Contacts of the helix formed by residues 273 - 288 (chain A) in PDB entry 3NA1
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 SER 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A LYS* 6.2 0.2 - - - +
271A LYS 3.8 2.4 + - - -
272A MET* 1.3 76.6 - - - +
274A PHE* 1.3 65.5 + - - +
275A GLU* 3.9 16.4 + - - +
276A ASP* 3.0 33.1 + - - -
277A ILE* 3.0 21.9 + - - +
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Residues in contact with PHE 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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242A THR* 3.9 31.6 - - + -
243A GLN* 4.9 10.8 - - + -
246A TYR* 3.4 45.8 - + + -
267A LEU* 3.7 17.7 - - + -
273A SER* 1.3 72.5 - - - +
275A GLU* 1.3 75.9 + - + +
277A ILE* 3.3 9.9 + - + +
278A LYS* 3.0 53.5 + - + +
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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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97A PRO* 4.8 12.7 - - + +
273A SER* 3.9 17.4 - - - +
274A PHE* 1.3 95.8 + - + +
276A ASP* 1.3 65.4 + - - +
278A LYS* 3.7 4.6 + - - +
279A ALA* 3.2 23.7 + - - +
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Residues in contact with ASP 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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98A ILE 5.0 1.4 - - - +
103A LYS* 3.1 25.0 + - - +
110A LYS* 5.2 8.5 - - - +
111A ASP* 3.8 8.8 - - - +
272A MET* 3.4 24.3 - - + -
273A SER* 3.0 27.0 + - - +
275A GLU* 1.3 76.8 - - - +
277A ILE* 1.3 64.7 + - - +
279A ALA* 3.5 4.7 + - - +
280A ASN* 2.8 32.3 + - - +
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Residues in contact with ILE 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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242A THR* 5.2 2.0 - - + -
263A LEU* 3.5 31.6 - - + -
266A LEU* 3.5 43.5 - - + +
267A LEU* 4.1 17.3 - - + +
270A SER* 3.9 2.5 - - - +
272A MET* 3.6 34.3 - - + +
273A SER 3.0 19.6 + - - +
274A PHE* 3.3 10.3 + - + +
276A ASP* 1.3 76.3 - - - +
278A LYS* 1.3 58.7 + - - +
280A ASN* 3.2 5.1 + - - +
281A VAL* 2.9 31.2 + - + +
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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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97A PRO* 5.5 12.1 - - + -
238A ALA 5.3 0.2 - - - +
239A ASP* 3.3 48.4 + - - +
242A THR* 4.1 30.1 + - + +
243A GLN* 5.3 8.0 + - + +
274A PHE* 3.0 40.4 + - + +
275A GLU* 4.0 5.2 - - - +
277A ILE* 1.3 78.6 - - - +
279A ALA* 1.3 60.2 + - - +
281A VAL* 3.5 3.9 + - - +
282A THR* 2.9 29.0 + - - +
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Residues in contact with ALA 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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97A PRO* 3.7 22.7 - - + +
98A ILE 3.5 31.4 - - - +
99A GLY* 4.1 2.0 - - - -
235A PHE* 5.6 3.4 - - - -
275A GLU 3.2 18.7 + - - +
276A ASP* 3.8 5.6 - - - +
277A ILE 3.3 0.4 - - - -
278A LYS* 1.3 76.1 - - - +
280A ASN* 1.3 61.9 + - - +
282A THR* 3.4 9.1 - - - -
283A GLU* 3.2 24.8 + - - +
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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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99A GLY* 3.4 4.0 - - - -
100A VAL* 2.8 38.8 + - - +
111A ASP* 2.9 26.5 + - - -
115A LEU* 3.6 28.1 - - + +
266A LEU* 6.2 0.2 - - + -
272A MET* 3.1 10.9 - - - +
276A ASP* 2.8 27.0 + - - +
277A ILE* 3.8 3.1 - - - +
279A ALA* 1.3 73.8 - - - +
281A VAL* 1.3 59.4 + - - +
283A GLU* 3.3 6.0 + - - +
284A MET* 2.9 36.6 + - + +
424A LEU* 5.4 0.2 - - - +
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Residues in contact with VAL 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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175A ILE* 4.2 17.4 - - + +
176A PHE* 4.0 13.2 - - + -
238A ALA 5.1 1.6 - - - +
242A THR* 3.5 21.5 - - - +
262A ILE* 6.5 0.2 - - + -
263A LEU* 4.1 26.7 - - + -
266A LEU* 5.3 7.2 - - + -
277A ILE* 2.9 23.1 + - + +
278A LYS* 3.8 5.6 - - - +
279A ALA 3.4 0.2 - - - -
280A ASN* 1.3 74.7 - - - +
282A THR* 1.3 58.0 + - - +
284A MET* 3.3 8.3 + - - +
285A LEU* 2.9 48.2 + - + +
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Residues in contact with THR 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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194A PHE* 5.3 0.2 - - - -
231A TRP* 5.5 2.7 - - + -
234A ILE* 3.7 27.2 - - + +
235A PHE* 4.2 30.1 - - + -
238A ALA* 3.3 29.8 - - + +
239A ASP* 4.4 8.5 + - - -
278A LYS 2.9 14.0 + - - -
279A ALA* 3.4 10.5 - - - -
280A ASN 3.3 0.2 - - - -
281A VAL* 1.3 78.4 - - - +
283A GLU* 1.3 60.0 + - + +
285A LEU* 3.5 2.8 + - - +
286A ALA* 3.0 27.9 + - - +
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Residues in contact with GLU 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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91A HIS* 4.7 9.3 + - - +
97A PRO 5.4 0.2 - - - +
98A ILE* 4.4 2.8 - - - -
99A GLY* 3.0 34.7 + - - +
100A VAL* 3.2 4.0 + - - +
101A LEU* 3.0 40.7 + - + +
102A LEU* 4.4 8.8 + - - +
231A TRP* 6.0 3.1 - - + -
235A PHE* 6.1 2.4 - - + -
279A ALA 3.2 10.5 + - - +
280A ASN* 3.3 8.5 + - - +
281A VAL 3.3 0.2 - - - -
282A THR* 1.3 77.8 - - + +
284A MET* 1.3 61.7 + - - +
287A GLY* 2.9 27.0 + - - -
601A HEM 4.7 12.1 - - + +
602A HCD 3.6 26.2 - - + +
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Residues in contact with MET 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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115A LEU* 4.6 12.1 - - - -
119A VAL* 3.8 32.3 - - + -
171A ILE* 3.7 6.9 - - + +
175A ILE* 3.9 18.8 - - + -
262A ILE* 3.9 19.7 - - + -
266A LEU* 6.0 1.3 - - - -
280A ASN* 2.9 22.9 + - + +
281A VAL* 3.8 5.4 - - - +
283A GLU* 1.3 72.9 - - - +
285A LEU* 1.3 65.8 + - - +
287A GLY 3.5 0.2 + - - -
288A GLY 3.3 9.4 + - - -
424A LEU* 4.2 22.7 - - + -
428A ILE* 4.0 5.2 - - + -
601A HEM 3.2 51.0 - - + +
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Residues in contact with LEU 285 (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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168A PHE* 5.1 0.7 - - + -
171A ILE* 4.2 13.2 - - + +
172A THR* 3.6 31.2 - - + -
175A ILE* 3.9 19.7 - - + +
176A PHE* 4.1 14.1 - - + -
194A PHE* 4.1 18.2 - - + -
198A ILE* 4.5 1.8 - - - -
238A ALA* 4.1 20.9 - - + -
241A TYR* 4.3 11.7 - - + -
281A VAL* 2.9 34.3 + - + +
282A THR 3.7 3.4 - - - +
284A MET* 1.3 80.1 - - - +
286A ALA* 1.3 60.2 + - - +
288A GLY* 3.5 3.5 + - - -
289A VAL* 3.3 25.5 + - - +
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Residues in contact with ALA 286 (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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194A PHE* 5.1 0.4 - - + -
198A ILE* 3.5 42.6 - - + +
202A PHE* 4.2 10.0 - - - -
231A TRP* 5.4 1.6 - - + -
234A ILE* 4.3 19.7 - - + -
282A THR 3.0 17.2 + - - +
285A LEU* 1.3 75.9 - - - +
287A GLY* 1.3 60.3 + - - +
288A GLY 3.5 0.5 + - - -
289A VAL 4.2 3.3 + - - -
290A ASP 4.9 0.7 + - - -
602A HCD 4.1 23.1 - - + -
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Residues in contact with GLY 287 (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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202A PHE* 5.4 1.1 - - - -
283A GLU 2.9 18.4 + - - -
284A MET 3.5 0.9 + - - -
285A LEU 3.3 0.2 - - - -
286A ALA* 1.3 76.0 - - - +
288A GLY* 1.3 50.5 + - - +
289A VAL 3.7 0.4 - - - -
290A ASP 5.3 0.2 - - - -
291A THR* 2.7 35.1 + - - +
601A HEM 3.5 21.1 + - - -
602A HCD 3.8 25.6 - - - +
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Residues in contact with GLY 288 (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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167A ALA* 3.6 10.6 - - - +
171A ILE* 4.7 7.7 - - - +
284A MET 3.3 11.5 + - - -
285A LEU 3.5 1.7 + - - -
286A ALA 3.2 1.0 - - - -
287A GLY* 1.3 78.5 - - - +
289A VAL* 1.3 62.3 + - - +
291A THR* 3.4 7.9 - - - -
292A THR* 3.2 21.3 + - - -
432A GLU* 4.9 1.0 - - - +
601A HEM 3.5 22.0 - - - +
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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