Contacts of the helix formed by residues 38 - 48 (chain A) in PDB entry 1SLY
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 TYR 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A MET* 3.2 57.2 + - + +
30A PRO* 4.6 2.4 - - - +
32A LEU* 3.4 33.4 - - + +
33A LYS* 3.9 39.7 - - + +
35A TYR* 2.9 14.2 + - - +
37A LEU* 1.3 73.2 - - - +
39A PRO* 1.4 67.2 - - + +
41A LEU* 3.0 25.1 + - + +
42A GLU* 3.1 42.0 + - + +
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Residues in contact with PRO 39 (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 4.7 0.2 - - - +
36A PRO 3.4 17.0 - - - +
37A LEU* 3.4 2.9 - - - -
38A TYR* 1.4 88.9 - - + +
40A TYR* 1.3 51.2 + - - +
42A GLU* 3.2 9.2 + - - +
43A TYR* 2.8 32.6 + - - +
61A PHE* 3.3 16.9 - - + -
65A ASN* 3.6 25.1 - - - +
68A LEU* 3.7 31.2 - - + -
387A ARG* 5.0 5.8 - - - +
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Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 5.1 6.3 - - - +
37A LEU* 3.0 33.8 + - + +
39A PRO* 1.3 75.6 - - + +
41A LEU* 1.3 66.7 + - + +
43A TYR* 3.6 12.0 - + - +
44A ARG* 2.9 28.6 + - - +
68A LEU* 3.8 20.9 - - + -
69A PRO* 4.5 1.7 - - - +
70A PRO* 3.5 33.4 - - + +
387A ARG* 4.2 9.9 - - - -
391A LEU* 4.0 11.8 - - + +
399A THR* 3.5 30.5 - - + +
403A GLU* 2.7 25.7 + - - -
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Residues in contact with LEU 41 (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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10A TYR* 3.6 42.4 - - + +
13A ILE* 4.1 16.4 - - + -
14A LYS* 4.6 14.8 - - + -
17A TRP* 3.4 30.0 - - + -
29A MET* 4.3 11.7 - - + -
32A LEU* 4.4 12.1 - - + -
35A TYR* 5.8 0.2 - - + -
37A LEU 3.7 4.6 + - - +
38A TYR* 3.0 23.2 + - + +
40A TYR* 1.3 81.9 - - + +
42A GLU* 1.3 58.3 + - - +
44A ARG* 3.2 11.9 + - - +
45A GLN* 2.9 26.2 + - - +
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Residues in contact with GLU 42 (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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29A MET* 4.3 6.0 - - + +
38A TYR* 3.1 52.1 + - + +
39A PRO* 3.5 15.6 - - - +
41A LEU* 1.3 76.2 - - - +
43A TYR* 1.3 61.6 + - - +
45A GLN* 3.1 12.6 + - - +
46A ILE* 3.0 33.2 + - + +
61A PHE* 3.7 23.0 - - + -
65A ASN* 4.7 4.9 + - - +
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Residues in contact with TYR 43 (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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39A PRO 2.8 20.0 + - - +
40A TYR* 3.6 13.9 - + - +
42A GLU* 1.3 70.3 - - - +
44A ARG* 1.3 59.8 + - - +
46A ILE* 3.8 4.0 - - - +
47A THR* 2.9 52.5 + - + +
61A PHE* 3.9 19.3 - + + -
68A LEU* 5.5 0.4 - - + -
70A PRO* 3.4 45.8 - - + -
73A THR* 4.0 13.2 - - - +
74A LEU* 3.4 27.4 - - + -
77A ARG* 2.7 27.4 + - - -
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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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14A LYS* 4.0 23.6 + - - +
17A TRP* 3.5 61.8 + - + +
18A ASP* 2.9 33.3 + - - +
20A ARG* 4.5 6.1 - - - +
40A TYR 2.9 21.9 + - - +
41A LEU* 3.2 13.3 + - - +
43A TYR* 1.3 76.0 - - + +
45A GLN* 1.3 56.9 + - - +
47A THR* 3.1 7.5 + - - +
48A ASP* 2.9 39.8 + - - +
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Residues in contact with GLN 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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17A TRP* 3.6 16.8 - - + -
25A VAL* 5.6 2.8 - - - +
29A MET* 3.7 32.5 - - - +
41A LEU 2.9 13.1 + - - +
42A GLU* 3.1 13.2 + - - +
44A ARG* 1.3 73.9 - - - +
46A ILE* 1.3 65.4 + - + +
48A ASP* 3.3 16.9 + - - +
49A ASP* 3.6 15.1 + - - +
53A GLN* 4.7 0.6 + - - -
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Residues in contact with ILE 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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42A GLU* 3.0 20.9 + - + +
43A TYR* 3.8 4.0 - - - +
45A GLN* 1.3 74.5 - - + +
47A THR* 1.3 65.3 + - - +
48A ASP 3.1 1.8 + - - -
49A ASP 3.5 4.2 + - - -
50A LEU* 3.4 25.4 + - + -
53A GLN* 4.0 21.3 + - + +
57A THR* 4.7 15.0 - - + +
58A VAL* 4.0 19.7 - - + -
61A PHE* 3.7 41.7 - - + -
74A LEU* 4.0 19.7 - - + -
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Residues in contact with THR 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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43A TYR* 2.9 62.7 + - + +
44A ARG* 3.1 12.0 + - - +
46A ILE* 1.3 72.8 - - - +
48A ASP* 1.3 63.1 + - - +
49A ASP 3.5 0.2 + - - -
50A LEU* 3.6 18.3 + - + +
74A LEU* 4.0 11.7 - - + -
77A ARG* 3.7 27.6 + - - +
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Residues in contact with ASP 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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17A TRP* 3.0 35.6 + - - -
20A ARG* 4.4 15.8 + - - -
22A MET* 5.0 3.3 - - - +
44A ARG* 2.9 21.5 + - - +
45A GLN* 3.3 11.7 - - - +
46A ILE 3.1 0.8 - - - -
47A THR* 1.3 78.3 + - - +
49A ASP* 1.3 62.0 + - - +
50A LEU 3.9 0.5 + - - -
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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