Contacts of the helix formed by residues 300 - 315 (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 GLU 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A LYS* 2.8 28.2 + - + +
299A LEU* 1.3 75.7 - - - +
301A SER* 1.3 77.7 + - - +
302A LEU* 2.9 44.2 + - - +
303A HIS* 2.7 37.8 + - + +
304A LEU* 3.1 24.6 + - - +
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Residues in contact with SER 301 (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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300A GLU* 1.3 81.2 - - - +
302A LEU* 1.3 60.3 + - - +
304A LEU* 4.6 4.4 - - - +
305A GLN* 2.9 30.4 + - - +
401A GOL 3.2 25.7 + - - -
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Residues in contact with LEU 302 (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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300A GLU* 2.9 27.3 + - - +
301A SER* 1.3 75.9 + - - +
303A HIS* 1.3 63.8 + - + +
305A GLN* 3.4 7.2 + - + +
306A LEU* 3.1 23.4 + - - +
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Residues in contact with HIS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TYR* 5.1 3.8 + - - -
275A PHE* 3.5 56.6 - + + -
277A GLU* 4.8 4.8 + - - -
278A LEU* 3.8 16.7 - - + +
298A LYS* 3.6 44.8 + - - +
299A LEU* 5.0 4.5 - - + -
300A GLU* 2.7 36.5 + - - +
302A LEU* 1.3 76.3 - - + +
304A LEU* 1.3 62.6 + - + +
306A LEU* 3.4 2.3 + - - +
307A ILE* 3.2 28.8 + - + +
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Residues in contact with LEU 304 (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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299A LEU* 3.9 43.7 - - + +
300A GLU 3.1 20.8 + - - +
301A SER* 3.8 4.9 - - - +
303A HIS* 1.3 81.2 - - - +
305A GLN* 1.3 55.4 + - - +
307A ILE* 3.2 11.7 + - + +
308A ARG* 2.9 27.5 + - - +
324A TRP* 3.7 8.8 - - + -
329A LEU* 3.9 23.3 - - + -
332A LEU* 4.0 22.9 - - + -
333A ASN* 5.2 3.4 - - - +
401A GOL 3.9 19.1 - - - +
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Residues in contact with GLN 305 (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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301A SER* 2.9 17.9 + - - +
302A LEU* 3.8 9.2 - - + +
304A LEU* 1.3 71.8 - - - +
306A LEU* 1.3 61.6 + - - +
308A ARG* 3.3 16.1 + - - +
309A ASN* 2.8 58.6 + - - +
312A GLU* 5.2 1.8 + - - -
401A GOL 2.5 39.4 + - - -
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PRO* 3.7 29.8 - - + -
243A PRO* 5.3 0.7 - - + -
246A TYR* 3.6 37.5 - - + +
274A LEU* 4.5 3.1 - - + -
275A PHE* 4.1 17.3 - - + -
302A LEU 3.1 14.0 + - - +
303A HIS 3.7 8.7 - - - +
305A GLN* 1.3 76.1 - - - +
307A ILE* 1.3 62.0 + - - +
309A ASN* 3.2 16.7 + - + +
310A TYR* 3.2 42.5 + - + -
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Residues in contact with ILE 307 (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* 3.8 36.3 - - + +
270A LEU* 4.2 4.9 - - + -
271A LEU* 3.9 42.2 - - + +
274A LEU* 4.2 11.0 - - + -
275A PHE* 4.0 13.7 - - + -
299A LEU* 6.0 0.2 - - + -
303A HIS* 3.2 18.7 + - + +
304A LEU* 3.2 13.7 + - + +
306A LEU* 1.3 75.8 - - - +
308A ARG* 1.3 56.7 + - - +
310A TYR* 3.2 10.4 + - - +
311A VAL* 2.9 29.4 + - + +
324A TRP* 4.4 7.0 - - + -
332A LEU* 4.3 9.9 - - + -
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Residues in contact with ARG 308 (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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304A LEU 2.9 14.0 + - - +
305A GLN* 3.5 18.3 + - - +
307A ILE* 1.3 77.8 - - - +
309A ASN* 1.3 55.9 + - - +
311A VAL* 3.2 2.8 + - - +
312A GLU* 2.9 54.4 + - - +
318A VAL* 2.9 24.4 + - + -
319A LYS* 3.1 20.2 + - - +
321A THR* 3.2 32.5 + - - +
324A TRP* 3.6 51.9 - - + -
401A GOL 2.9 29.1 + - - -
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Residues in contact with ASN 309 (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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305A GLN* 2.8 52.8 + - - +
306A LEU* 3.2 20.2 + - + +
308A ARG* 1.3 73.8 - - - +
310A TYR* 1.3 63.3 + - + +
312A GLU* 3.5 20.8 + - - +
313A VAL* 3.7 14.4 + - - +
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Residues in contact with TYR 310 (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 PRO* 3.9 7.6 - - + +
246A TYR 2.7 28.9 + - - -
247A GLN* 3.4 8.2 + - - -
248A LEU* 3.0 38.7 + - + -
253A LEU* 4.0 34.1 - - + +
266A LEU* 4.9 0.9 - - - +
270A LEU* 3.7 15.0 - - + -
274A LEU* 3.9 24.2 - - + -
306A LEU* 3.2 38.0 + - + -
307A ILE* 3.6 5.4 - - - +
309A ASN* 1.3 74.2 - - + +
311A VAL* 1.3 67.2 + - - +
313A VAL* 3.2 23.9 + - + +
314A TYR* 4.2 2.8 + - - -
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Residues in contact with VAL 311 (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* 4.3 4.5 - - - +
266A LEU* 4.0 9.9 - - + -
267A ALA* 4.0 26.7 - - + +
270A LEU* 3.8 16.2 - - + -
307A ILE* 2.9 23.4 + - + +
308A ARG* 3.6 8.5 - - - +
310A TYR* 1.3 75.5 - - - +
312A GLU* 1.3 58.2 + - - +
314A TYR* 3.2 5.4 + - - +
315A TYR* 2.9 38.6 + - + +
318A VAL* 3.8 28.7 - - + -
324A TRP* 4.7 2.2 - - + -
328A CYS* 4.2 9.4 - - - -
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Residues in contact with GLU 312 (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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305A GLN* 5.2 1.7 + - - -
308A ARG* 2.9 51.6 + - - +
309A ASN* 3.8 17.9 - - - +
310A TYR 3.2 0.6 - - - -
311A VAL* 1.3 73.9 - - - +
313A VAL* 1.3 64.5 + - - +
314A TYR 3.2 0.7 + - - -
315A TYR 3.5 7.6 - - - +
316A PRO* 3.4 19.9 - - - +
318A VAL* 3.4 14.0 - - + +
319A LYS* 3.5 52.4 + - + +
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Residues in contact with VAL 313 (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* 4.0 13.9 - - + -
309A ASN 3.7 10.7 + - - +
310A TYR* 3.2 18.1 + - + +
312A GLU* 1.3 78.5 - - - +
314A TYR* 1.3 84.4 + - + +
316A PRO* 4.7 3.8 - - - +
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Residues in contact with TYR 314 (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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250A ALA* 4.5 4.2 + - - +
253A LEU* 3.7 22.4 - - + -
254A LYS* 3.2 48.5 + - + +
257A VAL* 3.6 37.5 - - + -
266A LEU* 4.9 0.9 - - + -
310A TYR 4.7 1.8 - - - -
311A VAL 3.2 3.9 + - - +
313A VAL* 1.3 101.0 - - + +
315A TYR* 1.3 75.2 + - + +
316A PRO* 3.5 11.4 - - - +
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Residues in contact with TYR 315 (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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257A VAL* 5.2 8.0 + - + +
260A SER* 4.6 8.5 + - - -
261A LEU 4.7 0.5 - - - -
262A SER* 3.4 21.2 + - - -
263A GLY* 3.5 30.3 - - - -
266A LEU* 3.8 25.8 - - + -
311A VAL* 2.9 17.8 + - + +
312A GLU* 3.5 7.3 - - - -
314A TYR* 1.3 88.4 - - + +
316A PRO* 1.3 62.5 - - - +
317A SER* 3.2 8.3 - - - +
318A VAL* 3.0 39.0 + - + +
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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