Contacts of the strand formed by residues 37 - 41 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26S TYR* 2.8 33.4 + - + -
31S SER* 3.7 3.8 - - - +
36S ALA* 1.3 72.1 - - - +
38S VAL* 1.3 59.1 + - - +
39S TYR* 4.0 21.1 + - + -
301S GLU 3.1 18.5 + - - +
302S LYS* 3.6 5.4 - - + +
303S ILE* 3.1 25.8 + - - +
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Residues in contact with VAL 38 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26S TYR* 4.1 1.8 - - - -
27S LEU* 3.1 32.3 + - + +
30S ILE* 4.0 25.4 - - + -
31S SER* 3.0 24.9 + - - +
34S ILE* 4.6 5.2 - - + -
36S ALA 4.2 2.0 - - - +
37S ASP* 1.3 74.6 - - - +
39S TYR* 1.3 72.1 + - - +
287S PHE* 4.3 21.1 - - + -
290S LEU* 4.3 22.7 - - + -
303S ILE* 3.8 12.8 - - + +
305S PHE* 4.8 1.3 - - + -
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Residues in contact with TYR 39 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24S ILE* 4.0 10.5 - - + -
25S GLN 3.1 18.6 - - - +
26S TYR* 3.5 30.7 - + + -
37S ASP* 4.0 30.3 + - + -
38S VAL* 1.3 81.6 - - - +
40S ILE* 1.3 60.9 + - - +
180S VAL* 3.6 38.9 - - + +
181S LYS* 5.4 2.1 + - - -
182S PHE* 3.3 34.1 - + + -
302S LYS* 4.9 6.9 - - + +
303S ILE 3.0 9.3 + - - +
304S LEU* 3.8 2.4 - - + -
305S PHE* 3.1 23.9 + - - +
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Residues in contact with ILE 40 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23S PRO 3.8 0.5 - - - +
24S ILE* 3.4 3.4 - - - -
25S GLN* 2.9 43.6 + - + +
27S LEU* 3.5 37.0 - - + -
38S VAL 4.2 0.6 + - - -
39S TYR* 1.3 74.8 - - - +
41S LYS* 1.3 63.6 + - - +
42S ARG* 3.9 2.3 + - - +
270S VAL* 6.0 1.8 - - + -
276S ILE* 3.5 30.5 - - + -
278S LEU* 5.1 1.6 - - + -
287S PHE* 5.6 1.3 - - + -
304S LEU* 4.4 2.0 - - - -
305S PHE* 3.6 31.6 - - + +
307S HIS* 3.9 28.3 - - + -
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Residues in contact with LYS 41 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22S THR* 2.7 35.8 + - - +
23S PRO 3.5 7.9 - - - +
24S ILE* 4.1 6.3 - - + -
40S ILE* 1.3 73.2 - - - +
42S ARG* 1.3 61.7 + - - +
43S ASP* 3.0 23.1 + - - +
56S ARG* 4.0 4.0 - - - +
170S ALA* 4.6 4.9 - - - -
173S GLU* 3.1 7.0 + - - -
174S ILE* 3.4 33.7 - - + -
177S GLN* 2.5 34.7 - - - +
304S LEU* 3.8 16.7 - - + +
305S PHE 3.0 10.4 + - - +
306S ILE* 4.4 11.0 - - + -
307S HIS* 2.8 28.6 + - - +
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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