Contacts of the helix formed by residues 277 - 282 (chain A) in PDB entry 4H3I
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 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A MET* 1.3 71.1 - - - +
278A CYS* 1.3 62.6 + - - +
279A LYS* 2.9 28.3 + - - +
280A GLU* 2.9 41.6 + - + +
281A TYR 4.1 0.3 + - - -
442A ASP 5.3 0.7 - - - +
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Residues in contact with CYS 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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265A VAL* 3.7 18.4 - - - +
276A MET 3.0 5.0 + - - +
277A ASP* 1.3 76.3 + - - +
279A LYS* 1.3 61.7 + - - +
280A GLU 3.1 0.4 - - - -
281A TYR* 3.2 29.2 + - + +
282A ASN* 3.3 16.6 + - - -
439A ASP 5.0 1.6 - - - -
442A ASP* 4.5 4.3 - - - -
443A CYS* 2.0 55.6 - - + -
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ASP* 2.9 19.3 + - - +
278A CYS* 1.3 79.9 - - - +
280A GLU* 1.3 63.1 + - + +
282A ASN* 3.1 13.9 + - - -
283A TYR* 3.3 14.2 + - - +
442A ASP* 2.6 39.6 + - - +
443A CYS 3.4 12.9 - - - +
444A GLY 3.1 19.1 + - - +
445A TYR* 4.5 21.8 - - + +
446A ASN* 4.9 9.9 - - - +
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Residues in contact with GLU 280 (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 MET* 3.9 26.2 - - + -
277A ASP* 2.9 31.8 + - + +
279A LYS* 1.3 79.3 - - + +
281A TYR* 1.3 60.1 + - - +
282A ASN 3.3 0.5 + - - -
283A TYR* 3.4 26.0 + - - +
298A PRO* 3.6 8.8 - - - +
300A LYS* 2.8 44.0 + - + +
301A VAL* 3.4 14.3 - - + +
167B ASP* 4.4 2.1 - - - +
168B LYS* 3.5 15.5 + - - -
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Residues in contact with TYR 281 (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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264A ILE* 4.1 19.5 - - + +
265A VAL 4.4 0.2 - - - -
266A ARG* 3.9 27.4 - - - -
267A VAL* 3.7 33.2 + - + -
273A ASP* 4.3 2.6 + - - -
274A LEU* 3.6 19.5 - - + +
275A LYS 3.8 2.6 + - - -
276A MET* 3.2 50.2 + - + -
278A CYS* 3.4 34.1 - - + +
279A LYS 3.2 0.8 - - - -
280A GLU* 1.3 76.4 - - - +
282A ASN* 1.3 60.8 + - - +
283A TYR 3.6 0.8 + - - -
286A SER* 3.0 5.7 + - - -
298A PRO* 4.2 0.6 - - - +
301A VAL* 3.9 20.2 - - + -
392A THR* 2.7 27.4 + - - -
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Residues in contact with ASN 282 (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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255A ARG* 6.2 0.4 - - - +
261A GLU* 6.2 0.2 - - - +
262A VAL 5.0 1.3 - - - +
263A ILE* 3.7 12.4 - - + +
264A ILE* 2.8 48.8 + - - +
278A CYS 3.3 5.3 + - - -
279A LYS 3.1 6.8 + - - -
281A TYR* 1.3 78.2 - - - +
283A TYR* 1.3 56.2 + - - +
284A ASP 2.9 4.3 - - - -
285A LYS* 2.8 21.9 + - - -
286A SER* 2.6 32.6 + - - +
443A CYS 3.0 27.7 + - - +
444A GLY* 4.8 1.6 - - - -
445A TYR* 3.4 13.6 + - - +
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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