Contacts of the strand formed by residues 304 - 308 (chain F) in PDB entry 5IJ7
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 LEU 304 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B MET* 4.1 17.5 - - + -
42B PHE* 3.9 21.3 - - + -
45B ASN* 3.4 34.3 - - + +
300F TRP* 3.5 9.4 - - - -
301F LEU* 2.9 30.7 + - + +
303F ASP* 1.3 83.4 - - + +
305F ILE* 1.3 63.8 + - - +
316F CYS* 4.1 10.5 - - - -
317F TRP 3.7 5.8 - - - +
318F LYS* 4.0 22.4 - - + -
339F LEU* 3.7 34.1 - - + -
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Residues in contact with ILE 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238F MET* 3.7 28.5 - - + -
298F VAL* 3.6 28.9 - - + -
299F ARG 3.9 3.8 - - - +
300F TRP* 3.8 21.5 - - + -
303F ASP 4.1 1.3 - - - +
304F LEU* 1.3 81.3 - - - +
306F LEU* 1.3 66.6 + - - +
307F SER* 4.6 0.4 - - - -
315F VAL 3.4 1.7 - - - +
316F CYS* 3.3 7.4 - - - -
317F TRP* 2.8 68.4 + - + +
319F PRO* 3.6 30.5 - - + -
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Residues in contact with LEU 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298F VAL* 3.4 1.7 - - - +
299F ARG 2.9 38.1 + - - +
301F LEU* 3.9 27.1 - - + -
305F ILE* 1.3 71.2 - - - +
307F SER* 1.3 61.6 + - - +
314F ILE* 3.9 11.2 - - + -
315F VAL 3.4 1.6 - - - -
316F CYS* 3.8 20.9 - - + -
342F PHE* 3.8 28.3 - - + -
354F PHE* 3.3 15.4 - - + -
356F MET* 3.8 33.0 - - + -
363F LEU* 4.1 15.7 - - + -
377F LEU* 4.9 4.5 - - + -
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Residues in contact with SER 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F LEU* 3.8 23.4 - - - +
291F HIS* 2.8 32.6 + - - -
295F VAL* 3.9 2.0 - - - -
297F CYS 3.3 13.0 - - - -
298F VAL* 4.2 1.3 - - - -
306F LEU* 1.3 75.1 - - - +
308F LYS* 1.3 60.9 + - - +
314F ILE* 3.5 2.4 - - - +
315F VAL 2.8 34.4 + - - -
317F TRP* 3.1 20.8 + - - -
354F PHE* 4.0 5.7 - - - -
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Residues in contact with LYS 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F HIS* 3.7 7.0 - - - -
295F VAL* 3.2 19.4 - - - +
296F ASP* 2.8 44.2 + - - +
297F CYS* 3.2 8.3 + - + -
307F SER* 1.3 76.4 - - - +
309F SER* 1.3 71.7 + - - +
313F ALA 3.6 14.8 - - - +
314F ILE* 4.0 5.8 - - + -
344F TYR* 3.4 20.0 - - - +
347F CYS* 4.1 18.0 + - - -
349F ILE 5.1 1.4 + - - -
352F MET* 2.8 34.2 + - - +
354F PHE* 3.7 26.9 - - + -
365F LEU* 4.1 13.0 - - + -
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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