Contacts of the helix formed by residues 275 - 284 (chain A) in PDB entry 4NDI
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 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A LEU* 3.9 0.7 - - - +
274A LYS* 1.3 83.1 - - - +
276A LYS* 1.3 65.9 + - - +
277A LYS* 3.1 23.1 + - - +
278A HIS* 2.9 54.1 + - - +
279A TRP 3.2 9.4 + - - -
329A ILE* 3.6 16.1 - - - +
4E T 5.8 0.2 - - - -
5E C 5.9 1.6 - - - +
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Residues in contact with LYS 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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275A ASN* 1.3 74.9 - - - +
277A LYS* 1.3 58.0 + - - +
279A TRP* 3.3 0.9 + - - +
280A ASN* 2.9 53.0 + - - +
313A LEU 3.5 5.4 - - - +
314A LYS* 3.7 21.4 + - + +
315A LEU 3.4 16.3 + - - +
316A PRO* 4.5 9.3 - - - +
317A LEU* 4.0 32.1 - - + -
329A ILE* 3.9 3.8 - - + +
4E T 4.4 2.6 + - - -
5E C 2.7 41.9 + - - +
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Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ASN* 3.1 22.6 + - - +
276A LYS* 1.3 79.3 - - - +
278A HIS* 1.3 63.1 + - - +
280A ASN 3.8 0.2 - - - -
281A SER* 2.9 29.0 + - - -
313A LEU* 3.8 41.3 + - + +
1D G 2.7 47.3 + - - +
2D T 3.8 14.8 - - - +
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Residues in contact with HIS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLN* 3.5 30.5 - - - +
272A CYS 3.5 13.6 + - - -
273A LEU* 3.7 6.3 - - + -
274A LYS* 3.1 29.0 + - + -
275A ASN* 2.9 41.3 + - - +
277A LYS* 1.3 75.2 - - - +
279A TRP* 1.3 65.8 + - - +
281A SER* 3.0 20.4 + - - -
282A PHE* 3.4 15.1 - + - -
404A BME 5.7 0.9 - - - -
1D G 3.4 18.3 - - - -
2D T 3.0 28.7 + - - -
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Residues in contact with TRP 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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268A PHE* 3.7 29.4 - + + -
273A LEU* 3.8 18.6 - - + +
275A ASN 3.2 7.1 + - - +
276A LYS 3.6 6.7 - - - +
277A LYS 3.3 0.2 - - - -
278A HIS* 1.3 80.5 - - - +
280A ASN* 1.3 79.1 + - - +
282A PHE* 3.1 7.2 + - - -
283A ASN* 3.1 59.9 + - + +
317A LEU* 3.7 26.7 - - + -
318A ARG 3.0 36.8 + - - +
319A CYS* 4.2 3.1 - - - -
320A HIS* 3.5 30.7 - - - -
329A ILE* 4.7 0.2 - - + -
332A LEU* 3.6 17.5 - - + -
336A LEU* 4.0 18.2 - - + -
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Residues in contact with ASN 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 LYS* 2.9 19.5 + - - +
277A LYS 4.2 0.2 - - - +
279A TRP* 1.3 91.8 + - - +
281A SER* 1.3 65.6 + - - +
282A PHE 3.3 0.5 + - - -
283A ASN* 3.3 5.9 + - - +
284A THR* 2.7 40.6 + - + +
286A TYR* 3.8 0.2 - - - +
312A LEU 3.4 18.2 - - - +
313A LEU* 3.1 29.1 + - + -
315A LEU* 2.9 36.6 + - - +
316A PRO 4.5 3.6 - - - +
318A ARG 5.6 0.2 + - - -
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Residues in contact with SER 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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251A HIS* 3.1 37.9 + - - -
277A LYS* 2.9 18.1 + - - -
278A HIS* 3.0 18.0 + - - -
280A ASN* 1.3 78.1 - - - +
282A PHE* 1.3 68.3 + - - +
286A TYR* 3.8 24.0 - - - -
287A PHE* 3.3 15.3 + - - +
313A LEU* 3.7 6.9 - - - +
1D G 5.2 5.0 + - - -
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Residues in contact with PHE 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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197A GLN* 3.6 26.7 - - + -
201A HIS* 3.6 21.3 - + - -
247A ARG* 3.2 22.5 + - - -
251A HIS* 3.4 29.2 - + - -
262A HIS* 3.7 18.4 - + - -
264A ILE* 3.9 23.3 - - + -
268A PHE* 3.7 27.3 - + + -
278A HIS* 3.4 11.0 - + - +
279A TRP 3.1 3.1 + - - +
280A ASN 3.1 0.2 - - - -
281A SER* 1.3 90.8 + - - +
283A ASN* 1.3 65.2 + - - +
284A THR 3.8 1.6 - - - -
287A PHE* 3.6 32.7 - + - +
401A AMP 4.9 1.6 - - - -
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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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247A ARG* 4.7 8.8 + - - +
266A GLN* 4.7 0.9 - - - +
268A PHE* 3.6 16.1 - - - -
279A TRP* 3.1 72.2 + - + +
280A ASN* 3.3 1.0 + - - +
282A PHE* 1.3 88.1 - - - +
284A THR* 1.3 68.9 + - - +
318A ARG 5.2 1.1 - - - +
320A HIS* 3.3 26.7 - - + +
166B HIS* 5.2 3.1 - - - -
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Residues in contact with THR 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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247A ARG* 5.4 2.4 + - - -
280A ASN* 2.7 43.5 + - + +
283A ASN* 1.3 83.8 - - - +
285A GLU* 1.3 60.7 + - - +
286A TYR* 2.9 22.2 + - - +
287A PHE* 3.0 18.4 + - - +
312A LEU* 3.8 14.9 - - - +
315A LEU* 4.0 20.9 - - + -
166B HIS* 4.5 15.9 - - + -
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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