Contacts of the helix formed by residues 257 - 277 (chain P) in PDB entry 2IMW
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 257 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255P SER* 3.0 12.7 + - - +
256P ARG* 1.3 76.4 - - - +
258P LEU* 1.3 67.4 + - - +
259P GLU* 3.2 22.3 + - - +
260P GLU* 3.2 20.0 + - + +
261P ILE* 3.0 25.8 + - - +
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Residues in contact with LEU 258 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256P ARG 3.6 4.8 + - - -
257P ASN* 1.3 72.3 + - - +
259P GLU* 1.3 62.6 + - + +
261P ILE* 3.2 5.5 + - - +
262P LYS* 2.9 50.6 + - + +
316P VAL* 4.2 17.0 - - + -
319P LEU* 3.5 31.4 - - + -
320P GLN* 3.5 44.4 - - + +
323P LEU* 4.2 11.9 - - + +
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Residues in contact with GLU 259 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257P ASN* 3.2 9.7 + - - +
258P LEU* 1.3 80.3 - - + +
260P GLU* 1.3 60.4 + - - +
262P LYS* 2.8 41.8 + - - +
263P PRO* 3.1 24.3 - - - +
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Residues in contact with GLU 260 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251P MET* 5.3 1.1 - - - -
253P ARG* 3.4 43.8 + - - +
255P SER* 2.7 32.2 + - - +
257P ASN* 3.2 22.1 + - + +
259P GLU* 1.3 78.9 - - - +
261P ILE* 1.3 60.1 - - - +
263P PRO* 3.5 9.1 - - - +
264P TYR* 3.5 22.0 - - + -
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Residues in contact with ILE 261 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251P MET* 3.9 21.3 - - + -
255P SER* 3.5 31.6 - - - +
256P ARG* 4.1 4.3 - - - -
257P ASN 3.0 25.6 + - - +
258P LEU 3.8 4.3 - - - +
260P GLU* 1.3 78.8 - - - +
262P LYS* 1.3 64.1 + - - +
264P TYR* 3.0 16.5 + - - +
265P LEU* 3.2 7.5 + - + -
319P LEU* 3.7 23.8 - - + -
323P LEU* 4.5 6.5 - - + -
330P ILE* 4.3 18.6 - - + -
333P ILE* 3.8 30.1 - - + -
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Residues in contact with LYS 262 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258P LEU* 2.9 40.4 + - + +
259P GLU* 2.8 38.8 + - - +
261P ILE* 1.3 75.6 - - - +
263P PRO* 1.4 64.3 - - + +
265P LEU* 3.1 10.4 + - + +
266P PHE* 2.8 59.7 + - + -
316P VAL* 4.2 25.0 - - + +
319P LEU* 5.0 2.7 - - + +
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Residues in contact with PRO 263 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259P GLU 3.1 20.6 - - - +
260P GLU 3.5 7.9 - - - +
261P ILE 3.5 4.5 - - - -
262P LYS* 1.4 90.0 - - + +
264P TYR* 1.3 56.7 + - + +
266P PHE* 3.4 9.3 + - + +
267P ARG* 3.0 53.3 + - - +
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Residues in contact with TYR 264 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249P VAL* 3.5 35.2 - - + +
250P THR 4.0 5.4 - - - -
251P MET* 3.6 36.8 - - + -
252P LYS* 3.2 31.7 + - - +
260P GLU* 3.5 28.3 - - + -
261P ILE 3.0 6.1 + - - +
263P PRO* 1.3 74.3 - - + +
265P LEU* 1.3 65.7 + - - +
267P ARG* 3.3 36.7 + - - +
268P ALA* 3.0 19.6 + - - +
333P ILE* 3.6 9.9 - - + -
506P EDO 4.5 2.0 - - - -
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Residues in contact with LEU 265 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261P ILE* 3.2 8.9 + - + +
262P LYS* 3.1 11.3 + - + +
264P TYR* 1.3 78.3 - - - +
266P PHE* 1.3 67.7 + - + +
268P ALA* 3.4 7.1 - - - +
269P ILE* 3.1 27.5 + - + +
286P VAL* 4.2 14.8 - - + -
315P SER* 3.6 40.4 - - - +
316P VAL* 4.3 4.7 - - + +
319P LEU* 4.2 18.6 - - + -
333P ILE* 3.8 23.2 - - + +
334P GLY 3.8 25.1 - - - +
335P VAL* 4.6 4.9 - - + -
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Residues in contact with PHE 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262P LYS* 2.8 44.4 + - + +
263P PRO* 3.8 8.3 - - + +
265P LEU* 1.3 83.3 - - + +
267P ARG* 1.3 58.6 + - - +
269P ILE* 3.2 13.9 + - + +
270P GLU* 2.9 32.2 + - - +
312P TYR* 3.5 51.6 + + + +
315P SER* 4.0 4.7 - - - -
316P VAL* 3.9 30.3 - - + -
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Residues in contact with ARG 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263P PRO* 3.0 41.3 + - - +
264P TYR* 3.3 40.4 + - - +
266P PHE* 1.3 72.4 - - + +
268P ALA* 1.3 64.0 + - - +
270P GLU* 3.2 10.0 + - + +
271P GLU* 3.0 30.5 + - - +
506P EDO 2.5 69.3 + - - -
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Residues in contact with ALA 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247P ARG* 3.6 34.0 - - - +
249P VAL* 4.3 11.1 - - + +
264P TYR 3.0 13.6 + - - +
265P LEU* 3.4 10.3 - - - +
267P ARG* 1.3 75.6 - - - +
269P ILE* 1.3 53.9 + - - +
271P GLU* 3.9 1.2 - - - +
272P SER* 2.6 39.3 + - - -
333P ILE 4.4 0.2 - - - +
334P GLY* 4.0 15.5 - - - -
335P VAL* 4.0 4.5 - - + +
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Residues in contact with ILE 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265P LEU* 3.1 16.5 + - + +
266P PHE* 3.2 18.8 + - + +
268P ALA* 1.3 73.5 - - - +
270P GLU* 1.3 60.3 + - - +
272P SER* 3.2 2.6 + - - -
273P TYR* 2.8 50.4 + - + -
308P LYS* 4.1 4.3 - - + -
311P ALA* 3.7 15.9 - - + +
312P TYR* 3.6 31.9 - - + -
315P SER* 3.3 29.4 - - - +
335P VAL* 4.0 24.2 - - + -
337P PHE* 4.7 2.0 - - + -
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Residues in contact with GLU 270 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P PHE 2.9 17.7 + - - +
267P ARG* 3.2 10.5 + - + +
269P ILE* 1.3 75.2 - - - +
271P GLU* 1.3 64.1 + - + +
273P TYR* 3.4 4.5 + - - +
274P TYR* 3.0 23.1 + - - +
308P LYS* 3.1 31.7 + - - +
312P TYR* 2.3 38.5 + - - +
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Residues in contact with GLU 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247P ARG* 3.2 44.1 + - + +
249P VAL* 4.1 0.7 - - - +
267P ARG 3.0 16.7 + - - +
268P ALA 3.9 3.1 - - - +
270P GLU* 1.3 75.6 - - + +
272P SER* 1.3 59.7 + - - +
274P TYR* 3.2 10.8 + - - +
275P LYS* 2.9 38.7 + - + +
506P EDO 3.0 36.0 + - - -
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Residues in contact with SER 272 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245P ILE* 3.9 4.0 - - - +
246P GLY* 3.6 5.6 - - - -
247P ARG* 3.4 26.8 + - - +
268P ALA 2.6 22.7 + - - -
269P ILE 3.5 3.4 - - - -
271P GLU* 1.3 77.5 - - - +
273P TYR* 1.3 57.0 + - - +
275P LYS* 3.2 9.4 + - - +
276P LEU* 2.9 33.1 + - - +
335P VAL* 3.4 6.4 - - - +
337P PHE* 3.5 26.9 - - - -
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Residues in contact with TYR 273 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269P ILE* 2.8 31.5 + - + +
270P GLU 3.8 2.0 - - - +
272P SER* 1.3 69.3 - - - +
274P TYR* 1.3 66.4 + - - +
276P LEU* 3.4 29.5 + - + +
277P ASP* 3.6 6.8 + - - +
280P ILE* 6.1 3.8 - - + -
281P PRO* 4.6 4.5 - - + +
306P ILE* 2.6 37.6 + - - +
307P SER* 3.1 10.5 + - - -
308P LYS* 3.6 47.3 - - + +
311P ALA* 3.6 10.5 - - + -
337P PHE* 3.6 30.9 - + - -
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Residues in contact with TYR 274 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270P GLU 3.0 13.8 + - - +
271P GLU* 3.2 13.9 + - - +
273P TYR* 1.3 76.3 - - - +
275P LYS* 1.3 73.0 + - + +
277P ASP* 3.2 15.8 + - - +
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Residues in contact with LYS 275 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242P ARG* 4.7 4.0 + - - +
245P ILE* 3.6 19.1 - - + +
246P GLY 2.8 28.1 + - - -
247P ARG* 4.5 16.4 - - - +
271P GLU* 2.9 22.6 + - + +
272P SER* 3.6 7.9 - - - +
274P TYR* 1.3 86.0 - - + +
276P LEU* 1.3 65.7 + - - +
277P ASP* 3.0 4.3 + - - +
279P ARG* 3.2 14.7 + - - -
502P EDO 4.8 8.8 - - - -
1802S G 4.0 20.4 + - - -
1803S G 4.0 13.1 + - - +
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Residues in contact with LEU 276 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245P ILE* 4.0 18.2 - - + -
272P SER 2.9 19.5 + - - +
273P TYR* 3.6 28.3 - - + +
274P TYR 3.3 0.4 - - - -
275P LYS* 1.3 76.3 - - - +
277P ASP* 1.3 63.2 + - - +
278P LYS 3.0 0.9 + - - -
279P ARG* 3.0 51.9 + - + +
281P PRO* 4.1 15.5 - - + -
337P PHE* 4.0 27.1 - - + -
340P PHE* 3.4 37.9 - - + -
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Residues in contact with ASP 277 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273P TYR 3.6 5.6 + - - +
274P TYR 3.2 12.2 + - - +
275P LYS 3.0 8.0 + - - +
276P LEU* 1.3 79.3 - - - +
278P LYS* 1.3 86.8 + - - +
279P ARG* 4.5 8.3 - - - +
280P ILE* 5.8 1.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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