Contacts of the helix formed by residues 262 - 275 (chain A) in PDB entry 5JNO
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 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A SER* 3.3 2.6 + - - -
261A LEU* 1.3 82.4 - - - +
263A GLY* 1.3 59.2 + - - +
264A GLY* 3.4 4.2 + - - -
265A ASP* 3.1 21.1 + - - +
266A LEU* 2.9 28.8 + - - +
315A TYR* 3.4 14.7 + - - -
327A GLU* 3.9 10.9 + - - -
331A GLN* 4.1 7.9 + - - -
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Residues in contact with GLY 263 (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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262A SER* 1.3 73.6 - - - +
264A GLY* 1.3 56.4 + - - +
266A LEU* 3.4 3.5 + - - +
267A ALA* 2.9 27.4 + - - +
311A VAL* 4.3 4.3 - - - +
315A TYR* 3.5 36.8 - - - -
318A VAL* 5.8 0.4 - - - -
327A GLU* 3.6 8.2 + - - -
328A CYS* 3.8 15.1 - - - -
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Residues in contact with GLY 264 (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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262A SER* 3.2 0.8 + - - -
263A GLY* 1.3 74.1 - - - +
265A ASP* 1.3 63.0 + - - +
267A ALA* 3.2 3.8 + - - +
268A CYS* 3.0 28.4 + - - -
327A GLU* 3.2 26.8 + - - -
328A CYS* 4.2 12.3 - - - -
331A GLN* 3.5 19.4 - - - +
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Residues in contact with ASP 265 (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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260A SER* 3.4 0.8 - - - -
261A LEU* 3.0 26.1 + - + +
262A SER* 3.1 20.2 + - - +
264A GLY* 1.3 72.3 - - - +
266A LEU* 1.3 61.4 + - - +
268A CYS* 3.1 8.2 + - - +
269A ARG* 2.9 49.9 + - - +
331A GLN* 3.7 5.2 + - - +
11B GLU 3.5 9.0 - - - +
12B ALA* 3.5 18.0 - - + +
13B LEU* 2.9 26.7 + - - +
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Residues in contact with LEU 266 (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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253A LEU* 5.1 1.1 - - + -
256A ILE* 3.5 22.2 - - + -
257A VAL* 3.8 28.9 - - + +
260A SER* 3.2 25.6 + - - +
262A SER 2.9 16.1 + - - +
263A GLY* 3.5 4.7 - - - +
265A ASP* 1.3 76.3 - - - +
267A ALA* 1.3 61.6 + - - +
269A ARG* 3.4 1.6 + - - +
270A LEU* 2.9 39.3 + - + +
310A TYR 4.9 2.0 - - - +
311A VAL* 4.0 26.2 - - + +
314A TYR* 4.9 0.9 - - + -
315A TYR* 3.8 25.4 - - + -
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Residues in contact with ALA 267 (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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263A GLY 2.9 14.6 + - - +
264A GLY* 3.5 9.2 - - - +
265A ASP 3.2 0.4 - - - -
266A LEU* 1.3 78.1 - - - +
268A CYS* 1.3 56.3 + - - +
270A LEU* 3.4 2.9 + - - +
271A LEU 2.9 21.8 + - - -
307A ILE* 3.8 20.5 - - + +
311A VAL* 4.0 9.6 - - + +
324A TRP* 4.8 0.4 - - + -
328A CYS* 4.3 11.4 - - + -
332A LEU* 3.4 31.5 - - + +
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Residues in contact with CYS 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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264A GLY 3.0 19.9 + - - -
265A ASP* 3.1 13.0 + - - +
267A ALA* 1.3 72.8 - - - +
269A ARG* 1.3 66.0 + - + +
271A LEU* 3.1 12.6 + - - +
272A VAL* 3.2 19.7 + - - +
331A GLN* 3.7 35.0 - - - -
332A LEU* 4.0 11.2 - - - -
335A PHE* 3.7 36.7 - - + -
13B LEU* 5.0 2.9 - - + +
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Residues in contact with ARG 269 (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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256A ILE* 3.7 17.5 - - + -
259A GLN* 3.4 25.4 + - - +
260A SER* 3.2 22.4 - - - -
265A ASP* 2.9 35.0 + - - +
266A LEU 3.8 1.3 - - - +
268A CYS* 1.3 74.6 - - - +
270A LEU* 1.3 57.8 + - - +
272A VAL* 3.2 4.9 + - - +
273A GLN* 2.9 32.0 + - - +
10B ALA 4.5 2.0 + - - -
11B GLU* 2.8 27.9 + - - +
12B ALA 4.0 0.4 - - - -
13B LEU* 3.6 34.1 - - + +
50B ILE 5.2 3.4 + - - -
51B PHE* 3.7 47.6 - - + +
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Residues in contact with LEU 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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248A LEU* 3.6 31.0 - - + -
253A LEU* 4.0 12.1 - - + -
256A ILE* 4.0 11.7 - - + -
266A LEU* 2.9 36.5 + - + +
267A ALA 3.6 4.0 - - - +
269A ARG* 1.3 77.4 - - - +
271A LEU* 1.3 57.5 + - - +
273A GLN* 4.5 3.8 - - + +
274A LEU* 2.8 42.1 + - + +
307A ILE* 3.9 11.0 - - + +
310A TYR* 3.7 27.4 - - + -
311A VAL* 3.8 24.7 - - + +
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Residues in contact with LEU 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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267A ALA 2.9 14.1 + - - +
268A CYS 3.1 8.5 + - - +
270A LEU* 1.3 75.0 - - - +
272A VAL* 1.3 57.8 + - - +
275A PHE* 3.0 51.4 + - + +
278A LEU* 4.2 5.8 - - + -
279A PHE* 3.7 26.1 - - + -
299A LEU* 3.7 29.4 - - + -
303A HIS* 6.0 0.4 - - + -
307A ILE* 3.9 15.4 - - + +
332A LEU* 4.0 22.0 - - + +
335A PHE* 4.1 17.3 - - + -
336A PHE* 4.2 12.6 - - + -
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Residues in contact with VAL 272 (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 CYS 3.2 13.8 + - - +
269A ARG* 3.5 8.1 - - - +
271A LEU* 1.3 78.9 - - - +
273A GLN* 1.3 61.8 + - - +
276A PRO* 3.7 22.0 - - - +
279A PHE* 4.1 13.7 - - + -
335A PHE* 3.8 26.0 - - + -
13B LEU* 3.9 8.7 - - + -
18B ALA* 3.9 15.0 - - + -
21B TYR* 4.0 29.9 - - + -
22B LEU* 4.0 13.6 - - + +
51B PHE* 4.3 11.0 - - + -
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Residues in contact with GLN 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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248A LEU* 5.3 7.6 - - + +
256A ILE* 4.0 21.0 - - + +
269A ARG 2.9 12.0 + - - +
270A LEU* 4.1 2.7 - - - +
272A VAL* 1.3 76.8 - - - +
274A LEU* 1.3 65.8 + - + +
276A PRO* 3.8 6.9 - - - +
21B TYR* 3.1 32.4 + - - -
51B PHE* 3.6 38.5 - - + -
53B ASN* 3.3 31.4 + - - +
55B LYS* 5.6 1.7 - - - +
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Residues in contact with LEU 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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245A GLU 4.8 1.9 - - - +
246A TYR* 3.1 63.2 - - + +
248A LEU* 4.0 22.2 - - + -
270A LEU* 2.8 31.1 + - + +
273A GLN* 1.3 74.7 - - + +
275A PHE* 1.3 79.8 + - + +
276A PRO* 3.4 6.8 - - - +
306A LEU* 4.5 3.1 - - + -
307A ILE* 4.2 19.1 - - + -
310A TYR* 3.9 29.6 - - + -
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Residues in contact with PHE 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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246A TYR* 3.5 37.0 - + - -
271A LEU* 3.0 33.1 + - + +
274A LEU* 1.3 95.6 - - + +
276A PRO* 1.3 66.2 - - - +
277A GLU* 3.2 11.2 - - - +
278A LEU* 3.0 32.8 + - + +
279A PHE* 3.4 6.6 - - - -
303A HIS* 3.5 60.6 - + + -
306A LEU* 4.1 18.4 - - + -
307A ILE* 4.0 11.7 - - + -
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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