Contacts of the helix formed by residues 344 - 364 (chain A) in PDB entry 4CKG
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 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A GLU* 2.6 32.3 + - - -
254A GLU* 4.2 13.0 - - - -
327A PHE* 4.4 14.1 - - - -
342A ALA 3.5 2.2 + - - -
343A ASP* 1.4 79.8 - - - +
345A GLU* 1.3 68.7 + - - +
346A ARG* 3.4 3.8 + - - +
347A LEU* 3.2 14.9 + - - +
348A LEU* 3.0 28.3 + - - +
160B ARG* 4.3 6.7 + - - -
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Residues in contact with GLU 345 (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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327A PHE* 4.2 29.5 - - + -
344A SER* 1.3 77.1 + - - +
346A ARG* 1.4 58.1 + - - +
348A LEU* 3.8 4.8 - - - +
349A GLN* 3.3 22.3 + - - +
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Residues in contact with ARG 346 (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 GLU* 5.9 4.3 - - + +
256A GLU* 2.7 50.5 + - + +
344A SER* 3.4 3.5 + - - +
345A GLU* 1.4 74.9 - - + +
347A LEU* 1.3 67.1 + - + +
349A GLN* 2.9 35.5 + - - +
350A LEU* 3.0 59.5 + - - +
353A SER* 6.4 0.2 - - - -
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Residues in contact with LEU 347 (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 GLU* 5.5 0.9 - - - +
254A GLU* 3.7 27.6 - - + +
255A PRO 3.5 22.4 - - - +
256A GLU* 4.8 1.8 - - - -
257A PRO* 3.9 31.4 - - + -
270A GLY* 6.3 0.7 - - - -
271A HIS 5.5 6.3 - - - +
342A ALA* 3.9 11.9 - - + -
343A ASP* 4.6 14.6 - - + +
344A SER* 3.2 18.7 + - - +
346A ARG* 1.3 83.6 - - + +
348A LEU* 1.3 55.4 + - - +
350A LEU* 4.5 4.3 - - + -
351A TRP* 2.8 44.7 + - + +
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Residues in contact with LEU 348 (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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319A LEU* 4.1 24.9 - - + -
327A PHE* 3.2 56.1 - - + +
328A CYS 3.8 5.2 - - - +
329A PHE* 3.8 22.0 - - + -
342A ALA* 3.5 12.7 - - + +
344A SER 3.0 15.4 + - - +
345A GLU 3.8 7.4 - - - +
347A LEU* 1.3 73.9 - - - +
349A GLN* 1.3 67.9 + - + +
351A TRP* 4.0 1.9 - - - +
352A VAL* 3.1 33.0 + - + +
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Residues in contact with GLN 349 (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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345A GLU 3.3 15.6 + - - +
346A ARG* 2.9 42.3 + - - +
348A LEU* 1.3 84.6 - - + +
350A LEU* 1.4 58.7 + - - +
352A VAL* 3.9 4.1 - - - +
353A SER* 2.9 36.8 + - - +
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Residues in contact with LEU 350 (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 GLU* 3.5 27.4 - - + +
257A PRO* 3.4 35.2 - - + +
259A LEU* 4.2 24.9 - - + -
268A MET* 4.4 14.8 - - + -
346A ARG* 3.0 37.9 + - + +
347A LEU* 3.9 3.8 - - - +
349A GLN* 1.4 78.0 + - - +
351A TRP* 1.4 57.9 + - + +
353A SER* 2.9 8.2 + - - -
354A ALA* 2.7 39.5 + - + +
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Residues in contact with TRP 351 (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 PRO* 3.9 19.1 - - + +
268A MET* 3.7 40.2 - - + -
269A GLU 4.2 0.9 - - - -
270A GLY* 3.6 32.6 - - - -
271A HIS 4.6 3.8 + - - -
272A LEU* 3.9 37.4 - - + +
288A PHE* 3.7 24.5 - - + -
290A ILE* 4.2 9.6 - - + -
295A LEU* 4.4 6.3 - - + -
329A PHE* 4.0 17.9 - + + -
340A LEU* 6.4 0.2 - - + -
347A LEU* 2.8 43.0 + - + +
348A LEU 4.0 1.8 - - - +
350A LEU* 1.4 71.8 - - + +
352A VAL* 1.4 52.6 + - - +
354A ALA* 3.8 0.7 - - - +
355A VAL* 2.8 65.6 + - + +
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Residues in contact with VAL 352 (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 VAL* 4.4 10.1 - - + -
319A LEU* 4.6 21.8 - - + +
329A PHE* 3.4 46.4 - - + -
348A LEU* 3.1 27.5 + - + +
349A GLN* 3.9 4.7 - - - +
351A TRP* 1.4 71.4 - - - +
353A SER* 1.4 58.1 + - - +
355A VAL* 4.4 1.7 - - - +
356A GLN* 2.8 58.8 + - - +
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Residues in contact with SER 353 (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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346A ARG* 6.4 0.2 - - - -
349A GLN* 2.9 25.5 + - - +
350A LEU* 2.9 12.2 + - - -
352A VAL* 1.4 75.9 - - - +
354A ALA* 1.4 52.4 + - - +
356A GLN* 3.3 9.6 + - - +
357A SER* 2.7 36.1 + - - -
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Residues in contact with ALA 354 (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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259A LEU* 5.2 5.4 - - + -
266A LEU* 3.3 17.4 - - + +
268A MET* 3.9 31.2 - - + -
290A ILE* 4.0 8.3 - - + -
350A LEU* 2.7 23.8 + - + +
351A TRP 3.8 2.5 - - - +
353A SER* 1.4 68.9 - - - +
355A VAL* 1.3 61.4 + - - +
357A SER* 3.3 7.5 + - - -
358A SER* 2.8 26.7 + - - -
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Residues in contact with VAL 355 (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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290A ILE* 3.9 15.5 - - + -
295A LEU* 4.4 24.9 - - + -
312A LEU* 4.5 19.3 - - + -
317A VAL* 4.1 18.4 - - + -
329A PHE* 5.1 8.3 - - + -
331A VAL* 5.1 7.4 - - + -
340A LEU* 6.2 0.2 - - + -
351A TRP* 2.8 44.7 + - + +
352A VAL* 4.4 3.8 - - - +
354A ALA* 1.3 75.1 - - - +
356A GLN* 1.4 59.1 + - - +
358A SER* 3.4 6.4 + - - -
359A ILE* 3.3 20.5 + - + +
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Residues in contact with GLN 356 (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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316A THR* 5.6 0.9 + - - -
317A VAL* 3.7 36.5 + - + +
352A VAL* 2.8 46.0 + - - +
353A SER* 3.7 6.5 + - - +
355A VAL* 1.4 70.4 - - - +
357A SER* 1.4 59.8 + - - +
359A ILE* 3.3 13.0 + - + +
360A ALA* 3.2 18.9 + - - +
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Residues in contact with SER 357 (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 PRO* 3.9 20.3 - - - +
266A LEU* 4.1 8.1 - - - +
353A SER 2.7 20.1 + - - -
354A ALA* 3.3 10.7 + - - -
356A GLN* 1.4 71.5 - - - +
358A SER* 1.3 62.2 + - - +
360A ALA* 3.0 19.8 + - - +
361A SER* 3.1 13.4 + - - -
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Residues in contact with SER 358 (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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266A LEU* 3.9 11.0 - - - +
290A ILE* 3.6 13.2 - - - +
293A ASN* 3.1 32.7 + - - +
312A LEU* 3.3 22.4 - - - +
354A ALA 2.8 19.1 + - - -
355A VAL* 3.4 8.0 + - - -
357A SER* 1.3 70.9 - - - +
359A ILE* 1.3 56.9 + - - +
361A SER* 3.3 4.4 + - - -
362A ALA* 3.0 31.6 + - - +
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Residues in contact with ILE 359 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A LEU* 3.5 41.0 - - + +
313A ARG 4.6 6.1 - - - +
315A CYS* 3.7 36.1 - - + +
316A THR* 4.3 3.1 - - - -
317A VAL* 3.6 31.0 - - + -
355A VAL* 3.3 11.7 + - + +
356A GLN* 3.3 11.0 + - + +
358A SER* 1.3 71.8 - - - +
360A ALA* 1.4 60.5 + - - +
362A ALA* 3.8 1.3 - - - +
363A PHE* 2.9 36.4 + - + +
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Residues in contact with ALA 360 (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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356A GLN 3.2 9.6 + - - +
357A SER* 3.0 13.6 + - - +
359A ILE* 1.4 76.0 - - - +
361A SER* 1.3 59.7 + - - +
363A PHE* 3.4 5.9 + - - +
364A SER* 2.7 31.1 + - - +
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Residues in contact with SER 361 (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 PRO* 2.7 37.4 + - - +
264A GLY* 4.1 3.6 - - - -
293A ASN* 3.1 23.3 - - - -
357A SER 3.1 10.7 + - - -
358A SER 3.3 6.3 + - - -
360A ALA* 1.3 75.9 - - - +
362A ALA* 1.4 62.8 + - - +
364A SER* 3.2 21.5 + - - -
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Residues in contact with ALA 362 (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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293A ASN* 4.2 17.0 - - + +
311A ASP* 5.7 0.4 - - - +
312A LEU* 4.2 8.7 - - + -
313A ARG* 2.7 53.9 + - + +
358A SER 3.0 18.1 + - - +
359A ILE 3.8 3.8 - - - +
361A SER* 1.4 77.2 - - - +
363A PHE* 1.4 51.4 + - - +
364A SER 3.5 0.9 + - - +
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Residues in contact with PHE 363 (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 ARG* 3.0 59.3 + - + +
314A LEU* 5.6 6.3 - - + -
359A ILE* 2.9 24.5 + - + +
360A ALA* 4.1 5.6 - - - +
362A ALA* 1.4 70.5 - - - +
364A SER* 1.3 62.4 - - - +
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Residues in contact with SER 364 (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 ARG* 2.8 28.5 + - - -
360A ALA* 2.7 23.3 + - - +
361A SER* 3.2 15.2 + - - -
362A ALA 4.0 0.6 - - - +
363A PHE* 1.3 76.3 - - - +
365A GLN 1.3 51.5 + - - +
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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