Contacts of the strand formed by residues 33 - 38 (chain A) in PDB entry 3TNH
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 VAL 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LYS* 3.7 3.7 - - - +
25A ILE* 2.8 40.1 + - + +
26A GLY* 3.7 10.5 + - - +
29A THR* 4.3 12.8 - - - +
30A PHE 6.1 0.2 - - - -
31A GLY* 3.2 15.6 + - - +
32A GLU* 1.3 76.4 - - - +
34A PHE* 1.3 63.5 + - - +
46A ALA* 4.2 21.3 - - + -
47A LEU 3.1 10.3 - - - +
48A LYS* 4.1 21.8 - - + +
103A PHE* 6.1 0.2 - - + -
400A F18 4.4 26.9 - - + +
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Residues in contact with PHE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 4.3 44.4 - - + -
23A ALA 3.4 4.7 - - - -
24A LYS* 3.3 44.0 - - + -
25A ILE* 4.1 4.0 - - - -
32A GLU* 3.5 38.1 - - + -
33A VAL* 1.3 75.4 - - - +
35A LYS* 1.3 68.5 + - - +
36A ALA 3.7 0.3 + - - -
46A ALA* 3.3 5.7 - - - +
47A LEU* 2.9 46.9 + - + +
49A LYS* 5.3 2.7 - - + -
100A TYR* 4.7 12.3 - + - -
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 3.7 0.9 - - - -
22A LEU* 2.6 49.8 + - + +
23A ALA* 2.8 21.3 + - + +
25A ILE* 3.6 12.2 - - + +
34A PHE* 1.3 74.3 - - - +
36A ALA* 1.3 59.5 + - - +
44A LYS* 4.0 21.2 - - + +
45A VAL 3.5 5.2 - - - +
105A PHE* 3.7 37.5 - - + -
107A GLU* 4.2 5.9 + - - -
159A ARG* 3.2 31.1 - - - +
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 4.1 6.7 - - + -
20A GLU 3.2 21.3 - - - +
21A LYS* 3.9 3.6 - - + -
22A LEU* 4.0 6.1 - - - +
34A PHE 3.7 0.6 + - - +
35A LYS* 1.3 75.6 - - - +
37A ARG* 1.3 60.2 + - - +
44A LYS* 3.4 7.3 - - - +
45A VAL* 2.8 37.9 + - + +
47A LEU* 3.7 33.2 - - + -
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 4.1 2.7 - - - -
20A GLU* 2.9 65.3 + - + +
22A LEU* 3.9 20.4 - - + -
36A ALA* 1.3 75.2 - - - +
38A HIS* 1.3 76.5 + - - +
39A ARG* 3.1 14.1 + - - +
40A LYS 5.6 1.4 + - - -
41A THR 4.8 1.0 - - - +
42A GLY* 3.7 35.2 + - - +
43A GLN 3.6 3.8 - - - -
44A LYS* 4.4 10.6 - - + +
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Residues in contact with HIS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 4.0 29.0 + - + +
19A TYR* 3.7 31.1 - + + -
37A ARG* 1.3 73.9 + - - +
39A ARG* 1.3 60.1 + - + +
40A LYS* 2.9 57.4 + - + -
41A THR* 3.3 30.4 + - + +
42A GLY* 2.9 25.6 + - - -
43A GLN* 2.9 27.3 + - + +
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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