Contacts of the strand formed by residues 28 - 31 (chain B) in PDB entry 6DBT
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 28 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 4.7 13.2 - - + -
22B LEU 3.3 14.1 - - - +
23B ASP* 3.4 40.2 - - - +
24B LEU 4.8 0.4 - - - +
26B GLY 3.4 9.0 - - - +
27B ASP* 1.3 72.7 - - - +
29B TYR* 1.3 69.5 + - - +
47B GLY* 3.7 0.2 - - - -
48B VAL* 3.0 50.6 + - + +
321B SER 5.5 0.4 - - - +
322B LEU* 3.9 28.3 - - + +
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Residues in contact with TYR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.7 1.7 - - - -
22B LEU* 2.9 42.1 + - + +
24B LEU* 3.7 37.0 + - + +
25B GLU* 4.7 6.8 + - - +
27B ASP* 3.5 25.0 + - + +
28B VAL* 1.3 80.6 - - - +
30B LEU* 1.3 60.9 + - - +
31B PHE 3.9 0.3 + - - -
45B ILE* 3.8 14.8 - - + -
46B PHE 2.9 12.3 - - - +
47B GLY* 3.9 15.0 - - - -
48B VAL* 4.7 1.3 - - - -
60B ILE* 4.7 6.3 - - + -
109B LEU* 5.8 2.2 - - + -
111B VAL* 5.2 0.7 - - - +
114B ARG* 5.6 2.1 + - - -
120B VAL* 3.2 37.4 - - + +
122B LEU* 3.6 32.8 - - + -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU 5.1 6.3 - - - +
15B VAL* 4.4 20.0 - - + -
19B PHE* 3.6 29.4 - - + -
20B SER 3.6 5.4 - - - +
21B LEU* 3.7 16.2 - - + -
28B VAL 4.2 1.2 + - - -
29B TYR* 1.3 74.7 - - - +
31B PHE* 1.3 70.2 + - - +
32B GLY 4.7 2.9 - - - +
33B GLN* 4.7 12.1 - - + +
44B GLY 4.9 2.9 - - - +
45B ILE* 3.5 7.2 - - - +
46B PHE* 2.9 55.8 + - + +
48B VAL* 4.4 12.2 - - + +
57B LEU* 5.5 7.6 - - + -
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.8 3.6 - - - +
20B SER* 2.9 44.4 + - - +
22B LEU* 4.8 15.0 - - + -
29B TYR 3.9 0.4 + - - +
30B LEU* 1.3 77.4 - - - +
32B GLY* 1.3 74.9 + - - +
33B GLN 4.0 0.2 - - - -
43B THR 5.6 2.7 - - - -
44B GLY 5.2 1.1 - - - -
45B ILE* 3.5 38.8 - - + +
62B PHE* 5.9 0.9 - + - -
69B LEU* 4.5 24.7 - - + -
70B PRO 3.8 19.1 - - - -
71B PRO* 4.4 3.8 - - + -
72B LEU* 3.9 32.1 - - + -
75B PRO* 5.2 8.1 - - + -
92B ILE* 4.2 28.7 - - + -
109B LEU* 5.3 2.5 - - + -
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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