Contacts of the strand formed by residues 18 - 26 (chain M) in PDB entry 6O81
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 18 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M GLU 3.9 5.6 + - - +
17M ASP* 1.3 70.6 - - - +
19M VAL* 1.3 63.8 + - - +
37M GLU* 4.2 3.8 - - - +
69M CYS* 3.7 19.3 - - + -
70M VAL 3.4 9.6 - - - +
71M VAL* 4.1 17.3 - - + +
89M VAL* 3.9 22.9 - - + -
93M GLU* 4.5 12.6 - - + +
97M CYS* 3.7 31.7 - - + +
100M LYS* 5.0 7.6 + - - +
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Residues in contact with VAL 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M PRO* 3.9 14.6 - - + -
17M ASP* 3.8 12.3 - - + +
18M VAL* 1.3 78.5 - - - +
20M MET* 1.3 61.2 + - - +
21M VAL* 3.8 13.8 + - + -
35M LEU* 4.0 20.0 - - + -
37M GLU* 3.3 20.9 - - + +
38M TYR* 3.8 19.3 - - + -
68M GLU 3.8 0.3 - - - +
69M CYS* 3.4 4.1 - - - -
70M VAL* 2.9 41.0 + - - +
72M VAL* 5.7 0.2 - - + -
84M LEU* 4.3 15.5 - - + -
97M CYS* 5.4 0.9 - - - -
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Residues in contact with MET 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M VAL* 1.3 74.7 - - - +
21M VAL* 1.3 64.1 + - - +
35M LEU* 4.2 1.0 - - - -
36M LEU* 3.3 25.1 + - + +
37M GLU* 4.0 10.8 + - - +
67M ASN* 4.4 12.6 - - + +
68M GLU* 3.5 28.9 - - - +
69M CYS* 3.8 16.6 - - + -
94M ALA 4.8 0.2 - - - +
97M CYS* 3.7 32.2 - - + +
98M GLU* 3.8 15.0 - - + +
101M PHE* 3.7 45.3 - - + -
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Residues in contact with VAL 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M VAL* 4.1 7.0 - - + -
20M MET* 1.3 78.0 - - - +
22M ASN* 1.3 60.4 + - - +
23M VAL* 5.6 1.5 - - + +
33M VAL* 3.9 20.2 - - + -
34M SER 3.4 14.8 - - - +
35M LEU* 3.8 17.0 - - + -
36M LEU* 4.6 4.7 - - - +
45M ILE* 4.2 19.3 - - + -
67M ASN* 3.2 6.9 - - - +
68M GLU* 2.9 47.6 + - + +
70M VAL* 4.4 9.0 - - + -
84M LEU* 3.8 24.2 - - + -
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Residues in contact with ASN 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M VAL* 1.3 74.4 - - - +
23M VAL* 1.3 68.7 + - - +
24M ARG* 3.5 3.8 + - - +
33M VAL* 3.4 2.9 - - - -
34M SER* 2.4 54.3 + - - +
36M LEU* 3.4 21.2 - - - +
65M GLY* 5.2 5.9 - - - -
66M ARG 3.6 7.9 - - - +
67M ASN* 3.4 23.8 - - - +
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Residues in contact with VAL 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M VAL* 5.6 2.2 - - + -
22M ASN* 1.3 75.5 + - - +
24M ARG* 1.3 61.1 + - - +
25M SER 4.1 11.4 - - - +
26M ILE* 4.1 10.3 - - + -
31M ALA* 4.1 16.4 - - + -
32M TYR 3.9 8.3 - - - +
33M VAL* 3.7 16.4 - - + -
45M ILE* 5.0 7.9 - - + -
62M ILE* 3.8 21.8 - - + +
63M ARG 4.2 0.2 - - - +
64M ILE* 3.3 25.1 - - + +
65M GLY* 3.1 24.2 + - - +
66M ARG 3.6 12.9 + - - +
68M GLU* 5.7 5.4 - - + -
86M LYS* 5.8 2.9 - - - +
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Residues in contact with ARG 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M ASN* 3.5 7.7 + - - +
23M VAL* 1.3 73.7 - - - +
25M SER* 1.3 63.8 + - - +
32M TYR* 2.9 17.8 + - + +
33M VAL* 4.7 5.8 - - - -
34M SER* 5.0 6.1 - - - +
42M GLU* 5.2 7.4 - - - +
64M ILE* 3.5 14.8 - - - +
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Residues in contact with SER 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M VAL* 3.9 2.1 - - - +
24M ARG* 1.3 80.9 - - - +
26M ILE* 1.3 75.3 + - - +
31M ALA* 3.6 0.9 - - - +
32M TYR* 2.9 54.2 + - - +
42M GLU* 4.9 0.9 + - - -
64M ILE* 4.9 2.7 - - - -
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Residues in contact with ILE 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M VAL* 4.1 7.0 - - + -
25M SER* 1.3 86.6 - - - +
27M ALA* 1.3 72.3 + - - +
30M GLY 4.0 1.8 - - - +
31M ALA* 3.7 19.3 - - + -
58M ILE* 4.0 21.5 - - + +
59M ASN* 4.9 12.3 - - + +
62M ILE* 3.6 31.0 - - + -
64M ILE* 5.0 8.5 - - + -
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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