Contacts of the strand formed by residues 46 - 51 (chain B) in PDB entry 5E95
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 GLN 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B THR* 3.2 4.2 - - - -
36B TYR* 2.8 76.3 + - + +
44B PRO 4.5 6.5 + - - +
45B VAL* 1.3 75.8 + - - +
47B LYS* 1.3 62.9 + - - +
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Residues in contact with LYS 47 (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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138A GLY* 6.2 2.6 - - - -
33B VAL* 4.7 9.9 - - + -
34B ILE 3.3 8.3 - - - +
35B THR* 3.6 20.2 - - + +
36B TYR* 5.4 0.2 - - - -
45B VAL* 3.5 26.2 + - + +
46B GLN* 1.3 84.4 - - - +
48B PHE* 1.3 67.6 + - - +
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Residues in contact with PHE 48 (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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33B VAL* 3.5 5.8 - - - +
34B ILE* 2.8 74.5 + - + +
36B TYR* 3.8 27.8 - + - -
47B LYS* 1.3 74.3 - - - +
49B GLU* 1.3 74.1 + - - +
50B VAL* 4.1 6.1 - - + -
57B ALA* 3.8 17.9 - - + -
58B THR 3.5 20.9 - - - -
59B ILE* 4.0 9.6 - - + -
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Residues in contact with GLU 49 (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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135A ARG* 2.7 48.4 + - - +
31B TYR* 3.7 21.0 - - + -
32B TYR 3.1 13.0 - - - +
33B VAL* 3.9 12.5 - - + +
34B ILE* 4.4 0.4 - - - -
48B PHE* 1.3 82.2 - - - +
50B VAL* 1.3 70.0 + - - +
51B PRO* 4.8 0.5 - - - +
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Residues in contact with VAL 50 (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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22B TRP* 3.9 29.6 - - + -
31B TYR* 3.4 7.9 - - - -
32B TYR* 2.9 37.8 + - + +
34B ILE* 4.1 11.9 - - + -
48B PHE* 4.1 13.2 - - + -
49B GLU* 1.3 79.3 - - - +
51B PRO* 1.3 79.9 - - + +
54B LYS* 4.1 16.2 - - + +
56B THR 4.2 14.8 - - - +
57B ALA* 4.3 2.9 - - + -
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Residues in contact with PRO 51 (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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30B ASP 3.9 1.8 - - - +
31B TYR* 3.8 22.4 - - + -
49B GLU 4.8 0.2 - - - +
50B VAL* 1.3 92.5 - - + +
52B GLY* 1.3 58.4 + - - +
53B SER* 3.1 18.2 - - - +
54B LYS* 3.0 38.8 + - + +
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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