR 45 (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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43D ILE* 4.6 0.4 - - + -
44D THR* 1.3 80.5 - - - +
46D GLY* 1.3 59.8 + - - +
53D PRO 4.1 0.9 - - - +
54D VAL* 3.5 5.0 - - - +
55D GLN* 2.9 81.7 + - + +
57D PHE* 3.8 29.1 - + - -
68D ILE* 3.5 34.8 - - + -
69D SER* 3.6 15.7 + - - -
70D GLY 5.6 0.9 - - - -
71D LEU* 3.9 17.7 - - + -
77D TYR* 4.5 8.3 - + + -
78D THR 3.2 10.8 - - - +
79D ILE* 3.8 18.6 - - + -
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Residues in contact with GLY 46 (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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45D TYR* 1.3 76.6 - - - +
47D GLU* 1.3 69.0 + - - -
52D SER* 5.5 0.4 - - - -
53D PRO 4.0 13.7 - - - -
54D VAL* 4.5 11.7 - - - +
77D TYR* 3.3 12.1 - - - -
78D THR* 2.8 29.0 + - - +
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Residues in contact with GLU 47 (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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46D GLY* 1.3 71.5 - - - +
48D THR* 1.3 67.1 + - - +
49D GLY 3.3 0.9 + - - -
50D GLY* 3.1 20.5 + - - +
52D SER* 3.2 37.0 + - - +
53D PRO 4.9 0.2 + - - -
72D LYS* 2.9 40.9 + - - +
75D VAL* 3.8 18.2 - - + +
76D ASP 3.5 7.0 - - - +
77D TYR* 3.4 21.9 + - + -
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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