Contacts of the strand formed by residues 29 - 36 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20N PHE* 4.0 20.9 - - + -
21N GLU 3.4 10.8 - - - +
22N GLN* 3.7 26.7 - - + +
27N GLY 4.6 0.2 - - - +
28N PRO* 1.3 76.1 - - - +
30N LYS* 1.3 72.7 + - - +
31N VAL* 3.8 3.7 + - + +
100N GLU* 3.5 3.4 - - - -
101N ASP 2.8 33.2 + - - +
104N ILE* 3.6 44.6 - - + +
105N SER* 3.9 7.4 - - - -
106N LEU* 4.4 7.6 - - + +
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Residues in contact with LYS 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N ASN 3.5 0.3 - - - +
20N PHE* 3.1 5.2 - - - -
21N GLU* 2.7 55.0 + - + +
23N LYS* 6.3 3.4 - - + -
28N PRO* 5.5 2.0 - - + +
29N VAL* 1.3 74.5 - - - +
31N VAL* 1.3 60.6 + - - +
32N TRP* 3.8 18.0 - - + -
99N ILE 3.7 8.1 - - - +
100N GLU* 3.9 25.8 - - + +
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Residues in contact with VAL 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N ILE* 3.7 20.0 - - + -
19N ASN 3.0 9.2 - - - +
20N PHE* 3.9 20.6 - - + -
29N VAL 4.0 10.1 - - - +
30N LYS* 1.3 78.9 - - - +
32N TRP* 1.3 64.4 + - - +
45N PHE* 4.2 20.4 - - + -
84N LEU* 5.1 4.0 - - + -
97N VAL* 4.2 7.6 - - + -
98N SER* 3.5 1.0 + - - -
99N ILE* 2.9 49.4 + - + +
101N ASP* 5.1 0.9 - - + +
104N ILE* 4.4 14.4 - - + -
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Residues in contact with TRP 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3N LYS* 4.9 10.1 - - - -
18N ILE* 3.5 6.4 - - - -
19N ASN* 2.7 81.5 + - + +
20N PHE 4.5 2.5 - - - -
21N GLU* 3.7 42.2 - - + -
30N LYS* 3.8 22.9 - - + -
31N VAL* 1.3 77.2 - - - +
33N GLY* 1.3 62.6 + - - +
97N VAL* 3.2 15.7 - - - +
98N SER* 4.2 9.0 - - - +
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Residues in contact with GLY 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N ILE 3.3 11.4 - - - -
18N ILE* 4.2 1.3 - - - -
19N ASN* 4.1 4.0 - - - -
32N TRP* 1.3 84.0 - - - +
34N SER* 1.3 58.2 + - - -
96N ASP* 3.7 3.6 - - - +
97N VAL* 2.7 37.1 + - - +
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Residues in contact with SER 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N GLY* 3.2 3.1 - - - -
17N ILE 3.2 28.9 + - - -
18N ILE* 4.1 0.6 - - - +
33N GLY* 1.3 75.1 - - - -
35N ILE* 1.3 66.1 + - - +
36N LYS* 6.1 0.3 - - - +
94N VAL* 4.7 9.2 - - - +
95N ALA 3.1 15.0 - - - -
96N ASP* 3.8 15.9 - - - -
97N VAL* 4.3 1.1 - - - +
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Residues in contact with ILE 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N LEU* 4.9 7.9 - - + -
14N VAL* 3.7 20.2 - - + -
15N GLN 3.5 12.8 - - - +
16N GLY* 4.5 5.2 - - - +
18N ILE* 4.2 16.2 - - + -
34N SER* 1.3 82.7 - - - +
36N LYS* 1.3 62.6 + - - +
38N LEU* 3.5 21.4 - - + +
45N PHE* 4.1 25.1 - - + -
87N VAL* 4.4 11.0 - - + -
93N GLY 3.7 1.2 - - - +
94N VAL* 3.4 2.6 - - - +
95N ALA* 2.7 37.5 + - + +
97N VAL* 4.5 5.6 - - + -
119N VAL* 4.3 21.3 - - + -
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Residues in contact with LYS 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N PRO 3.5 1.7 - - - +
14N VAL* 3.2 6.8 - - - +
15N GLN* 2.8 70.7 + - + +
34N SER* 6.1 0.2 - - - +
35N ILE* 1.3 76.1 - - - +
37N GLY* 1.3 64.0 + - - +
38N LEU* 3.3 2.6 + - - -
93N GLY 3.4 4.5 - - - -
94N VAL* 4.0 20.0 - - + +
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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