Contacts of the strand formed by residues 37 - 41 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26X TYR* 3.7 20.4 + - + -
31X SER* 3.7 2.0 - - - -
36X ALA* 1.3 92.9 - - - +
38X VAL* 1.3 55.6 + - - +
39X TYR* 3.6 25.2 + - + +
301X GLU* 2.8 16.9 + - + +
302X LYS* 3.3 12.2 - - + +
303X ILE* 2.7 33.6 + - - +
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Residues in contact with VAL 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X TYR* 3.5 5.4 - - - -
27X LEU* 3.0 40.4 + - + +
30X ILE* 3.9 23.3 - - + +
31X SER* 2.9 21.2 + - - +
34X ILE* 5.4 2.2 - - + -
36X ALA* 6.2 0.9 - - + -
37X ASP* 1.3 75.5 - - - +
39X TYR* 1.3 77.5 + - - +
287X PHE* 4.8 2.5 - - + -
290X LEU* 4.6 15.3 - - + -
303X ILE* 3.1 23.8 - - + +
305X PHE* 4.4 14.4 - - + +
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Residues in contact with TYR 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X ILE* 3.8 20.2 - - + -
25X GLN* 2.7 16.6 - - - +
26X TYR* 3.5 38.9 - + + -
27X LEU* 4.4 0.7 - - - +
37X ASP* 3.6 34.2 + - + +
38X VAL* 1.3 78.8 - - - +
40X ILE* 1.3 53.0 + - - +
180X VAL* 3.9 31.1 - - + +
182X PHE* 3.3 27.8 - + + -
302X LYS* 4.9 7.0 - - + +
303X ILE 2.9 5.8 + - - -
304X LEU* 3.2 7.0 - - + -
305X PHE* 2.7 32.4 + - - -
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Residues in contact with ILE 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X ILE* 3.5 1.2 - - - -
25X GLN* 2.8 34.6 + - + +
27X LEU* 3.7 35.6 - - + +
39X TYR* 1.3 74.8 - - - +
41X LYS* 1.3 62.5 + - - +
42X ARG* 3.7 17.8 + - - +
270X VAL* 5.9 1.8 - - + -
276X ILE* 4.1 15.7 - - + -
278X LEU* 5.2 1.6 - - + -
287X PHE* 5.5 1.1 - - + -
304X LEU* 3.9 2.5 - - - -
305X PHE* 2.9 46.2 - - + +
307X HIS* 3.7 32.3 - - + -
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Residues in contact with LYS 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X THR* 2.6 46.2 + - - +
23X PRO 3.4 11.2 - - - +
24X ILE* 4.1 6.7 - - + +
40X ILE* 1.3 70.3 - - - +
42X ARG* 1.3 51.9 + - - +
43X ASP* 2.6 30.4 + - - +
56X ARG* 3.7 8.7 - - - +
170X ALA* 4.5 4.3 - - - -
173X GLU* 3.2 9.5 + - - -
174X ILE* 3.5 36.3 - - + -
177X GLN* 2.6 20.9 - - - +
304X LEU* 3.6 16.3 - - + +
305X PHE 2.7 11.7 + - - +
306X ILE* 3.9 15.0 - - + -
307X HIS* 3.0 18.8 + - - -
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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