Contacts of the strand formed by residues 37 - 42 (chain T) in PDB entry 1J0B
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 ASP 37 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O LYS* 2.6 43.1 + - - +
26T TYR* 3.7 11.7 + - - -
31T SER* 3.7 2.5 - - - -
35T GLY 5.3 1.2 - - - +
36T ALA* 1.3 73.4 - - - +
38T VAL* 1.3 58.4 + - - +
39T TYR* 3.5 22.2 + - - +
301T GLU* 2.8 26.0 + - + +
302T LYS* 3.5 18.0 - - + -
303T ILE* 3.2 18.0 + - - +
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Residues in contact with VAL 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T TYR* 3.6 4.2 - - - -
27T LEU* 3.0 49.8 + - + +
30T ILE* 4.0 26.2 - - + +
31T SER* 3.5 7.3 + - - -
34T ILE* 5.2 2.0 - - + -
36T ALA* 3.5 7.0 + - + +
37T ASP* 1.3 73.7 - - - +
39T TYR* 1.3 69.1 + - - +
287T PHE* 4.7 1.6 - - + -
290T LEU* 3.8 35.9 - - + -
303T ILE* 3.3 18.8 - - + +
305T PHE 4.7 0.4 - - - +
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Residues in contact with TYR 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2O HIS* 3.8 6.8 - - - -
3O PRO* 4.0 29.4 - - + -
4O LYS* 4.3 5.0 - - + +
24T ILE* 4.1 15.0 - - + -
25T GLN 3.0 10.5 - - - +
26T TYR* 3.6 33.4 - + + +
27T LEU* 4.5 1.8 - - - -
37T ASP* 3.5 34.1 + - + +
38T VAL* 1.3 78.7 - - - +
40T ILE* 1.3 62.5 + - - +
180T VAL* 3.0 36.9 - - + +
182T PHE* 3.4 26.9 - + + -
302T LYS* 4.6 7.3 - - + -
303T ILE 3.0 5.0 + - - +
304T LEU* 3.4 3.9 - - + -
305T PHE* 2.8 26.2 + - - +
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Residues in contact with ILE 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23T PRO 3.9 0.2 - - - +
24T ILE* 3.0 2.1 - - - -
25T GLN* 2.4 77.1 + - + +
27T LEU* 3.7 26.5 - - + -
39T TYR* 1.3 71.7 - - - +
41T LYS* 1.3 70.1 + - - +
42T ARG* 3.9 14.5 + - - +
270T VAL* 6.2 0.9 - - + -
276T ILE* 3.5 28.3 - - + -
278T LEU* 5.4 1.3 - - + -
287T PHE* 6.4 0.2 - - + -
304T LEU* 3.9 4.0 - - - -
305T PHE* 3.3 20.4 - - + +
307T HIS* 3.9 22.4 - - + -
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Residues in contact with LYS 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T THR* 2.5 45.9 + - - +
23T PRO 3.3 7.4 - - - +
24T ILE* 3.8 6.3 - - + -
40T ILE* 1.3 73.4 - - - +
42T ARG* 1.3 57.7 + - - +
43T ASP* 3.0 22.7 + - - +
56T ARG* 3.8 4.9 - - - +
167T TYR* 6.5 0.7 - - + -
170T ALA* 4.9 3.1 - - - -
173T GLU* 2.6 28.2 + - - -
174T ILE* 3.7 29.6 - - + -
177T GLN* 2.7 17.8 - - - +
304T LEU* 3.6 15.8 - - + +
305T PHE 2.9 9.8 + - - +
306T ILE* 3.9 12.7 - - + -
307T HIS* 3.0 23.0 + - - +
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Residues in contact with ARG 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20S TRP* 4.3 2.8 - - + -
47S GLY* 3.0 37.6 + - - -
22T THR* 3.2 11.1 - - - -
23T PRO* 2.9 32.4 + - + +
25T GLN* 2.4 41.3 - - + +
40T ILE* 3.9 15.5 - - - +
41T LYS* 1.3 66.3 - - - +
43T ASP* 1.3 56.4 + - - +
44T ASP* 2.8 54.7 + - - +
45T LEU* 2.9 40.1 + - + +
276T ILE* 3.9 18.8 - - - +
277T ILE 5.8 0.2 - - - +
307T HIS* 3.6 13.5 - - - -
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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