Contacts of the helix formed by residues 48 - 55 (chain A) in PDB entry 1JSA
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ILE* 4.7 10.1 - - + -
44A THR 3.5 11.7 + - - +
45A ARG* 3.2 18.3 + - + +
47A GLU* 1.3 80.2 - - - +
49A GLN* 1.3 62.4 + - - +
50A THR 3.3 0.3 + - - -
51A ILE* 3.3 25.0 + - + +
52A TYR* 4.0 25.4 + + - -
65A ALA* 2.9 31.9 - - + +
66A GLN* 5.8 0.7 - - - -
68A VAL* 3.6 30.3 - - + -
69A PHE* 4.0 8.5 - + + -
80A LEU* 3.5 33.4 - - + -
85A TYR* 4.3 23.6 - + - -
88A ALA* 6.1 2.0 - - + -
89A LEU* 5.4 3.4 - - + -
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Residues in contact with GLN 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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45A ARG 4.2 1.2 + - - -
46A GLN* 3.4 30.5 + - - +
48A PHE* 1.3 75.7 - - - +
50A THR* 1.3 68.8 + - - +
51A ILE 2.9 7.0 + - - -
52A TYR* 3.4 12.0 + - - +
53A SER* 3.7 9.2 + - - -
62A LYS* 4.0 42.3 - - + +
65A ALA* 3.8 26.9 - - + -
66A GLN* 3.5 28.5 - - + +
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Residues in contact with THR 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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46A GLN* 4.1 5.9 + - - -
47A GLU* 2.9 40.8 + - + +
49A GLN* 1.3 81.7 - - - +
51A ILE* 1.3 61.8 + - - +
53A SER* 3.8 14.6 - - - -
54A LYS* 5.0 4.5 - - - +
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Residues in contact with ILE 51 (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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43A ILE* 5.3 12.6 - - + -
47A GLU* 4.0 9.0 - - + +
48A PHE* 3.6 22.0 - - + +
49A GLN 2.9 0.4 - - - -
50A THR* 1.3 80.7 - - - +
52A TYR* 1.3 56.7 + - + +
53A SER 2.4 18.2 + - - -
54A LYS* 2.6 38.8 + - + +
55A PHE* 4.2 17.2 + - + -
85A TYR* 3.6 38.1 - - + +
89A LEU* 5.7 0.7 - - + -
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Residues in contact with TYR 52 (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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48A PHE* 4.0 33.2 - + - -
49A GLN 3.4 9.1 + - - +
51A ILE* 1.3 82.1 - - + +
53A SER* 1.3 56.4 + - - +
54A LYS 3.0 1.8 - - - -
55A PHE* 3.5 10.7 + + - +
56A PHE* 3.1 63.0 + + - +
61A PRO* 3.9 22.8 - - + +
64A TYR* 3.8 34.1 + + - -
65A ALA* 4.2 18.2 - - + -
68A VAL* 4.0 12.5 - - + +
89A LEU* 4.9 14.1 - - + +
92A THR* 4.5 16.6 + - - +
131A MET* 4.9 2.5 - - + -
188A GLU* 5.1 3.3 - - + +
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Residues in contact with SER 53 (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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49A GLN 3.7 6.0 + - - -
50A THR* 3.8 19.3 - - - -
51A ILE 2.4 8.9 + - - -
52A TYR* 1.3 76.0 - - - +
54A LYS* 1.3 60.5 + - - -
56A PHE 4.2 7.4 - - - -
57A PRO* 3.7 23.9 - - - +
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Residues in contact with LYS 54 (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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50A THR 5.0 3.6 - - - +
51A ILE* 2.6 37.1 + - + +
53A SER* 1.3 78.0 - - - +
55A PHE* 1.3 85.8 + - + +
56A PHE 3.4 0.6 + - - -
57A PRO* 3.7 10.8 - - - +
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Residues in contact with PHE 55 (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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30A TRP* 5.9 5.2 - + - -
51A ILE* 4.4 24.9 - - + -
52A TYR* 3.5 10.9 + + - -
54A LYS* 1.3 104.2 - - + +
56A PHE* 1.3 101.4 + + + +
57A PRO* 3.4 5.9 - - - +
85A TYR* 5.0 2.5 - - - -
89A LEU* 4.4 26.0 - - + -
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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