Contacts of the helix formed by residues 310 - 324 (chain A) in PDB entry 2JJD
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 PRO 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A PHE 4.4 3.1 - - - +
309A THR* 1.3 83.3 - - - +
311A ILE* 1.3 67.5 + - - +
312A GLY 3.4 2.2 - - - -
313A MET* 3.3 6.8 + - + +
314A LEU* 3.3 22.1 + - - +
386A PHE* 3.8 27.6 - - + -
389A GLN* 4.0 16.2 - - + +
390A ALA* 3.8 37.9 - - + +
393A GLU* 4.2 19.3 - - + +
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Residues in contact with ILE 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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309A THR* 3.2 17.4 - - - -
310A PRO* 1.3 80.8 - - + +
312A GLY* 1.3 65.6 + - - +
314A LEU* 3.1 13.3 + - - +
315A LYS* 3.3 11.4 + - - +
393A GLU* 5.1 14.6 - - - +
660A GLN* 5.3 8.1 - - - +
663A LYS* 6.0 1.8 - - - +
664A SER* 6.1 5.4 - - - -
667A LEU* 6.3 0.9 - - + -
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Residues in contact with GLY 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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271A ASP* 4.7 17.9 - - - +
272A TYR* 5.4 1.0 - - - -
298A PHE* 4.1 10.4 - - - -
309A THR* 5.0 1.8 + - - -
310A PRO 3.4 0.4 - - - -
311A ILE* 1.3 78.2 - - - +
313A MET* 1.3 57.0 + - - +
315A LYS* 3.2 8.9 + - - +
316A PHE* 3.0 28.2 + - - +
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Residues in contact with MET 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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233A LEU* 3.9 7.9 - - + -
298A PHE* 4.1 29.7 - - + -
301A TRP* 3.6 30.3 - - + -
307A PRO* 6.0 1.6 - - + -
310A PRO* 3.3 11.5 + - + +
311A ILE 3.2 0.4 - - - -
312A GLY* 1.3 75.4 - - - +
314A LEU* 1.3 58.4 + - + +
316A PHE* 3.7 11.2 - - - +
317A LEU* 3.0 29.3 + - + +
344A THR* 4.9 0.7 - - - +
345A PHE* 3.5 44.2 - - + +
348A ILE* 4.5 13.7 - - + -
386A PHE* 4.4 24.7 - - + -
390A ALA* 6.1 0.2 - - + -
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Residues in contact with LEU 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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310A PRO 3.3 11.6 + - - +
311A ILE* 3.1 8.5 + - - +
313A MET* 1.3 76.8 - - + +
315A LYS* 1.3 65.1 + - - +
317A LEU* 3.3 5.6 + - - +
318A LYS* 3.1 21.8 + - - +
348A ILE* 4.3 13.5 - - + -
352A MET* 3.6 38.4 - - + +
390A ALA* 3.5 29.6 - - + +
393A GLU* 3.9 24.5 - - + -
394A TYR* 3.9 24.5 - - + +
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Residues in contact with LYS 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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272A TYR* 5.1 9.6 + - + +
311A ILE 3.3 8.4 + - - +
312A GLY* 3.2 11.1 + - - +
314A LEU* 1.3 75.7 - - - +
316A PHE* 1.3 65.0 + - - +
318A LYS* 3.1 9.4 + - - +
319A LYS* 3.0 21.9 + - - +
649A ARG* 5.9 7.2 - - - +
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Residues in contact with PHE 316 (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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231A VAL* 3.8 24.2 - - + -
233A LEU* 4.0 9.6 - - + -
272A TYR* 3.6 47.7 - + + -
296A LEU* 3.7 39.9 - - + -
298A PHE* 3.6 34.3 - + + -
312A GLY 3.0 16.5 + - - +
313A MET* 3.7 11.0 - - - +
315A LYS* 1.3 77.0 - - - +
317A LEU* 1.3 63.2 + - - +
319A LYS* 3.2 5.6 + - - +
320A VAL* 3.1 25.6 + - + +
345A PHE* 3.8 16.8 - + - -
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Residues in contact with LEU 317 (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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313A MET* 3.0 20.3 + - + +
314A LEU* 3.7 6.5 - - - +
315A LYS 3.2 0.2 - - - -
316A PHE* 1.3 76.7 - - - +
318A LYS* 1.3 60.8 + - - +
320A VAL* 3.7 5.2 + - - +
321A LYS* 3.4 18.7 + - + +
345A PHE* 3.8 40.2 - - + +
348A ILE* 3.7 28.0 - - + -
349A ASP* 3.8 26.0 - - + +
352A MET* 3.7 29.8 - - + -
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Residues in contact with LYS 318 (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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314A LEU 3.1 11.6 + - - +
315A LYS* 3.1 11.2 + - - +
317A LEU* 1.3 79.1 - - - +
319A LYS* 1.3 58.9 + - - +
320A VAL 3.2 0.2 - - - -
321A LYS* 3.2 9.0 + - - +
322A THR* 3.0 29.8 + - - -
352A MET* 6.2 2.9 - - + -
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Residues in contact with LYS 319 (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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272A TYR* 3.9 20.2 - - + +
274A ILE* 4.1 13.9 - - + -
296A LEU* 3.9 20.6 - - + -
315A LYS 3.0 12.5 + - - +
316A PHE* 3.2 10.7 + - - +
318A LYS* 1.3 73.5 - - - +
320A VAL* 1.3 65.2 + - - +
322A THR* 3.3 15.9 + - + +
323A LEU* 3.1 34.0 + - + +
653A GLU* 3.5 25.4 - - - +
655A LEU* 6.2 1.3 - - + -
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Residues in contact with VAL 320 (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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204A PHE* 6.1 0.2 - - + -
229A THR* 4.5 5.6 + - + -
231A VAL* 3.8 25.1 - - + -
296A LEU* 3.7 30.4 - - + +
316A PHE* 3.1 18.3 + - + +
317A LEU 3.8 8.5 - - - +
318A LYS 3.2 0.4 - - - -
319A LYS* 1.3 75.6 - - - +
321A LYS* 1.3 68.2 + - - +
322A THR 3.2 0.7 + - - -
323A LEU* 3.2 1.7 + - - +
324A ASN* 3.2 22.0 + - - +
331A ILE* 3.9 26.9 - - + -
345A PHE* 4.3 17.7 - - + -
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Residues in contact with LYS 321 (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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317A LEU* 3.4 11.9 + - + +
318A LYS* 3.2 12.2 + - - +
320A VAL* 1.3 79.7 - - - +
322A THR* 1.3 62.5 + - - +
324A ASN* 3.8 14.8 - - - +
331A ILE* 6.3 0.2 - - - -
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Residues in contact with THR 322 (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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318A LYS 3.0 15.1 + - - -
319A LYS* 3.4 19.1 - - + +
321A LYS* 1.3 78.0 - - - +
323A LEU* 1.3 80.0 + - + +
324A ASN 3.7 3.3 + - - +
655A LEU* 6.1 1.2 - - - +
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Residues in contact with LEU 323 (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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229A THR* 4.0 2.9 + - - +
274A ILE* 3.4 35.0 - - + -
276A LYS* 4.1 23.4 + - + +
294A SER* 3.9 21.8 + - - +
296A LEU* 4.0 20.9 - - + -
319A LYS* 3.1 20.4 + - + +
320A VAL 3.2 2.2 + - - +
322A THR* 1.3 91.2 - - + +
324A ASN* 1.3 59.4 + - - +
325A PRO* 3.3 11.5 - - - +
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Residues in contact with ASN 324 (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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228A ALA* 4.0 7.8 + - - +
229A THR* 2.9 26.9 + - - +
320A VAL 3.2 15.4 + - - +
321A LYS* 3.8 12.3 - - - +
322A THR 3.4 3.3 - - - +
323A LEU* 1.3 77.5 - - - +
325A PRO* 1.3 79.7 + - - +
326A VAL* 3.7 1.6 + - - -
328A ALA* 4.1 3.9 + - - +
329A GLY 4.6 9.7 + - - +
330A PRO 5.7 0.2 - - - -
331A ILE* 3.7 32.8 - - + +
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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