Contacts of the helix formed by residues 309 - 324 (chain A) in PDB entry 2JDQ
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 ASP 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A THR* 3.3 27.7 + - + +
307A HIS* 3.1 20.8 + - + +
308A ASN* 1.3 79.4 - - + +
310A TYR* 1.3 62.4 + - - +
311A LYS* 3.0 40.2 + - - +
312A VAL* 3.0 19.9 + - - +
313A VAL* 3.1 15.4 + - - +
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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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307A HIS 6.0 0.2 - - - -
308A ASN 4.0 6.9 + - - -
309A ASP* 1.3 74.3 + - - +
311A LYS* 1.3 56.6 + - - +
312A VAL 3.1 0.2 - - - -
313A VAL* 3.8 13.7 - - + -
314A SER* 2.9 38.9 + - - +
346A LEU* 6.2 2.7 - - + -
349A SER* 4.1 13.7 - - - -
350A PRO* 3.2 32.2 - - + +
351A LYS* 3.9 38.4 - - + -
354A ILE* 4.3 14.8 - - + -
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 4.7 6.1 - - + -
269A ASP* 5.5 6.3 - - - +
272A ALA* 3.3 18.0 - - + +
276A TRP* 4.7 2.1 + - - -
309A ASP* 3.0 26.6 + - - +
310A TYR* 1.3 79.1 - - + +
312A VAL* 1.3 57.7 + - - +
314A SER* 5.3 0.4 - - - -
315A PRO* 3.1 21.1 - - - +
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Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 3.6 39.9 - - + +
271A LEU* 4.2 12.3 - - + -
272A ALA* 4.1 5.8 - - - +
275A CYS* 4.7 5.8 - - - -
304A LEU* 3.9 39.3 - - + -
307A HIS* 3.9 25.6 - - + +
309A ASP 3.0 7.5 + - - +
311A LYS* 1.3 78.6 - - - +
313A VAL* 1.3 65.1 + - - +
314A SER 3.4 0.2 - - - -
315A PRO* 3.2 6.6 - - - +
316A ALA* 3.0 20.3 + - - +
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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
----------------------------------------------------------
304A LEU 3.8 17.7 - - - +
305A LEU* 3.8 21.1 - - - +
307A HIS* 3.5 22.7 - - + +
309A ASP 3.1 18.0 + - - +
310A TYR* 3.4 13.2 + - + +
312A VAL* 1.3 72.6 - - - +
314A SER* 1.3 57.6 + - - +
316A ALA* 3.8 1.5 - - - +
317A LEU* 2.7 40.6 + - + +
346A LEU* 4.0 25.4 - - + -
354A ILE* 4.0 16.4 - - + -
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Residues in contact with SER 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TRP* 5.0 9.9 - - - -
310A TYR* 2.9 19.9 + - - +
311A LYS* 5.3 0.2 - - - -
313A VAL* 1.3 76.5 - - - +
315A PRO* 1.4 66.8 - - - +
318A ARG* 3.0 25.4 + - - +
351A LYS* 5.1 4.9 - - - +
353A SER* 5.2 2.1 + - - -
354A ILE* 3.3 19.3 - - - +
357A GLU* 3.1 25.3 + - - +
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Residues in contact with PRO 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 ALA 3.7 9.2 - - - +
275A CYS* 3.6 19.8 - - + +
276A TRP* 3.7 45.3 - - + +
279A SER* 4.1 0.3 - - - -
311A LYS* 3.1 27.8 - - - +
312A VAL* 3.2 11.2 - - - +
314A SER* 1.4 89.9 - - - +
316A ALA* 1.3 62.4 + - - +
318A ARG* 3.2 8.7 + - + +
319A ALA* 3.0 23.6 + - - +
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Residues in contact with ALA 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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275A CYS* 3.7 16.0 - - - +
301A LEU* 4.0 12.2 - - + +
304A LEU* 3.9 29.2 - - + -
305A LEU* 3.9 8.1 - - + -
312A VAL 3.0 20.3 + - - +
313A VAL 3.8 2.5 - - - +
315A PRO* 1.3 74.1 - - - +
317A LEU* 1.3 58.7 + - - +
319A ALA* 3.2 6.7 + - - +
320A VAL* 3.0 31.4 + - - +
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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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305A LEU* 3.5 16.5 - - + +
313A VAL 2.7 21.1 + - - +
314A SER 3.5 4.3 - - - +
316A ALA* 1.3 74.0 - - - +
318A ARG* 1.3 54.8 + - - +
320A VAL* 3.8 2.4 - - + +
321A GLY* 3.0 24.8 + - - -
343A LEU* 3.7 26.2 - - + -
346A LEU* 4.1 17.7 - - + -
354A ILE* 3.8 24.9 - - + +
357A GLU* 3.6 35.7 - - + +
358A ALA* 3.9 3.6 - - - +
360A TRP* 3.8 1.4 - - - -
361A THR* 3.6 19.6 + - + +
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TRP* 3.4 38.0 - - - -
279A SER* 3.9 15.3 + - - -
280A TYR* 5.4 4.6 - - - -
314A SER 3.0 15.8 + - - +
315A PRO* 3.2 7.1 + - + +
317A LEU* 1.3 76.7 - - - +
319A ALA* 1.3 62.7 + - - +
321A GLY 3.6 0.3 + - - -
322A ASN* 3.1 29.1 + - - -
357A GLU* 4.1 18.5 + - - +
360A TRP* 3.6 10.9 - - + -
741E SER* 3.8 41.3 + - - +
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Residues in contact with ALA 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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275A CYS 4.3 3.1 - - - +
278A LEU* 4.3 5.6 - - + +
279A SER* 3.7 29.3 - - - +
282A SER* 3.9 3.0 + - - +
301A LEU* 4.1 24.2 - - + -
315A PRO 3.0 12.6 + - - +
316A ALA 3.5 7.9 - - - +
318A ARG* 1.3 72.6 - - - +
320A VAL* 1.3 65.0 + - - +
322A ASN* 3.2 4.9 + - - +
323A ILE* 3.0 29.7 + - + +
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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
----------------------------------------------------------
301A LEU* 4.0 23.3 - - + -
302A VAL* 4.3 13.2 - - + -
305A LEU* 4.2 22.2 - - + -
316A ALA 3.0 23.5 + - - +
317A LEU* 3.8 6.7 - - + +
319A ALA* 1.3 75.5 - - - +
321A GLY* 1.3 63.4 + - - +
323A ILE* 3.1 9.8 + - - +
324A VAL* 3.1 23.8 + - + +
334A ILE* 4.1 25.6 - - + -
339A ALA* 5.2 2.0 - - + -
343A LEU* 5.4 0.2 - - + -
361A THR* 4.0 18.6 - - + -
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Residues in contact with GLY 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 3.0 10.9 + - - -
319A ALA 3.3 0.2 - - - -
320A VAL* 1.3 76.2 - - - +
322A ASN* 1.3 60.2 + - - +
324A VAL* 3.2 10.5 - - - +
325A THR* 3.4 1.4 - - - +
360A TRP* 3.5 17.7 - - - -
361A THR* 3.4 30.7 - - - -
364A ASN* 3.2 22.5 + - - -
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Residues in contact with ASN 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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279A SER* 3.0 27.5 + - - -
282A SER* 3.5 19.4 - - - +
283A ASP* 3.8 6.7 - - - +
289A ILE* 3.2 8.3 - - - +
318A ARG* 3.1 18.0 + - - +
319A ALA 3.5 7.9 - - - +
320A VAL 3.1 0.4 - - - -
321A GLY* 1.3 76.3 - - - +
323A ILE* 1.3 61.4 + - - +
325A THR* 2.6 28.2 + - - -
360A TRP* 3.8 2.9 - - - -
740E ASP* 3.2 20.3 - - - +
741E SER* 3.2 35.2 + - - -
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Residues in contact with ILE 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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282A SER* 4.0 16.4 - - - -
289A ILE* 3.8 23.6 - - + +
292A VAL* 4.4 14.4 - - + -
293A ILE* 3.9 19.3 - - + -
297A VAL* 5.1 0.2 - - + -
298A CYS* 4.0 15.0 - - - -
301A LEU* 3.9 26.9 - - + -
319A ALA* 3.0 22.9 + - + +
320A VAL* 3.1 7.6 + - - +
322A ASN* 1.3 76.4 - - - +
324A VAL* 1.3 54.3 + - - +
326A GLY* 2.8 29.1 + - - -
330A GLN* 4.2 7.0 - - - +
334A ILE* 3.9 20.4 - - + -
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Residues in contact with VAL 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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320A VAL* 3.1 15.3 + - + +
321A GLY* 3.2 19.3 - - - +
323A ILE* 1.3 72.2 - - - +
325A THR* 1.3 54.2 + - - -
326A GLY 3.1 4.7 - - - -
331A THR* 3.9 20.2 - - - +
334A ILE* 3.7 37.0 - - + -
361A THR* 3.7 16.6 - - + +
364A ASN* 3.3 22.9 - - + +
365A ILE* 4.0 17.5 - - + -
738E LYS* 3.0 21.4 + - - -
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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