Contacts of the strand formed by residues 20 - 26 (chain D) in PDB entry 4OM5
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 LEU 20 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D CYS* 3.8 3.1 - - - -
14D CYS* 4.4 0.5 - - - -
19D ASN* 1.3 82.3 - - + +
21D CYS* 1.3 64.7 + - - +
38D CYS* 3.4 7.1 - - - +
39D ILE* 3.0 36.3 + - + +
40D ASP 3.5 23.1 - - - +
41D VAL* 3.8 16.6 - - + -
42D CYS* 4.0 9.6 - - + +
53D CYS* 4.8 9.6 - - + -
54D CYS* 3.5 10.8 - - - +
55D ASN* 3.6 28.9 - - + -
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Residues in contact with CYS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ARG* 3.9 5.6 - - - -
2D LYS 3.4 12.8 - - - -
3D CYS* 2.0 44.0 - - - -
20D LEU* 1.3 73.9 - - - +
22D TYR* 1.3 62.7 + - - +
37D GLY 3.3 6.3 - - - -
53D CYS* 3.3 6.1 - - - +
54D CYS* 3.0 28.5 + - - -
56D THR 3.8 16.8 - - - -
58D ARG 4.3 0.7 - - - -
59D CYS* 3.8 13.0 - - - -
60D ASN* 3.6 19.7 - - - +
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Residues in contact with TYR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D CYS* 1.3 78.3 - - - +
23D LYS* 1.3 71.3 + - - +
24D MET* 4.1 18.0 - - + +
35D LYS* 4.0 34.3 - - + +
36D ARG* 3.4 9.8 - - - -
37D GLY* 3.3 36.5 + - - -
38D CYS 3.3 26.0 - - - -
39D ILE* 3.9 17.3 - - + -
51D TYR* 4.0 20.9 - + + -
52D VAL 3.1 9.9 - - - +
53D CYS* 4.1 15.5 - - - -
60D ASN* 2.9 23.3 + - - -
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Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D TYR* 1.3 79.4 - - - +
24D MET* 1.3 60.1 + - - +
25D PHE* 3.6 33.6 - - + -
33D PRO* 3.7 13.5 - - + -
35D LYS 3.6 5.4 - - - -
36D ARG* 3.9 18.4 - - + +
50D LYS 3.8 0.5 - - - +
51D TYR* 3.5 3.1 - - - -
52D VAL* 2.9 52.3 + - + +
59D CYS 5.8 0.9 - - - -
60D ASN* 3.5 30.2 + - + +
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Residues in contact with MET 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D TYR* 4.0 7.4 - - + +
23D LYS* 1.3 74.3 - - - +
25D PHE* 1.3 65.0 + - - +
26D MET* 5.0 3.8 - - - -
33D PRO* 3.4 3.5 - - - +
34D VAL* 2.8 46.9 + - - +
35D LYS* 2.8 47.9 + - + +
49D VAL* 3.5 28.5 - - + -
50D LYS 3.4 3.8 - - - +
51D TYR* 3.5 39.5 - - + +
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Residues in contact with PHE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LYS* 3.6 43.3 - - + -
24D MET* 1.3 78.1 - - - +
26D MET* 1.3 69.3 + - - +
29D ASN 3.7 15.9 - - - +
30D LEU* 3.5 36.3 - - + -
31D THR 4.8 0.4 - - - -
32D VAL 4.6 0.2 - - - -
33D PRO* 3.8 27.8 - - + -
34D VAL* 4.5 4.9 - - - +
49D VAL* 3.4 6.7 - - - +
50D LYS* 2.8 55.1 + - + +
52D VAL* 3.8 19.1 - - + -
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Residues in contact with MET 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D MET* 5.0 3.4 - - - -
25D PHE* 1.3 73.7 - - - +
27D VAL* 1.3 65.3 + - - +
28D SER* 4.1 15.5 - - - +
29D ASN* 3.1 29.7 + - + +
30D LEU* 3.8 0.2 - - - +
32D VAL 5.5 0.2 + - - -
34D VAL* 3.9 40.2 - - + +
48D LEU* 3.6 13.0 - - + +
49D VAL* 4.1 21.5 - - + -
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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