Contacts of the strand formed by residues 46 - 51 (chain D) in PDB entry 6DBV
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 PHE 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D CYS* 5.8 2.9 - - - -
14D LEU* 4.3 13.9 - - + -
29D TYR* 3.3 2.7 - - - -
30D LEU* 2.8 52.7 + - + +
33D GLN* 3.0 42.6 - - + -
40D SER* 6.2 3.1 - - - -
41D CYS* 4.0 26.0 - - + -
44D GLY 3.4 11.0 + - - +
45D ILE* 1.3 85.0 - - - +
47D GLY* 1.3 63.5 + - - +
48D VAL 3.3 0.9 + - - -
57D LEU* 3.9 35.0 - - + -
58D ARG 3.5 13.5 - - - +
59D ALA* 4.4 4.7 - - + -
60D ILE* 3.9 2.9 - - - -
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Residues in contact with GLY 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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27D ASP* 6.0 3.8 - - - -
28D VAL 3.6 8.1 - - - -
29D TYR* 3.9 5.2 - - - -
46D PHE* 1.3 69.9 - - - +
48D VAL* 1.3 58.9 + - - -
49D ARG* 5.2 5.9 + - - +
56D LYS 3.8 0.5 - - - +
57D LEU* 3.4 7.0 - - - +
58D ARG* 2.9 41.9 + - - +
60D ILE* 3.3 21.8 - - - +
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Residues in contact with VAL 48 (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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21D LEU* 4.9 6.3 - - + -
27D ASP* 4.3 1.0 - - - +
28D VAL* 3.0 61.4 + - + +
29D TYR 4.3 0.2 - - - -
30D LEU* 3.9 22.4 - - + +
46D PHE 3.3 1.1 + - - +
47D GLY* 1.3 72.0 - - - -
49D ARG* 1.3 70.9 + - - +
50D ILE* 5.7 0.4 - - + -
55D LEU* 3.5 26.5 - - + -
57D LEU* 3.6 16.6 - - + -
322D LEU* 5.5 8.5 - - + -
328D LEU* 6.2 4.7 - - + -
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Residues in contact with ARG 49 (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 ASP* 3.6 31.6 + - - +
28D VAL* 5.4 0.2 - - - -
47D GLY* 5.2 3.9 + - - -
48D VAL* 1.3 81.4 - - - +
50D ILE* 1.3 67.0 + - - +
51D LYS* 3.9 23.5 + - + +
55D LEU* 3.2 7.9 - - - +
56D LYS* 2.9 58.7 + - + +
58D ARG* 3.4 47.5 - - - +
322D LEU* 5.8 0.9 - - - -
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Residues in contact with ILE 50 (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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6D LEU* 3.5 21.1 - - + -
48D VAL* 5.7 0.7 - - + -
49D ARG* 1.3 73.5 - - - +
51D LYS* 1.3 70.5 + - - +
52D LYS 4.4 0.6 + - - +
53D GLY 4.3 12.6 - - - +
54D GLU 3.5 8.3 - - - +
55D LEU* 4.7 9.2 - - + -
322D LEU* 3.6 36.8 - - + +
328D LEU* 5.6 3.1 - - + -
347D GLN* 3.3 48.9 - - + +
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Residues in contact with LYS 51 (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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49D ARG* 3.9 23.8 - - + +
50D ILE* 1.3 79.9 + - - +
52D LYS* 1.3 85.3 + - + +
53D GLY 3.2 0.7 - - - -
54D GLU* 2.9 27.0 + - + +
56D LYS* 5.5 9.2 - - + -
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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