Contacts of the strand formed by residues 302 - 307 (chain H) 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 LYS 302 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H ASP* 3.4 24.8 + - + +
39H TYR* 5.2 1.5 + - - -
180H VAL* 3.8 20.9 - - + +
181H LYS* 2.7 51.5 - - + +
182H PHE* 3.0 20.1 - - - +
183H ASP* 2.9 34.8 + - - +
301H GLU* 1.3 92.8 - - + +
303H ILE* 1.3 57.8 + - - +
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Residues in contact with ILE 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H ILE* 5.8 0.7 - - + -
36H ALA* 4.6 13.5 - - + -
37H ASP 3.2 14.8 + - - +
38H VAL* 3.5 5.6 - - + +
39H TYR* 2.9 27.7 + - - +
182H PHE* 4.0 0.7 - - - -
184H SER* 3.5 9.2 - - - +
186H VAL* 3.3 18.4 - - + -
290H LEU* 3.3 33.7 - - + -
294H ALA* 3.9 12.8 - - + -
299H LEU* 2.9 54.7 - - + +
300H GLY 4.6 2.7 - - - +
301H GLU 4.4 3.8 - - - +
302H LYS* 1.3 70.9 - - - +
304H LEU* 1.3 60.7 + - - +
305H PHE 3.9 0.2 + - - -
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Residues in contact with LEU 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H ILE* 4.8 5.4 - - + -
39H TYR* 3.5 15.5 - - + +
40H ILE 4.3 0.9 - - - -
41H LYS* 3.9 19.7 - - + +
174H ILE* 4.2 20.0 - - + -
182H PHE* 3.2 40.4 - - + -
184H SER 3.0 10.3 + - - +
185H ILE* 3.0 71.8 - - + +
186H VAL 3.0 2.5 + - - -
302H LYS 3.7 0.4 + - - -
303H ILE* 1.3 71.4 - - - +
305H PHE* 1.3 71.4 + - - +
306H ILE* 4.2 7.2 - - + -
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Residues in contact with PHE 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H VAL* 4.7 2.0 - - + -
39H TYR 2.8 10.0 + - - +
40H ILE* 3.1 36.0 - - + -
41H LYS 3.1 20.4 + - - -
186H VAL* 3.1 33.2 - - + +
187H VAL* 4.9 2.7 - - - -
188H ALA* 4.9 0.9 - - + -
278H LEU* 4.6 7.9 - - + -
283H THR* 4.2 27.6 - - + -
286H ALA* 3.7 24.7 - - + -
287H PHE* 3.6 31.9 - + + -
290H LEU* 4.1 20.6 - - + -
303H ILE* 3.9 2.0 - - - +
304H LEU* 1.3 75.9 - - - +
306H ILE* 1.3 80.4 + - - +
307H HIS* 4.1 2.2 - - - -
308H THR* 5.5 0.7 - - - -
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Residues in contact with ILE 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H LYS* 4.1 16.4 - - + +
43H ASP* 4.3 14.8 - - + -
167H TYR* 4.4 28.3 - - + +
174H ILE* 4.4 15.0 - - + -
185H ILE* 3.5 29.2 - - + -
186H VAL 3.3 5.9 + - - +
187H VAL* 4.5 19.5 - - + +
194H THR* 5.6 0.2 - - + -
198H LEU* 5.1 7.0 - - + -
304H LEU* 4.2 7.4 - - + -
305H PHE* 1.3 99.1 - - - +
307H HIS* 1.3 76.4 + - - +
308H THR* 3.3 13.2 + - + +
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Residues in contact with HIS 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ILE* 3.8 14.1 - - + +
41H LYS 3.0 16.1 + - - +
42H ARG* 4.3 2.5 - - - -
43H ASP* 3.1 27.0 - - - +
44H ASP* 2.8 37.9 + - + +
276H ILE* 3.4 29.4 - - + +
277H ILE 3.6 24.0 + - - -
278H LEU* 3.9 14.4 - - + +
283H THR* 4.1 3.4 - - + +
305H PHE* 4.0 8.3 + - - -
306H ILE* 1.3 69.8 - - - +
308H THR* 1.3 58.0 + - - +
309H GLY* 2.8 46.7 + - - -
311H ILE* 5.9 1.1 - - + -
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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