Contacts of the strand formed by residues 30 - 39 (chain I) in PDB entry 4EMG
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 ARG 30 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I LYS* 3.4 12.0 - - - +
26I LEU* 3.0 55.6 + - + +
27I ARG 4.5 4.8 + - - +
28I GLY 3.2 11.3 + - - +
29I ASP* 1.3 81.0 - - - +
31I GLU* 1.3 66.7 + - - +
32I LEU* 5.0 0.7 - - + -
52I GLU* 2.6 49.8 + - + +
53I ILE 3.7 1.3 - - - +
54I VAL* 3.4 24.6 - - + +
25J LYS* 3.2 40.0 - - - +
28J GLY 5.9 0.8 - - - +
29J ASP 5.7 0.2 - - - +
86J ILE* 5.0 11.3 - - - +
87J LEU* 4.6 8.3 - - - -
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Residues in contact with GLU 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I TYR* 2.7 42.5 + - + +
24I VAL 3.3 6.1 - - - +
25I LYS* 4.0 9.6 - - + +
26I LEU 4.7 0.2 - - - +
29I ASP 5.7 0.4 - - - -
30I ARG* 1.3 79.7 - - - +
32I LEU* 1.3 73.7 + - - +
33I ASN* 5.4 0.9 - - - +
52I GLU* 3.4 1.2 - - - +
53I ILE* 2.9 50.5 + - + +
55I THR* 4.0 21.1 - - + +
73L LYS* 4.3 10.6 - - - +
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Residues in contact with LEU 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I VAL 4.4 0.4 - - - -
23I TYR* 3.5 3.1 - - - -
24I VAL* 2.8 37.8 + - + +
26I LEU* 4.0 24.2 - - + -
30I ARG* 5.0 0.7 - - + -
31I GLU* 1.3 83.0 - - - +
33I ASN* 1.3 73.3 + - - +
47I LEU* 3.9 17.9 - - + -
51I GLU 3.2 7.0 - - - +
52I GLU* 3.7 29.6 - - + -
78I LEU* 3.8 17.7 - - + -
80I VAL* 3.4 42.0 - - + -
87J LEU* 4.4 4.3 - - + -
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Residues in contact with ASN 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I ILE* 5.0 9.5 - - + +
22I VAL 3.3 7.8 - - - +
23I TYR* 3.8 26.9 + - - +
31I GLU* 5.4 0.6 - - - +
32I LEU* 1.3 82.0 + - - +
34I GLY* 1.3 58.8 + - - +
47I LEU* 4.6 1.8 - - - -
49I ASP 4.0 1.3 - - - +
50I ALA* 3.0 4.4 - - - +
51I GLU* 2.8 55.8 + - + +
53I ILE* 4.0 16.6 - - - +
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Residues in contact with GLY 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I ILE* 3.2 12.0 - - - +
22I VAL* 2.8 34.0 + - - +
33I ASN* 1.3 75.6 - - - +
35I ARG* 1.3 62.2 + - - -
36I LEU 3.6 0.9 + - - -
47I LEU* 3.9 15.7 - - - +
48I GLY 3.5 10.5 - - - -
49I ASP 4.0 5.8 - - - -
50I ALA* 4.1 1.3 - - - -
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Residues in contact with ARG 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I ASP* 2.9 48.8 + - - +
20I GLU* 3.4 5.6 - - - +
21I ILE* 3.8 31.8 - - + +
34I GLY* 1.3 71.0 - - - -
36I LEU* 1.3 60.7 + - - +
37I HIS* 3.0 33.6 + - + +
47I LEU* 3.4 2.6 - - - -
48I GLY 2.8 40.8 + - - +
49I ASP* 5.6 4.8 - - + +
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Residues in contact with LEU 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I VAL* 3.4 39.3 - - + +
17I SER* 3.6 26.9 - - - +
18I LEU* 3.7 13.3 - - + +
19I ASP* 2.7 32.1 + - - -
20I GLU 3.0 10.7 + - - +
22I VAL* 4.2 13.7 - - + -
34I GLY 3.6 2.8 + - - -
35I ARG* 1.3 68.6 - - - +
37I HIS* 1.3 59.1 + - - +
38I ALA 3.4 26.2 - - - +
39I TYR* 4.4 2.0 - - + -
45I MSE 3.8 27.8 - - + -
46I VAL 3.9 1.6 - - - +
47I LEU* 4.0 9.6 - - + -
88I ILE* 6.1 1.3 - - + -
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Residues in contact with HIS 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I LEU* 3.9 10.2 - - - +
19I ASP* 4.2 20.0 + - - +
35I ARG* 3.0 25.5 + - + -
36I LEU* 1.3 75.6 - - - +
38I ALA* 1.3 64.0 + - + +
46I VAL* 2.9 21.7 + - + +
47I LEU 4.4 0.2 - - - -
48I GLY* 3.6 36.4 + - - -
77I MSE 3.7 23.2 - - + -
9J GLU* 4.8 4.3 - - - +
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Residues in contact with ALA 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I LEU* 4.0 7.0 - - - +
36I LEU* 3.4 7.8 - - - +
37I HIS* 1.3 83.5 - - + +
39I TYR* 1.3 64.8 + - - +
45I MSE 3.2 4.5 - - - -
46I VAL* 3.0 31.4 + - + -
9J GLU* 3.5 31.4 - - + +
10J PRO* 3.9 17.7 - - + -
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Residues in contact with TYR 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I LEU* 4.7 13.4 + - + +
14I VAL* 3.7 27.1 - - + -
15I ARG* 3.1 43.6 - - - +
18I LEU* 3.5 34.1 - - + -
36I LEU* 4.4 3.6 - - + -
38I ALA* 1.3 78.2 - - - +
40I ASP* 1.3 76.8 + - - +
43I LEU* 5.0 5.8 - - + -
44I ASN 3.0 13.7 - - - +
45I MSE 3.9 11.9 - - + -
9J GLU* 4.9 3.5 - - - +
10J PRO* 3.3 13.8 - - - +
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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