Contacts of the helix formed by residues 395 - 411 (chain A) in PDB entry 3CKI
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 LEU 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A THR 5.2 2.9 - - - +
394A ILE* 1.3 76.2 - - - +
396A THR* 1.3 66.2 + - - +
397A LYS* 3.4 43.1 - - + +
398A GLU* 2.9 24.4 + - - +
399A ALA* 2.8 20.3 + - - +
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Residues in contact with THR 396 (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 TYR* 4.1 25.8 - - + -
257A ARG* 4.0 21.1 + - - +
394A ILE 3.9 1.2 + - - -
395A LEU* 1.3 72.4 - - - +
397A LYS* 1.3 66.4 + - - +
399A ALA* 3.6 7.8 - - - +
400A ASP* 2.8 38.1 + - - +
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Residues in contact with LYS 397 (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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395A LEU* 3.4 32.8 - - + +
396A THR* 1.3 83.3 + - - +
398A GLU* 1.3 76.2 - - + +
400A ASP* 3.8 10.1 + - - +
401A LEU* 3.4 27.6 + - - +
441A SER* 4.9 2.2 + - - +
442A GLY* 4.7 21.3 - - - +
443A ASP* 3.5 32.4 + - - +
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Residues in contact with GLU 398 (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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348A LEU* 5.9 2.9 - - + -
394A ILE* 3.5 18.3 - - + +
395A LEU* 2.9 46.3 + - + +
397A LYS* 1.3 92.8 - - + +
399A ALA* 1.3 65.4 + - - +
401A LEU* 3.1 7.7 + - - +
402A VAL* 3.0 27.6 + - + +
439A ALA* 6.0 3.3 - - + +
440A VAL* 5.7 0.2 - - - -
441A SER* 4.4 29.4 + - - +
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Residues in contact with ALA 399 (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 TYR* 3.2 26.9 - - - +
254A LEU* 4.0 9.2 - - + -
385A THR* 4.5 1.9 - - + +
387A THR* 3.8 10.8 - - + -
394A ILE* 3.5 24.1 - - + +
395A LEU 2.8 10.0 + - - +
396A THR 3.6 5.2 - - - +
398A GLU* 1.3 77.8 - - - +
400A ASP* 1.3 62.8 + - - +
402A VAL* 3.1 14.8 + - - +
403A THR* 3.2 16.6 + - - -
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Residues in contact with ASP 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 3.2 23.0 - - + +
257A ARG* 2.6 56.6 + - + +
258A VAL* 3.7 9.7 - - + +
261A ILE* 6.0 1.8 - - + -
396A THR* 2.8 33.0 + - - +
397A LYS* 3.9 9.8 - - - +
398A GLU 3.2 0.2 - - - -
399A ALA* 1.3 71.7 - - - +
401A LEU* 1.3 59.1 + - + +
403A THR 3.6 0.7 + - - -
404A THR* 2.7 36.3 + - - +
448A LYS* 5.9 1.6 + - - +
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ILE* 4.1 24.7 - - + -
397A LYS 3.4 13.2 + - - +
398A GLU* 3.1 8.8 + - - +
400A ASP* 1.3 79.9 - - + +
402A VAL* 1.3 66.0 + - - +
404A THR* 3.7 4.1 - - - +
405A HIS* 3.1 24.4 + - - +
434A VAL* 3.9 11.1 - - + +
439A ALA* 5.8 3.8 - - + +
441A SER 4.6 4.7 - - - +
442A GLY* 4.0 17.7 - - - +
447A ASN* 3.5 43.5 - - + +
448A LYS* 4.3 12.3 - - + +
2B THR* 5.2 0.2 - - - +
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Residues in contact with VAL 402 (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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348A LEU* 3.7 44.0 - - + +
349A GLY* 4.3 0.9 - - - +
385A THR* 3.7 25.1 - - + +
394A ILE* 4.4 5.2 - - + -
398A GLU 3.0 19.3 + - - +
399A ALA* 3.1 10.5 + - - +
401A LEU* 1.3 77.8 - - - +
403A THR* 1.3 58.9 + - - +
405A HIS* 3.2 5.3 + - - +
406A GLU* 2.9 35.0 + - + +
439A ALA* 5.0 6.5 - - + -
2B THR* 3.6 22.9 - - - +
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Residues in contact with THR 403 (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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254A LEU* 3.8 19.8 - - + +
255A ILE* 4.5 3.1 - - + -
258A VAL* 4.3 2.5 - - + -
336A HIS* 4.0 17.9 - - + +
338A PHE* 3.6 25.2 - - + -
385A THR* 2.9 20.7 + - - +
399A ALA 3.2 10.2 + - - -
400A ASP 4.0 2.7 - - - -
402A VAL* 1.3 75.5 - - - +
404A THR* 1.3 65.6 + - - +
406A GLU* 4.0 2.4 - - - +
407A LEU* 2.8 44.7 + - + +
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Residues in contact with THR 404 (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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258A VAL* 3.6 21.8 - - - +
261A ILE* 3.8 26.0 - - + +
262A TYR* 2.8 28.3 + - + -
400A ASP 2.7 24.7 + - - -
401A LEU* 3.7 6.5 - - - -
402A VAL 3.3 0.2 - - - -
403A THR* 1.3 74.2 - - - +
405A HIS* 1.3 53.4 + - - +
408A GLY* 2.7 30.0 + - - -
434A VAL* 3.7 20.6 - - + -
450A PHE* 3.9 14.8 - - + -
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Residues in contact with HIS 405 (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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401A LEU 3.1 16.0 + - - +
402A VAL 3.4 3.8 - - - +
404A THR* 1.3 77.4 - - - +
406A GLU* 1.3 71.5 + - - +
408A GLY* 3.0 8.8 + - - -
409A HIS* 3.2 15.3 + - - -
415A HIS* 3.7 2.9 - + - -
434A VAL* 2.6 25.8 + - - +
435A MET* 3.2 34.6 - - + +
436A TYR 3.1 24.5 + - - -
501A ZN 2.2 37.3 - - - -
1B CYS 3.0 5.6 + - - -
2B THR* 3.2 20.3 - - + +
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Residues in contact with GLU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A HIS* 3.9 20.4 - - + -
349A GLY* 3.4 6.3 - - - -
350A LEU* 3.2 37.0 - - - +
351A ALA* 3.4 21.4 + - + +
384A LEU 3.9 10.8 - - - +
385A THR* 4.6 0.4 - - - +
402A VAL* 2.9 21.7 + - + +
403A THR 4.0 0.4 - - - +
405A HIS* 1.3 73.8 - - - +
407A LEU* 1.3 68.3 + - - +
409A HIS* 3.0 14.8 + - - -
410A ASN* 3.2 8.6 + - - -
1B CYS 3.3 11.6 + - - -
2B THR* 2.9 39.7 + - - +
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Residues in contact with LEU 407 (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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227A LEU* 4.6 19.1 - - + -
255A ILE* 4.9 1.8 - - + -
258A VAL* 3.8 23.8 - - + -
262A TYR* 3.3 14.6 - - + +
277A ILE* 4.1 20.0 - - + -
334A LEU* 3.8 24.5 - - + -
336A HIS* 4.1 20.0 - - + +
403A THR* 2.8 37.7 + - + +
404A THR 3.8 0.2 - - - +
406A GLU* 1.3 72.7 - - - +
408A GLY* 1.3 57.0 + - - +
410A ASN* 3.1 15.2 - - - +
411A PHE* 2.8 32.1 + - + -
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Residues in contact with GLY 408 (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 TYR* 2.9 12.3 + - - -
404A THR 2.7 13.0 + - - -
405A HIS 3.3 6.7 - - - -
406A GLU 2.9 1.2 - - - -
407A LEU* 1.3 77.9 - - - +
409A HIS* 1.3 58.1 + - - +
411A PHE* 3.1 13.4 + - - +
412A GLY 3.3 0.3 + - - -
413A ALA* 2.9 29.0 + - - +
435A MET* 3.9 10.8 - - - -
450A PHE* 4.4 6.5 - - - -
458A ILE* 4.1 0.6 - - - +
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Residues in contact with HIS 409 (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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351A ALA* 4.2 4.7 - - + -
352A TYR 4.1 3.1 - - - +
353A VAL* 3.2 13.2 - - - +
354A GLY 2.6 30.7 + - - -
405A HIS* 3.2 10.8 + - - -
406A GLU* 3.0 19.7 + - - +
408A GLY* 1.3 71.2 - - - +
410A ASN* 1.3 55.1 + - - +
412A GLY* 2.7 12.6 + - - -
413A ALA 2.7 26.0 + - - +
414A GLU* 4.1 2.2 + - - -
415A HIS* 3.5 17.9 - + - -
435A MET* 3.5 12.0 - - + +
501A ZN 2.2 36.2 - - - -
1B CYS 2.9 10.4 + - - -
65B GLU* 4.0 6.7 - - - -
66B SER* 3.6 26.6 - - - -
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Residues in contact with ASN 410 (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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334A LEU* 3.4 41.6 - - + +
335A ALA 4.9 0.7 - - - +
336A HIS* 4.9 1.4 + - - -
351A ALA* 3.5 7.9 - - - +
352A TYR 2.8 28.7 + - - -
354A GLY* 3.3 8.7 - - - -
363A GLY* 3.8 6.8 - - - -
364A VAL* 3.0 24.5 + - - +
382A SER 3.2 29.2 + - - +
383A GLY* 4.5 1.7 + - - -
406A GLU 3.2 9.0 + - - -
407A LEU* 3.1 23.8 + - - +
409A HIS* 1.3 80.3 - - - +
411A PHE* 1.3 55.9 + - - -
412A GLY 3.3 3.3 + - - -
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Residues in contact with PHE 411 (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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225A CYS* 3.9 15.0 - - + -
262A TYR* 4.0 20.2 - + + -
267A TRP* 5.4 0.2 - + - -
275A TYR* 5.5 3.4 - - + -
276A GLY 4.4 5.6 - - - -
277A ILE* 3.7 37.7 - - + -
334A LEU* 4.1 11.0 - - + -
364A VAL* 3.8 20.9 - - + -
407A LEU* 2.8 22.4 + - + +
408A GLY* 3.6 10.1 - - - +
409A HIS 3.1 0.8 - - - -
410A ASN* 1.3 74.5 - - - +
412A GLY* 1.3 56.6 + - - +
413A ALA 3.6 0.4 - - - -
458A ILE* 3.6 25.8 - - + +
461A THR* 3.1 25.7 - - - +
462A ILE* 3.9 29.2 - - + -
470A PHE* 3.8 20.2 - + - -
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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