Contacts of the helix formed by residues 273 - 284 (chain A) in PDB entry 3Q29
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 ASN 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLU 3.1 17.6 + - - -
5A GLU* 3.4 12.6 - - - +
6A GLY* 2.9 22.3 + - - -
7A LYS 2.9 25.0 + - - -
8A LEU* 3.7 12.3 - - + -
59A ASP* 3.0 21.3 + - - +
271A SER* 2.9 5.8 + - - +
272A PRO* 1.3 81.7 - - - +
274A LYS* 1.3 64.5 + - - +
275A GLU 3.0 3.8 + - - -
276A LEU* 3.1 20.2 + - + +
277A ALA* 2.9 21.9 + - - +
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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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78A ALA* 3.6 24.7 - - + -
267A ILE* 4.0 26.2 - - + +
268A ASN 3.5 11.9 - - - +
269A ALA* 2.9 29.4 + - - +
270A ALA 4.3 0.4 - - - -
271A SER* 2.6 30.5 + - - +
272A PRO 3.5 3.0 + - - -
273A ASN* 1.3 76.8 - - - +
275A GLU* 1.3 60.3 + - - +
277A ALA* 3.9 1.9 - - - +
278A LYS* 3.1 27.0 + - - +
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Residues in contact with GLU 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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273A ASN 3.1 1.0 - - - -
274A LYS* 1.3 80.9 - - - +
276A LEU* 1.3 66.2 + - + +
278A LYS* 3.5 26.8 + - - +
279A GLU* 3.1 26.5 + - - +
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Residues in contact with LEU 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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6A GLY* 4.3 5.8 - - - +
8A LEU* 4.1 13.7 - - + -
28A PHE* 3.9 11.5 - - + -
32A THR* 5.9 2.2 - - + -
34A ILE* 4.0 42.4 - - + -
273A ASN* 3.1 29.3 + - + +
275A GLU* 1.3 78.9 - - + +
277A ALA* 1.3 56.1 + - - +
279A GLU* 3.0 10.7 + - + +
280A PHE* 2.7 35.9 + - - +
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Residues in contact with ALA 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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8A LEU* 3.9 15.5 - - + +
59A ASP* 4.9 2.0 - - + -
60A ILE* 3.6 32.1 - - + -
267A ILE* 4.2 16.2 - - + -
273A ASN 2.9 17.1 + - - +
274A LYS* 3.9 6.5 - - - +
276A LEU* 1.3 78.1 - - - +
278A LYS* 1.3 61.9 + - - +
280A PHE* 3.4 1.4 + - - +
281A LEU* 3.1 30.5 + - - +
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Residues in contact with LYS 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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81A THR* 2.8 39.5 + - - +
82A PRO* 4.7 0.4 - - - +
83A ASP 5.4 0.4 - - - +
107A TYR* 3.5 11.4 - - - +
267A ILE* 4.1 11.4 - - + +
274A LYS 3.1 20.4 + - - +
275A GLU* 3.7 28.1 + - - +
276A LEU 3.2 0.2 - - - -
277A ALA* 1.3 76.1 - - - +
279A GLU* 1.3 64.1 + - - +
281A LEU* 3.4 3.1 + - - +
282A GLU* 3.0 54.0 + - - +
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Residues in contact with GLU 279 (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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28A PHE* 3.7 15.9 - - - -
32A THR* 4.4 8.5 - - - +
275A GLU 3.1 13.8 + - - +
276A LEU* 3.0 14.0 + - - +
278A LYS* 1.3 75.9 - - - +
280A PHE* 1.3 66.5 + - - +
282A GLU* 5.1 0.7 - - - -
283A ASN* 2.9 59.8 + - - +
284A TYR* 3.8 20.3 + - - -
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Residues in contact with PHE 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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8A LEU* 4.0 11.7 - - + -
10A ILE* 3.5 27.8 - - + -
21A LEU* 4.0 22.2 - - + -
24A VAL* 3.9 24.9 - - + -
25A GLY* 4.0 19.1 - - - -
28A PHE* 3.8 36.9 - + + -
36A VAL* 4.7 4.7 - - + -
60A ILE* 4.2 7.9 - - + -
62A PHE* 5.2 0.9 - + - -
276A LEU 2.7 20.1 + - - +
277A ALA 3.6 2.9 - - - +
279A GLU* 1.3 74.0 - - - +
281A LEU* 1.3 82.5 + - + +
284A TYR* 3.2 10.2 + - + +
285A LEU* 3.0 30.7 + - + -
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Residues in contact with LEU 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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60A ILE* 4.0 16.6 - - + -
62A PHE* 4.3 3.4 - - + -
107A TYR* 3.6 38.6 - - + -
109A ILE* 5.4 1.8 - - + -
265A ALA* 4.1 23.6 - - + +
267A ILE* 4.4 12.3 - - + -
277A ALA 3.1 18.2 + - - +
278A LYS 3.9 3.1 - - - +
279A GLU 3.1 0.2 - - - -
280A PHE* 1.3 96.5 - - + +
282A GLU* 1.3 61.1 + - - +
285A LEU* 3.8 24.4 - - + +
286A LEU* 3.0 36.9 + - + +
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Residues in contact with GLU 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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82A PRO* 3.8 8.7 - - - +
83A ASP* 5.2 1.7 + - - +
86A PHE* 3.4 53.3 - - + +
89A LYS* 5.3 3.1 + - - -
107A TYR* 2.6 41.0 + - + -
278A LYS* 3.0 41.8 + - - +
279A GLU* 5.1 0.2 - - - -
281A LEU* 1.3 77.8 - - - +
283A ASN* 1.3 71.4 + - - +
286A LEU* 3.9 10.9 - - - +
287A THR* 4.3 3.3 - - - +
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Residues in contact with ASN 283 (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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86A PHE* 5.7 0.7 - - - -
89A LYS* 5.8 1.6 + - - -
279A GLU* 2.9 45.1 + - - +
282A GLU* 1.3 90.7 - - - +
284A TYR* 1.3 73.6 + - + +
287A THR* 3.6 18.2 + - - +
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Residues in contact with TYR 284 (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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24A VAL* 3.8 19.0 - - + +
27A LYS* 3.1 32.8 - - + -
28A PHE* 3.3 41.2 - + + -
31A ASP* 3.2 29.8 + - - +
32A THR* 4.3 4.9 - - - +
279A GLU* 3.8 27.1 + - - -
280A PHE* 3.2 13.2 + - + +
283A ASN* 1.3 88.0 - - + +
285A LEU* 1.3 64.3 + - - +
287A THR* 2.7 22.6 + - - -
290A GLY* 3.5 9.5 + - - -
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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