Contacts of the strand formed by residues 43 - 50 (chain A) in PDB entry 2JQY
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 TRP 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ALA 3.7 1.7 - - - +
40A ASN* 3.0 34.7 + - + +
41A GLY 3.2 2.8 + - - -
42A PRO* 1.3 80.9 - - + +
44A ARG* 1.3 61.0 + - - +
45A ILE* 3.9 24.8 + - + +
73A VAL* 3.2 51.4 - - + +
74A HIS 3.2 23.3 - - - -
75A TYR* 3.5 37.2 - + + -
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Residues in contact with ARG 44 (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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2A GLU* 5.3 9.3 + - - -
35A TYR* 4.9 1.6 + - - -
37A ASN* 3.6 26.8 + - - +
38A ALA 3.1 3.6 - - - +
39A ALA* 3.5 32.2 - - + +
40A ASN 4.7 0.2 - - - +
41A GLY 5.4 4.3 - - - +
43A TRP* 1.3 71.1 - - - +
45A ILE* 1.3 62.0 + - - +
72A GLU 3.2 14.6 - - - +
73A VAL* 3.2 13.4 - - - -
74A HIS* 3.2 59.5 + - + +
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Residues in contact with ILE 45 (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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6A TRP* 6.0 5.2 - - + +
36A PHE* 5.2 1.0 - - - -
37A ASN* 3.1 3.7 - - - -
38A ALA* 2.6 55.3 + - + +
40A ASN* 5.5 9.4 - - + +
43A TRP* 3.9 29.2 - - + +
44A ARG* 1.3 71.8 - - - +
46A ALA* 1.3 61.0 + - - +
47A LEU* 4.2 22.1 + - + +
71A LEU* 6.2 2.7 - - + -
72A GLU 3.7 4.5 - - - +
73A VAL* 4.8 4.3 - - + -
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Residues in contact with ALA 46 (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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35A TYR* 4.6 4.9 - - + +
36A PHE 3.1 10.5 - - - +
37A ASN* 3.6 21.3 - - - +
45A ILE* 1.3 75.2 - - - +
47A LEU* 1.3 63.0 + - - +
71A LEU* 3.5 5.2 - - - +
72A GLU* 2.8 66.5 + - + +
74A HIS* 4.6 5.8 - - - +
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Residues in contact with LEU 47 (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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34A VAL* 5.1 1.9 - - - +
35A TYR* 3.7 1.1 - - - -
36A PHE* 2.8 47.0 + - + +
45A ILE* 4.2 20.3 + - + +
46A ALA* 1.3 74.8 - - - +
48A ALA* 1.3 61.0 + - - +
69A PRO* 5.1 11.0 - - + -
70A GLU 3.6 15.0 - - - +
71A LEU* 4.1 24.5 - - + -
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Residues in contact with ALA 48 (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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34A VAL 3.3 15.9 - - - +
35A TYR* 4.1 19.5 - - + +
46A ALA 4.2 1.2 - - - -
47A LEU* 1.3 75.3 - - - +
49A TYR* 1.3 59.6 + - - +
50A TYR* 3.9 4.8 + - + -
69A PRO* 3.2 4.4 - - - +
70A GLU* 2.7 46.7 + - + +
72A GLU* 4.6 10.7 + - - +
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Residues in contact with TYR 49 (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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32A PRO 4.6 1.4 - - - +
33A SER* 4.0 8.3 - - - -
34A VAL* 3.1 53.5 + - + +
47A LEU 4.5 0.2 + - - -
48A ALA* 1.3 72.0 - - - +
50A TYR* 1.3 72.8 + - - +
51A GLN* 4.0 27.3 + - + +
68A ARG* 4.5 3.6 - - - +
69A PRO* 3.9 30.2 - - + +
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Residues in contact with TYR 50 (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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33A SER* 5.6 11.9 - - - +
48A ALA* 3.9 6.0 + - + -
49A TYR* 1.3 74.8 - - - +
51A GLN* 1.3 67.2 + - - +
52A GLU* 5.4 9.4 - - + -
67A ASP* 3.3 11.3 - - + +
68A ARG* 2.8 39.6 + - - +
70A GLU* 3.1 37.2 - - - +
94A TYR* 4.2 23.6 - + + -
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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