Contacts of the strand formed by residues 37 - 42 (chain C) in PDB entry 4AG1
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 37 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A THR* 2.7 43.9 + - - +
84A SER* 3.5 31.1 + - - +
11C TYR* 3.3 33.4 - + - -
15C ARG* 3.8 16.8 - - - -
18C ASP* 3.5 24.5 - - + -
33C GLY* 3.6 8.8 - - - -
36C ASP* 1.3 86.0 - - + +
38C TRP* 1.3 64.9 + - - +
50C TYR* 4.0 11.0 - - + -
51C ILE* 3.2 22.9 - - - +
52C PRO* 3.6 32.8 - - + +
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Residues in contact with TRP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 3.6 34.1 - + - -
29C ILE* 4.0 20.9 - - + -
31C GLU 3.4 8.7 - - - +
32C PHE* 3.3 61.1 + + + -
33C GLY 3.5 1.6 - - - -
35C GLY 3.9 9.4 + - - -
36C ASP* 5.0 0.4 - - - +
37C TRP* 1.3 77.6 - - - +
39C GLU* 1.3 63.3 + - - +
40C ALA 3.5 1.2 + - - -
50C TYR* 3.2 5.3 - - - -
51C ILE* 2.8 40.3 + - + +
53C SER* 3.3 31.6 + - - -
56C VAL* 4.0 12.8 - - + -
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Residues in contact with GLU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 5.7 0.6 - - - +
28A LYS* 2.7 34.5 + - - +
45A HIS 4.5 2.5 - - - +
47A ALA 4.1 6.4 - - - +
48A GLY* 5.6 0.9 - - - -
29C ILE* 3.6 3.3 - - - +
30C LEU* 2.7 45.0 + - + +
31C GLU* 2.9 34.0 + - + +
33C GLY 4.7 0.4 + - - -
38C TRP* 1.3 71.3 - - - +
40C ALA* 1.3 57.5 + - - +
48C THR* 3.4 27.7 - - + +
49C GLY* 3.6 9.4 - - - +
50C TYR* 3.6 23.8 + - + -
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 3.7 3.6 - - - +
27C PHE* 4.0 10.8 - - + -
28C GLN 3.3 11.4 - - - +
29C ILE* 3.8 8.7 - - + -
30C LEU* 4.2 5.6 - - - +
39C GLU* 1.3 77.6 - - - +
41C ARG* 1.3 60.4 + - - +
42C SER 4.2 0.2 - - - -
48C THR* 3.2 4.6 - - - +
49C GLY 2.9 33.4 + - - +
51C ILE* 3.6 35.4 - - + -
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Residues in contact with ARG 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 3.0 10.9 + - - +
24A ASN* 2.7 33.0 + - - +
25A GLY* 3.7 6.2 - - - -
26A PRO* 2.6 50.4 + - - +
27A SER 5.4 1.0 + - - -
28A LYS* 6.2 0.4 - - - +
27C PHE* 3.2 5.9 - - - -
28C GLN* 2.8 41.3 + - + +
30C LEU* 4.2 8.4 - - + +
40C ALA* 1.3 73.6 - - - +
42C SER* 1.3 73.6 + - - +
43C LEU* 3.5 10.4 + - + +
46C GLY* 2.8 36.4 + - - +
47C GLU 3.3 8.5 - - - +
48C THR* 3.3 24.5 + - - +
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Residues in contact with SER 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.2 6.3 - - - +
20C SER 6.0 0.7 - - - -
25C GLU* 2.5 29.4 + - - +
26C LYS 3.6 5.4 - - - -
27C PHE* 3.7 15.5 - - - -
41C ARG* 1.3 75.1 - - - +
43C LEU* 1.3 58.4 + - - +
44C THR 3.0 13.3 + - - -
45C THR* 3.0 23.8 + - - -
46C GLY* 2.9 27.9 + - - -
47C GLU 2.9 10.4 + - - -
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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