Contacts of the strand formed by residues 29 - 36 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20K PHE* 4.1 21.3 - - + -
21K GLU 3.3 11.2 - - - +
22K GLN* 3.7 25.1 - - + +
28K PRO* 1.3 76.6 - - - +
30K LYS* 1.3 72.2 + - - +
31K VAL* 3.8 3.4 + - + +
100K GLU* 3.5 2.3 - - - -
101K ASP* 2.9 33.4 + - - +
104K ILE* 3.5 43.3 - - + +
105K SER* 3.9 8.3 - - - -
106K LEU* 4.4 7.2 - - + +
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Residues in contact with LYS 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K ASN 3.6 0.3 - - - +
20K PHE* 3.1 5.0 - - - -
21K GLU* 2.7 54.5 + - + +
23K LYS* 6.2 3.3 - - + +
28K PRO* 4.1 2.0 - - + +
29K VAL* 1.3 74.2 - - - +
31K VAL* 1.3 60.0 + - - +
32K TRP* 3.7 17.5 - - + -
99K ILE 3.6 7.2 - - - +
100K GLU* 3.9 27.1 - - + +
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Residues in contact with VAL 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ILE* 3.8 18.8 - - + -
19K ASN 3.0 9.0 - - - +
20K PHE* 3.9 20.9 - - + -
29K VAL 3.9 9.6 - - - +
30K LYS* 1.3 76.5 - - - +
32K TRP* 1.3 62.7 + - - +
45K PHE* 4.1 13.9 - - + -
84K LEU* 5.1 4.3 - - + -
97K VAL* 4.0 13.8 - - + +
98K SER* 3.6 0.5 - - - -
99K ILE* 2.8 53.1 + - + +
101K ASP 5.0 0.4 - - - +
104K ILE* 4.4 13.5 - - + -
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Residues in contact with TRP 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K LYS* 5.0 9.9 - - - -
18K ILE* 3.5 6.6 - - - -
19K ASN* 2.7 73.8 + - + +
20K PHE 4.6 1.3 - - - -
21K GLU* 3.7 44.6 - - + -
30K LYS* 3.7 25.6 - - + -
31K VAL* 1.3 76.1 - - - +
33K GLY* 1.3 61.2 + - - +
97K VAL* 3.1 18.6 - - - +
98K SER* 4.2 8.1 - - - +
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Residues in contact with GLY 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K ILE 3.3 12.6 - - - -
18K ILE* 4.1 4.7 - - - -
19K ASN* 4.2 4.3 - - - -
32K TRP* 1.3 86.9 - - - +
34K SER* 1.3 63.2 + - - -
96K ASP* 3.8 3.5 - - - +
97K VAL* 2.8 25.9 + - - +
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Residues in contact with SER 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K GLY* 3.2 2.9 - - - -
17K ILE 3.1 29.7 + - - +
18K ILE* 4.1 0.4 - - - +
33K GLY* 1.3 75.8 - - - -
35K ILE* 1.3 66.8 + - - +
94K VAL* 4.8 7.6 - - - +
95K ALA 3.1 15.9 - - - -
96K ASP* 3.8 15.3 - - - -
97K VAL* 4.3 1.3 - - - +
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Residues in contact with ILE 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K LEU* 4.9 7.6 - - + -
14K VAL* 3.7 22.4 - - + -
15K GLN 3.5 12.3 - - - +
16K GLY* 4.5 4.0 - - - +
18K ILE* 4.1 16.2 - - + -
34K SER* 1.3 80.4 - - - +
36K LYS* 1.3 62.3 + - - +
38K LEU* 3.5 21.6 - - + +
45K PHE* 4.1 25.4 - - + -
87K VAL* 4.4 15.0 - - + -
93K GLY 3.7 1.0 - - - +
94K VAL* 3.4 3.4 - - - +
95K ALA* 2.7 37.0 + - + +
97K VAL* 4.4 11.7 - - + -
119K VAL* 4.4 14.6 - - + -
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Residues in contact with LYS 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J ASP* 3.0 43.0 + - - +
13K PRO 3.5 1.5 - - - +
14K VAL* 3.2 6.9 - - - +
15K GLN* 2.8 68.2 + - + +
35K ILE* 1.3 75.7 - - - +
37K GLY* 1.3 63.2 + - - +
38K LEU 3.2 2.8 + - - -
93K GLY 3.4 4.7 - - - -
94K VAL* 4.1 19.1 - - + +
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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