Contacts of the strand formed by residues 29 - 36 (chain M) in PDB entry 1OZT
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 29 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20M PHE* 4.1 21.5 - - + -
21M GLU 3.3 12.3 - - - +
22M GLN* 3.7 24.9 - - + +
28M PRO* 1.3 75.9 - - - +
30M LYS* 1.3 71.2 + - - +
31M VAL* 3.8 3.0 + - + +
100M GLU* 3.5 2.6 - - - -
101M ASP 2.9 35.0 + - - +
104M ILE* 3.5 45.1 - - + +
105M SER* 3.9 7.6 - - - -
106M LEU* 4.4 7.9 - - + +
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Residues in contact with LYS 30 (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 ASN 3.6 0.3 - - - +
20M PHE* 3.2 5.7 - - - -
21M GLU* 2.7 51.5 + - + +
23M LYS* 6.3 2.7 - - + -
28M PRO* 5.5 2.0 - - + +
29M VAL* 1.3 74.5 - - - +
31M VAL* 1.3 60.3 + - - +
32M TRP* 3.7 17.0 - - + -
99M ILE 3.6 7.6 - - - +
100M GLU* 3.9 27.1 - - + +
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Residues in contact with VAL 31 (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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18M ILE* 3.7 19.7 - - + -
19M ASN 3.0 8.1 - - - +
20M PHE* 3.9 21.1 - - + -
29M VAL 4.0 8.7 - - - +
30M LYS* 1.3 77.9 - - - +
32M TRP* 1.3 62.9 + - - +
45M PHE* 4.1 21.5 - - + -
84M LEU* 5.1 4.3 - - + -
97M VAL* 4.2 6.7 - - + -
98M SER* 3.5 0.9 + - - -
99M ILE* 2.8 51.4 + - + +
101M ASP* 5.0 1.3 - - + +
104M ILE* 4.5 14.1 - - + -
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Residues in contact with TRP 32 (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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3M LYS* 5.0 9.4 - - - -
18M ILE* 3.5 6.8 - - - -
19M ASN* 2.7 74.4 + - + +
20M PHE 4.5 2.2 - - - -
21M GLU* 3.7 36.3 - - + -
30M LYS* 3.7 31.2 - - + -
31M VAL* 1.3 78.1 - - - +
33M GLY* 1.3 61.4 + - - +
97M VAL* 3.2 16.8 - - - +
98M SER* 4.2 9.9 - - - +
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Residues in contact with GLY 33 (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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17M ILE 3.3 12.3 - - - -
18M ILE* 4.2 4.5 - - - -
19M ASN* 4.2 4.5 - - - -
32M TRP* 1.3 84.0 - - - +
34M SER* 1.3 63.5 + - - -
96M ASP* 3.7 3.0 - - - +
97M VAL 2.7 30.0 + - - +
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Residues in contact with SER 34 (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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16M GLY* 3.2 3.3 - - - -
17M ILE* 3.2 29.2 + - - +
18M ILE* 4.1 0.2 - - - +
33M GLY* 1.3 75.5 - - - -
35M ILE* 1.3 67.6 + - - +
94M VAL* 4.7 9.0 - - - +
95M ALA 3.1 14.6 - - - -
96M ASP* 3.8 16.6 - - - -
97M VAL* 4.3 1.3 - - - +
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Residues in contact with ILE 35 (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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8M LEU* 4.9 7.6 - - + -
14M VAL* 3.7 22.2 - - + -
15M GLN 3.5 11.0 - - - +
16M GLY* 4.5 4.9 - - - +
18M ILE* 4.2 12.3 - - + -
34M SER* 1.3 81.6 - - - +
36M LYS* 1.3 62.9 + - - +
38M LEU* 3.4 21.7 - - + +
45M PHE* 4.1 26.0 - - + -
87M VAL* 4.4 7.6 - - + -
93M GLY 3.7 1.0 - - - +
94M VAL* 3.4 3.5 - - - +
95M ALA* 2.7 37.5 + - + +
97M VAL* 4.4 13.7 - - + -
119M VAL* 4.4 21.8 - - + -
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Residues in contact with LYS 36 (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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13M PRO 4.2 1.3 - - - +
14M VAL* 3.2 6.9 - - - +
15M GLN* 2.8 69.9 + - + +
35M ILE* 1.3 75.9 - - - +
37M GLY* 1.3 64.6 + - - +
38M LEU 3.3 3.3 + - - -
93M GLY 3.5 4.9 - - - -
94M VAL* 4.1 19.5 - - + -
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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