Contacts of the strand formed by residues 21 - 28 (chain C) in PDB entry 1MJO
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 VAL 21 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 3.3 31.6 - - + -
17C LYS* 2.7 44.2 + - + +
18C SER* 4.3 5.2 - - - +
19C GLU 3.5 0.2 - - - -
20C GLN* 1.3 73.5 - - - +
22C LYS* 1.3 79.1 + - - +
23C LYS* 5.0 5.4 - - + +
27D SER* 3.5 33.4 - - - +
28D ILE 3.6 8.3 - - - +
29D PRO* 4.6 4.7 - - + -
9F T 4.2 6.5 - - - +
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Residues in contact with LYS 22 (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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18C SER 4.4 3.4 + - - -
19C GLU* 2.7 37.2 + - - +
21C VAL* 1.3 84.5 + - - +
23C LYS* 1.3 66.1 + - - +
27D SER* 3.5 4.7 - - - -
28D ILE* 2.8 39.2 + - - +
30D LEU* 3.4 36.1 - - + +
33D LEU* 4.1 24.0 - - + -
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Residues in contact with LYS 23 (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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21C VAL* 5.0 5.2 - - + +
22C LYS* 1.3 82.6 - - - +
24C ILE* 1.3 66.3 + - - +
25D THR* 3.6 19.7 - - + -
26D VAL 3.4 2.9 - - - +
27D SER* 3.7 25.4 - - - +
9F T 3.4 21.1 - - + +
10F G 3.3 40.7 + - - -
11F A 5.4 0.6 - - - +
3G A 4.2 7.8 + - - +
4G C 5.9 6.5 - - + -
6G T 5.3 2.2 + - - -
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Residues in contact with ILE 24 (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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23C LYS* 1.3 80.0 - - - +
25C THR* 1.3 64.8 + - - +
26C VAL* 3.7 20.5 + - + -
24D ILE 3.5 0.7 - - - +
25D THR* 3.6 3.5 - - - -
26D VAL* 2.9 46.3 + - + +
28D ILE* 3.8 29.6 - - + -
33D LEU* 3.8 26.9 - - + -
36D LEU* 4.4 8.1 - - + -
53D ASN* 5.2 5.4 - - + +
57D LEU* 4.1 12.1 - - + -
3G A 3.3 26.0 - - - +
4G C 6.3 0.4 - - - -
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Residues in contact with THR 25 (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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24C ILE* 1.3 73.2 - - - +
26C VAL* 1.3 63.2 + - - +
27C SER* 4.1 1.5 + - - +
23D LYS* 3.8 36.6 - - + -
24D ILE 3.4 7.2 - - - +
25D THR* 5.0 3.8 + - - +
54D SER* 4.1 5.9 + - - -
12F C 4.7 3.4 + - - +
13F G 5.5 1.3 - - - +
1G A 5.4 0.3 - - - +
2G G 3.5 30.2 + - + +
3G A 3.0 25.9 + - - +
4G C 3.0 29.1 + - - +
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Residues in contact with VAL 26 (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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24C ILE* 3.8 13.9 - - + -
25C THR* 1.3 76.6 - - - +
27C SER* 1.3 70.2 + - - +
28C ILE* 4.8 8.3 - - + +
57C LEU* 5.0 4.9 - - + -
22D LYS 3.3 2.1 - - - +
23D LYS* 3.2 2.7 - - - -
24D ILE* 2.8 43.4 + - + +
26D VAL* 3.4 32.8 - - + -
53D ASN* 6.2 0.9 - - + -
54D SER* 3.6 26.5 - - - +
57D LEU* 3.8 26.7 - - + -
58D CYS* 5.2 1.6 - - - -
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Residues in contact with SER 27 (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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25C THR* 5.1 1.0 + - - +
26C VAL* 1.3 71.4 - - - +
28C ILE* 1.3 60.9 + - - +
29C PRO* 4.4 1.5 - - - +
21D VAL* 3.8 13.0 - - - -
22D LYS 3.3 7.0 - - - -
23D LYS* 3.9 13.4 - - - +
54D SER* 3.0 28.0 + - - -
58D CYS* 3.8 8.7 - - - -
1G A 3.1 48.8 + - - +
2G G 5.2 0.9 - - - -
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Residues in contact with ILE 28 (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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26C VAL* 4.6 5.6 - - + +
27C SER* 1.3 75.3 - - - +
29C PRO* 1.3 87.3 - - + +
30C LEU* 3.3 0.7 + - - -
32C VAL* 3.6 24.2 - - + -
33C LEU* 3.7 29.4 - - + +
36C LEU* 4.0 20.9 - - + -
57C LEU* 5.2 8.1 - - + -
21D VAL* 4.0 3.0 - - - +
22D LYS* 2.8 40.8 + - - +
24D ILE* 4.1 26.9 - - + -
58D CYS* 3.9 10.5 - - - -
61D PHE* 6.1 0.2 - - + -
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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