Contacts of the strand formed by residues 44 - 49 (chain D) in PDB entry 1J8H
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 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D TYR* 3.1 5.6 - - - -
36D VAL* 2.8 41.6 + - + +
38D TYR* 4.2 23.3 - - + -
41D GLN* 3.9 18.1 - - + +
42D GLY 3.8 10.0 - - - +
43D LEU* 1.3 78.1 - - - +
45D LEU* 1.3 67.3 + - - +
46D LEU 3.3 0.3 + - - -
59D ILE* 4.4 17.8 - - - +
60D ASN* 4.8 1.8 - - - +
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Residues in contact with LEU 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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33D PHE* 4.6 10.3 - - + -
34D TRP 3.7 8.1 - - - +
35D TYR* 3.6 26.6 - - + +
44D GLN* 1.3 72.1 - - - +
46D LEU* 1.3 64.3 + - - +
47D LEU* 3.3 33.9 - - - +
48D LYS* 4.0 35.2 - - + +
59D ILE* 3.5 17.5 - - - +
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Residues in contact with LEU 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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34D TRP* 2.7 24.6 + - + +
36D VAL* 4.0 17.7 - - + -
38D TYR* 5.0 0.4 - - - +
44D GLN 3.3 2.4 + - - +
45D LEU* 1.3 74.1 - - - +
47D LEU* 1.3 66.1 + - + +
58D GLY* 3.8 1.0 - - - -
59D ILE* 3.4 61.1 + - + +
60D ASN* 3.5 15.9 - - - +
62D PHE* 3.6 31.2 - - + -
75D LEU* 3.6 28.5 - - + -
88D TYR* 3.9 11.4 - - + -
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Residues in contact with LEU 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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34D TRP* 3.0 51.9 + - + -
45D LEU* 3.3 10.8 - - - +
46D LEU* 1.3 89.1 - - + +
48D LYS* 1.3 64.7 + - - +
56D VAL* 3.7 26.9 - - + +
57D LYS 4.6 0.7 - - - +
58D GLY* 3.6 27.6 - - - +
62D PHE* 4.2 2.7 - - + +
63D GLU* 4.0 6.7 - - - -
64D ALA* 3.9 14.1 - - + +
73D PHE* 3.8 18.8 - - + -
75D LEU* 4.1 8.3 - - + -
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Residues in contact with LYS 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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66B ASP* 4.7 17.9 + - - -
32D LEU 3.3 13.2 - - - +
33D PHE* 4.0 23.1 - - + -
45D LEU* 4.0 26.6 - - + +
47D LEU* 1.3 82.6 - - - +
49D TYR* 1.3 60.7 + - - +
50D THR* 3.8 22.7 + - + +
56D VAL* 3.3 22.8 - - - +
73D PHE* 4.4 2.0 - - - -
97D PHE 5.8 3.1 + - - +
100E PRO 5.6 4.0 + - - -
104E TYR* 5.6 7.1 - - - +
105E GLY 5.8 1.4 - - - +
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Residues in contact with TYR 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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30D PRO* 3.5 23.3 - - + -
31D TYR* 3.5 8.5 - - - +
32D LEU* 3.0 30.2 + - + +
33D PHE* 6.0 0.2 - - - -
48D LYS* 1.3 72.8 - - - +
50D THR* 1.3 58.4 + - - +
51D SER* 3.2 37.2 + - - -
53D ALA 3.5 23.6 - - - -
54D THR* 4.5 0.9 - - - -
56D VAL* 4.1 6.7 - - + -
66D PHE* 3.4 63.4 - + + -
73D PHE* 3.5 24.0 - - + -
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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