Contacts of the helix formed by residues 273 - 278 (chain A) in PDB entry 3I5H
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 GLU 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ARG* 2.8 45.2 + - + +
271A LEU 3.6 0.4 + - - -
272A LEU* 1.3 72.5 - - - +
274A LYS* 1.3 66.3 + - - +
275A SER* 3.5 7.9 - - - +
276A ARG* 2.4 60.4 + - + +
287A TYR* 2.9 21.6 + - - +
476A GLU* 4.1 21.5 - - + +
479A CYS* 6.0 0.9 - - - +
480A ILE* 4.8 6.1 - - - +
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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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272A LEU* 2.7 21.2 + - + +
273A GLU* 1.3 70.5 - - - +
275A SER* 1.3 54.9 + - - +
277A VAL* 2.6 45.6 + - - +
431A LYS* 3.9 33.7 - - + +
432A SER* 5.1 6.3 - - - +
434A TYR* 5.8 1.3 - - + -
435A ASP* 4.3 31.4 - - + +
602A ASP* 2.9 37.3 + - - +
647A ILE* 5.3 9.9 - - + -
650A VAL* 4.8 24.1 - - - +
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLU* 4.8 9.1 - - - +
274A LYS* 1.3 75.6 + - - +
276A ARG* 1.3 52.2 + - - +
278A THR* 2.7 30.0 + - - -
279A TYR* 3.1 18.5 + - - +
431A LYS* 3.9 17.6 - - - +
475A PHE* 5.7 3.3 - - - -
476A GLU* 5.0 14.7 - - - +
599A LYS* 5.5 8.5 - - - +
647A ILE* 3.2 28.0 - - - +
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA* 4.3 9.4 - - - +
238A LYS 4.1 5.3 + - - -
239A THR* 4.7 3.2 - - - +
247A ARG* 3.7 34.2 - - - +
273A GLU* 2.4 53.4 + - + +
274A LYS 2.7 3.4 + - - -
275A SER* 1.3 75.9 - - - +
277A VAL* 1.3 55.0 + - - +
279A TYR 3.7 13.2 + - - +
280A GLN* 2.7 31.7 + - - +
281A GLN* 5.1 1.4 - - - +
284A GLU* 3.0 39.6 + - - +
285A ARG 3.5 29.9 + - - +
286A ASN* 2.9 10.8 + - - -
287A TYR* 3.9 12.1 - - + -
476A GLU* 4.9 9.7 - - - +
477A GLN* 6.1 0.6 - - - +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 2.6 23.6 + - - +
276A ARG* 1.3 72.7 - - - +
278A THR* 1.3 69.0 + - + +
286A ASN* 3.0 18.6 + - - +
287A TYR* 4.1 8.1 - - + -
290A PHE* 4.5 4.3 - - + -
316A PHE* 3.5 13.7 - - - +
360A ILE* 3.8 27.5 - - + +
430A ALA* 4.5 5.4 - - + -
431A LYS* 4.6 6.1 - - + +
434A TYR* 3.4 53.2 - - + -
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Residues in contact with THR 278 (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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275A SER 2.7 7.7 + - - -
277A VAL* 1.3 86.2 - - + +
279A TYR* 1.3 58.1 + - - +
280A GLN* 4.3 1.6 - - - -
316A PHE* 3.6 38.4 - - + -
319A GLN* 2.4 26.9 + - - -
427A ALA* 4.2 13.3 - - + +
430A ALA* 4.6 0.2 - - + -
431A LYS* 3.4 43.8 + - + -
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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