Contacts of the strand formed by residues 37 - 42 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D TYR* 2.8 34.7 + - + -
31D SER* 3.8 4.7 - - - -
36D ALA* 1.3 72.6 - - - +
38D VAL* 1.3 59.4 + - - +
39D TYR* 3.8 22.4 + - + -
301D GLU* 2.6 18.9 + - - +
302D LYS* 4.4 12.2 - - + +
303D ILE* 3.0 27.7 + - - +
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Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TYR* 3.9 1.4 - - - -
27D LEU* 2.9 31.8 + - + +
30D ILE* 4.0 15.3 - - + +
31D SER* 3.0 32.3 + - - +
34D ILE* 4.8 3.4 - - + -
36D ALA 3.9 2.7 - - - +
37D ASP* 1.3 76.5 - - - +
39D TYR* 1.3 71.2 + - - +
287D PHE* 4.2 13.7 - - + -
290D LEU* 3.8 29.4 - - + -
303D ILE* 3.6 14.8 - - + +
305D PHE* 4.8 2.2 - - + -
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Residues in contact with TYR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 4.1 15.3 - - + -
25D GLN 3.1 11.2 - - - +
26D TYR* 3.3 41.1 - + + +
27D LEU* 4.2 1.3 - - - +
37D ASP* 3.8 30.3 + - + +
38D VAL* 1.3 80.7 - - - +
40D ILE* 1.3 64.2 + - - +
180D VAL* 3.6 43.3 - - + +
182D PHE* 3.7 20.6 - + + -
302D LYS* 4.5 9.3 - - + +
303D ILE 3.0 10.5 + - - +
304D LEU* 4.0 3.6 - - + -
305D PHE* 3.1 24.6 + - - +
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Residues in contact with ILE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PRO 3.8 0.2 - - - +
24D ILE* 3.4 2.5 - - - -
25D GLN* 2.8 43.5 + - + +
27D LEU* 3.6 31.4 - - + -
39D TYR* 1.3 77.1 - - - +
41D LYS* 1.3 60.7 - - - +
42D ARG* 3.5 17.1 + - - +
270D VAL* 6.0 2.2 - - + -
276D ILE* 4.4 19.3 - - + -
278D LEU* 5.2 2.7 - - + -
287D PHE* 5.1 2.5 - - + -
304D LEU* 4.1 2.0 - - - -
305D PHE* 3.1 31.0 - - + +
307D HIS* 3.7 30.7 - - + -
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Residues in contact with LYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D THR* 2.4 47.6 + - - +
23D PRO 3.6 3.1 - - - -
24D ILE* 3.7 15.5 - - + -
40D ILE* 1.3 71.7 - - - +
42D ARG* 1.3 59.9 + - - +
43D ASP* 3.0 21.5 + - - +
56D ARG* 3.8 4.9 - - - +
167D TYR* 6.3 0.2 - - + -
170D ALA* 4.9 5.2 - - + -
173D GLU* 3.1 15.0 + - - -
174D ILE* 3.7 25.1 - - + -
177D GLN* 2.5 34.0 + - - +
304D LEU* 3.7 7.8 - - + +
305D PHE 2.8 9.3 + - - +
306D ILE* 3.6 19.6 - - + +
307D HIS 2.8 27.5 + - - -
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLY* 2.1 45.1 + - - -
22D THR* 3.3 15.6 - - - -
23D PRO* 2.9 22.3 + - + +
25D GLN* 2.7 32.5 - - + +
40D ILE* 4.0 22.4 - - - +
41D LYS* 1.3 69.9 - - - +
43D ASP* 1.3 57.0 + - - +
44D ASP* 2.7 60.2 + - - +
45D LEU* 3.1 34.0 + - + +
276D ILE* 3.6 26.7 - - - +
307D HIS* 3.8 8.9 - - - -
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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