Contacts of the strand formed by residues 273 - 277 (chain A) in PDB entry 6J8H
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 HIS 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A GLY 4.2 8.1 - - - -
270A ASN* 3.3 34.3 + - - +
271A LEU 3.4 2.0 - - - -
272A LYS* 1.3 74.4 - - - +
274A LYS* 1.3 62.6 + - - +
314A LEU* 3.0 29.6 - - + +
315A CYS* 3.4 37.2 - - - +
316A GLY* 4.7 3.1 - - - -
317A PHE* 3.8 31.5 - + - -
330A CYS* 4.3 5.5 - - - -
331A VAL 3.8 5.2 - - - -
332A LYS* 3.3 25.1 + - + +
373A ALA* 4.0 15.9 + - + -
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU 4.5 1.8 + - - -
272A LYS* 2.6 23.3 + - - +
273A HIS* 1.3 78.9 + - - +
275A CYS* 1.3 62.1 + - - +
276A PHE 3.5 0.7 + - - -
299A PHE* 5.6 9.0 - - + -
303A PHE* 3.5 33.2 - - + -
312A ALA* 4.0 25.4 - - + +
313A LEU 3.7 6.1 - - - -
314A LEU* 5.3 1.7 - - + +
315A CYS* 3.0 14.0 - - - -
331A VAL* 2.9 27.2 + - - +
333A ILE 2.5 29.1 + - - +
334A GLY* 3.8 6.8 - - - -
335A ARG* 3.3 28.4 + - - +
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Residues in contact with CYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LYS* 1.3 72.6 - - - +
276A PHE* 1.3 60.4 + - - +
303A PHE* 3.4 25.8 - - - +
304A TYR* 3.4 17.7 + - + +
312A ALA* 5.7 0.4 - - - +
313A LEU* 4.2 14.2 + - - -
315A CYS* 3.6 7.0 - - - -
323A GLN 4.7 1.3 - - - -
324A CYS* 1.9 59.0 - - + -
325A PRO* 4.7 3.6 - - - -
328A TYR* 3.6 16.9 - - + -
329A THR 3.2 6.5 - - - +
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Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LYS 3.5 2.0 + - - -
275A CYS* 1.3 73.7 - - - +
277A ARG* 1.3 74.4 + - - +
278A ASN 5.9 0.2 - - - -
280A LEU* 3.1 39.3 - - + -
286A LEU* 4.0 38.6 - - + -
289A ILE* 4.6 8.5 - - + -
302A TYR* 4.0 29.2 - + + -
303A PHE* 4.1 23.1 - + + -
328A TYR* 4.1 0.7 - - - -
329A THR* 2.5 44.3 + - + +
331A VAL* 3.1 27.8 - - + -
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Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A PHE* 1.3 87.5 - - + +
278A ASN* 1.3 61.6 + - - +
279A SER* 3.3 19.6 + - - +
280A LEU* 3.3 25.4 - - + +
281A GLU* 5.4 10.5 + - - +
301A LYS* 3.7 26.3 + - - +
302A TYR* 3.6 35.3 + - + +
327A GLY 3.9 2.5 - - - -
328A TYR* 3.7 19.9 - - + -
131B ASN* 4.0 23.6 + - - +
132B TYR* 3.7 46.4 - - + +
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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