Contacts of the helix formed by residues 267 - 283 (chain A) in PDB entry 2NUN
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 GLY 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ARG* 5.0 3.1 - - - -
113A PHE* 3.9 15.0 - - - -
266A ARG* 1.3 69.6 - - - +
268A SER* 1.3 60.4 + - - +
270A ALA* 3.4 3.3 + - - +
271A LYS* 3.2 32.2 + - - +
600A ADP 2.4 43.1 + - - -
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Residues in contact with SER 268 (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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92A TRP* 3.8 11.5 - - - -
258A ALA 5.0 1.6 - - - -
259A ALA* 5.3 2.5 - - - -
262A MET* 3.4 32.4 - - - +
263A PRO* 3.6 5.6 - - - -
264A ASP* 3.1 37.9 + - - -
266A ARG* 3.4 1.2 + - - +
267A GLY* 1.3 77.0 - - - +
269A ALA* 1.3 57.7 + - - +
271A LYS* 3.4 0.6 + - - -
272A ALA* 2.8 32.3 + - - +
600A ADP 3.4 2.2 + - - -
1503A TRS 5.3 3.5 + - - -
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A HIS* 5.0 1.0 + - - -
259A ALA* 5.6 1.3 - - - +
268A SER* 1.3 77.1 - - - +
270A ALA* 1.3 62.9 + - - +
272A ALA* 3.4 6.0 + - - +
273A GLU* 3.1 26.3 + - - +
296A SER* 5.2 1.9 + - - +
297A ASP* 3.4 41.5 - - + +
600A ADP 2.9 34.2 + - - +
1503A TRS 3.7 4.8 + - - +
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Residues in contact with ALA 270 (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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65A TYR* 3.5 14.1 - - - +
69A MET* 4.2 6.3 - - - +
98A TRP* 4.5 7.9 - - + -
99A ARG* 3.9 18.8 - - - +
267A GLY 3.4 8.6 + - - +
268A SER 3.3 0.4 - - - -
269A ALA* 1.3 76.9 - - - +
271A LYS* 1.3 58.9 + - + +
273A GLU* 3.9 4.1 - - - +
274A PHE* 2.9 30.9 + - - +
600A ADP 3.4 33.1 + - - +
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Residues in contact with LYS 271 (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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92A TRP* 3.5 28.6 - - + -
95A ALA* 3.9 26.9 - - + +
96A THR* 3.5 23.7 + - - +
99A ARG* 4.3 14.4 - - + -
113A PHE 2.7 29.2 + - - -
264A ASP* 2.7 30.2 + - - +
266A ARG 3.0 18.0 + - - -
267A GLY* 3.2 21.7 + - - +
270A ALA* 1.3 75.9 - - + +
272A ALA* 1.3 57.4 + - - +
274A PHE* 3.3 2.2 + - - +
275A ALA* 2.8 31.5 + - - +
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TRP* 3.6 9.5 - - + -
254A THR* 5.9 0.5 - - - +
255A HIS* 4.1 14.6 - - + -
258A ALA* 3.9 10.6 - - + +
259A ALA* 3.8 33.0 - - + +
268A SER 2.8 18.4 + - - +
269A ALA* 3.7 4.5 - - - +
271A LYS* 1.3 76.7 - - - +
273A GLU* 1.3 62.2 + - - +
275A ALA* 3.3 4.4 + - - +
276A ALA* 3.1 23.6 + - - +
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Residues in contact with GLU 273 (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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46A GLY* 2.9 36.7 + - - -
47A ALA 4.7 3.1 + - - +
69A MET* 3.7 6.9 - - + +
255A HIS* 3.7 24.4 + - + +
269A ALA 3.1 14.4 + - - +
270A ALA* 3.9 3.1 - - - +
272A ALA* 1.3 76.8 - - - +
274A PHE* 1.3 65.7 + - - +
276A ALA* 3.8 0.5 - - - +
277A ARG* 2.4 70.6 + - + +
290A PHE* 3.7 12.9 - - + -
296A SER* 3.6 12.7 + - - +
600A ADP 4.3 8.3 + - - -
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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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69A MET* 3.9 18.6 - - + +
72A SER* 3.7 42.2 - - - -
73A ILE* 2.9 39.9 - - + +
76A ALA* 4.0 21.1 - - + -
91A LEU* 4.4 6.7 - - + -
94A ARG* 4.3 10.3 - - + -
95A ALA* 3.5 30.7 - - + -
98A TRP* 3.9 26.0 - + + -
270A ALA 2.9 19.8 + - - +
271A LYS* 3.4 6.1 - - - +
273A GLU* 1.3 78.7 - - - +
275A ALA* 1.3 66.4 + - - +
278A ALA* 3.0 12.2 + - + +
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Residues in contact with ALA 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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88A PHE* 3.9 33.0 - - + -
91A LEU* 3.7 21.9 - - + +
92A TRP* 5.0 3.4 - - + +
95A ALA* 5.4 2.0 - - + -
254A THR* 5.2 1.1 - - + -
258A ALA* 5.9 0.2 - - + -
271A LYS 2.8 17.8 + - - +
272A ALA 3.6 5.2 - - - +
273A GLU 3.3 0.2 - - - -
274A PHE* 1.3 78.3 - - + +
276A ALA* 1.3 62.5 + - - +
278A ALA* 3.1 3.3 + - - +
279A ILE* 3.0 29.0 + - - +
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Residues in contact with ALA 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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251A ILE* 3.4 31.2 - - + +
254A THR* 5.0 3.5 - - - +
255A HIS* 3.8 34.1 - - + +
272A ALA 3.1 15.5 + - - +
273A GLU 3.8 4.3 - - - +
275A ALA* 1.3 78.1 - - - +
277A ARG* 1.3 63.1 + - + +
279A ILE* 3.4 9.5 + - - +
280A ALA* 3.2 16.5 + - - +
312A TYR* 4.1 3.1 - - - +
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Residues in contact with ARG 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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45A ILE* 3.3 32.4 - - - +
46A GLY 4.3 0.6 - - - +
69A MET* 4.3 2.7 - - - -
73A ILE* 3.4 18.9 - - + +
273A GLU* 2.4 57.3 + - + +
274A PHE 4.1 0.9 - - - +
276A ALA* 1.3 75.3 - - + +
278A ALA* 1.3 60.5 + - - +
280A ALA* 3.7 8.0 - - - +
281A SER* 2.8 30.5 + - - -
287A LEU* 3.3 26.8 + - + +
288A PRO 2.3 41.2 + - - -
289A PRO* 3.2 9.1 - - - +
290A PHE* 3.2 21.4 - - + -
312A TYR* 5.5 2.5 - - - +
316A LEU* 4.1 5.5 - - - +
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Residues in contact with ALA 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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73A ILE* 3.7 22.8 - - + +
76A ALA* 4.1 9.4 - - + -
77A GLY* 3.4 10.3 - - - +
80A ILE* 4.0 3.8 - - + -
91A LEU* 3.7 26.5 - - + -
274A PHE* 3.0 21.1 + - + +
275A ALA 3.1 5.6 + - - +
277A ARG* 1.3 75.4 - - - +
279A ILE* 1.3 65.3 + - - +
281A SER 3.3 0.5 + - - -
282A ALA* 3.0 19.8 + - - +
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Residues in contact with ILE 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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80A ILE* 4.2 6.3 - - + -
88A PHE* 5.0 1.8 - - + -
91A LEU* 3.8 15.9 - - + -
234A TYR* 4.2 25.4 - - + -
237A ALA* 3.8 34.5 - - + +
238A ILE* 5.4 4.3 - - + -
247A LEU* 5.1 0.4 - - + -
251A ILE* 4.4 15.3 - - + -
254A THR* 4.0 31.0 - - + +
275A ALA 3.0 15.9 + - - +
276A ALA* 3.6 8.3 - - - +
278A ALA* 1.3 77.0 - - - +
280A ALA* 1.3 61.2 + - - +
282A ALA* 3.3 8.5 + - + +
283A HIS* 3.2 20.9 - - + +
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Residues in contact with ALA 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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251A ILE* 3.5 27.5 - - + +
276A ALA 3.2 9.4 + - - +
277A ARG* 3.8 7.0 - - - +
278A ALA 3.3 0.2 - - - -
279A ILE* 1.3 78.4 - - - +
281A SER* 1.3 63.8 + - - +
283A HIS* 3.0 15.1 + - - +
285A ILE* 3.1 36.0 + - + +
287A LEU* 3.9 21.3 - - + -
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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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31A GLY 3.3 10.9 - - - +
32A PRO* 3.3 31.3 - - - +
73A ILE* 4.2 15.0 - - - -
74A ARG* 3.4 13.2 - - - +
77A GLY* 4.3 1.8 - - - -
277A ARG 2.8 19.6 + - - -
278A ALA 3.5 6.1 - - - -
280A ALA* 1.3 78.2 - - - +
282A ALA* 1.3 57.9 + - - +
284A GLY* 3.0 16.0 + - - -
285A ILE 3.6 11.6 + - - -
286A GLU* 4.7 5.9 + - - -
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Residues in contact with ALA 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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29A LEU* 3.5 19.7 - - + +
30A PRO 2.4 26.8 - - - +
31A GLY* 3.8 2.2 + - - -
77A GLY* 3.3 25.9 - - - +
80A ILE* 3.8 25.1 - - + -
81A SER* 3.9 2.9 - - - +
278A ALA 3.0 11.8 + - - +
279A ILE* 3.5 12.1 - - - +
280A ALA 3.2 0.4 - - - -
281A SER* 1.3 75.7 - - - +
283A HIS* 1.3 54.4 + - + +
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Residues in contact with HIS 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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29A LEU* 3.9 25.4 - - + +
30A PRO* 3.4 21.4 - - - +
237A ALA 2.6 24.9 + - - -
238A ILE* 4.1 0.8 - - - +
239A SER 3.2 27.6 - - - -
240A SER* 5.2 0.6 - - - -
242A LEU* 4.8 4.6 + - + +
247A LEU* 3.4 43.0 - - + +
279A ILE* 3.2 25.3 - - + +
280A ALA 3.0 7.3 + - - +
282A ALA* 1.3 79.5 - - + +
284A GLY* 1.3 57.3 + - - +
285A ILE* 3.2 10.8 + - - +
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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