Contacts of the helix formed by residues 351 - 366 (chain B) in PDB entry 2CT8
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 ILE 351 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320B TYR* 4.7 4.5 - - + +
346B GLU 3.0 9.8 + - - +
347B LEU* 3.7 30.5 - - + +
350B GLU* 1.3 74.4 - - - +
352B GLY* 1.3 66.9 + - - +
354B LEU* 3.1 19.8 + - - +
355B TYR* 3.2 32.7 - - + -
405B ILE* 4.7 3.1 - - + -
406B LEU* 4.4 18.6 - - + -
409B THR* 3.9 24.7 - - + +
447B LEU* 4.7 2.7 - - + -
451B LEU* 4.0 32.3 - - + -
492B PHE* 4.1 15.5 - - + -
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Residues in contact with GLY 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B LEU 2.9 18.5 + - - -
351B ILE* 1.3 76.1 - - - +
353B ASN* 1.3 62.2 + - - +
354B LEU 3.3 0.2 + - - -
355B TYR* 3.4 10.6 + - - +
356B SER* 3.2 17.0 + - - -
489B LYS 5.4 1.6 - - - +
491B LEU* 4.8 5.6 + - - +
492B PHE* 4.3 5.8 - - - -
36D U 3.2 31.1 - - - -
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Residues in contact with ASN 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ALA 3.1 12.2 + - - +
349B ASN 3.4 11.6 + - - +
351B ILE 3.3 0.8 - - - +
352B GLY* 1.3 76.8 - - - +
354B LEU* 1.3 57.9 + - - +
356B SER* 3.4 2.0 + - - -
357B ARG* 2.8 36.7 + - - +
413B ASN* 5.0 0.6 + - - -
35D A 2.7 57.4 + - - +
36D U 3.5 21.3 - - + +
38D A 2.9 31.6 + - - +
39D G 4.5 2.4 + - - -
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLU 3.2 13.4 + - - +
351B ILE 3.1 9.8 + - - +
353B ASN* 1.3 76.1 - - - +
355B TYR* 1.3 68.3 + - - +
357B ARG* 2.9 32.1 - - - +
358B VAL* 3.1 23.2 + - + +
409B THR* 4.1 16.6 - - + +
412B LEU* 3.8 39.0 - - + +
413B ASN* 3.3 27.8 - - - +
416B VAL* 4.4 1.1 - - + -
444B LEU* 3.7 14.6 - - + -
447B LEU* 4.0 15.3 - - + -
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Residues in contact with TYR 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ILE* 3.2 42.2 + - + -
352B GLY* 3.8 4.9 - - - +
354B LEU* 1.3 75.8 - - - +
356B SER* 1.3 65.8 + - - +
358B VAL* 3.0 3.1 + - - -
359B VAL* 2.9 29.6 + - - +
444B LEU* 3.5 40.5 + - + -
447B LEU* 4.0 11.6 - - + +
448B THR* 2.7 32.5 + - - -
459B MET* 2.9 24.9 - - + +
462B ALA* 3.9 15.5 - - + -
465B MET* 4.4 18.8 - - + -
466B LEU* 4.8 6.5 - - + -
489B LYS 5.7 0.9 - - - +
491B LEU* 3.9 23.6 - - + -
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Residues in contact with SER 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B GLY 3.2 10.6 + - - -
353B ASN* 3.5 9.9 - - - -
355B TYR* 1.3 79.8 - - - +
357B ARG* 1.3 59.7 + - - +
360B ASN* 3.2 11.6 + - - +
488B ARG* 3.0 49.8 + - - +
489B LYS 4.8 7.4 + - - -
490B ILE* 4.9 4.3 - - - +
35D A 3.1 24.2 + - - +
36D U 4.4 12.1 + - - -
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Residues in contact with ARG 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ASN* 2.8 19.0 + - - +
354B LEU* 2.9 39.7 - - - +
356B SER* 1.3 74.2 - - - +
358B VAL* 1.3 64.7 + - + +
361B MET* 3.1 30.6 + - - +
413B ASN* 3.1 31.2 + - - +
416B VAL* 3.6 19.9 - - + +
417B ASP* 4.7 3.2 - - - +
34D C 2.9 50.4 + - - +
35D A 3.4 39.1 + - - +
39D G 3.1 30.1 + - - -
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Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 3.3 27.6 - - + +
355B TYR 3.0 3.0 + - - +
357B ARG* 1.3 82.7 - - + +
359B VAL* 1.3 68.0 + - - +
360B ASN 3.1 1.6 - - - -
361B MET* 3.1 11.0 + - - +
362B ALA* 2.9 20.1 + - - +
416B VAL* 4.4 2.2 - - + -
437B LEU* 5.1 3.8 - - + +
440B LEU* 3.7 33.2 - - + +
441B VAL* 3.8 32.3 - - + +
444B LEU* 3.6 23.6 - - + -
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Residues in contact with VAL 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B TYR 2.9 22.6 + - - +
358B VAL* 1.3 72.4 - - + +
360B ASN* 1.3 63.0 + - - +
362B ALA* 3.2 8.6 - - - +
363B HIS* 2.9 41.4 + - + +
441B VAL* 6.4 0.2 - - + -
444B LEU* 4.0 16.2 - - + -
465B MET* 3.8 26.2 - - + -
466B LEU* 4.9 7.9 - - + -
485B LEU* 4.1 20.9 - - + -
486B GLY 4.5 0.7 - - - +
488B ARG* 4.1 25.6 - - + -
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Residues in contact with ASN 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B SER 3.2 19.1 + - - +
357B ARG 4.0 3.4 - - - +
358B VAL 3.1 1.0 - - - -
359B VAL* 1.3 77.0 - - - +
361B MET* 1.3 69.5 + - - +
363B HIS* 2.7 21.1 + - - +
364B LYS* 2.9 25.1 + - - +
488B ARG* 3.1 32.3 - - - +
34D C 3.4 25.3 + - - +
35D A 3.7 15.5 + - - +
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Residues in contact with MET 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B ARG 3.1 16.8 + - - +
358B VAL* 3.1 9.8 + - - +
360B ASN* 1.3 80.5 + - - +
362B ALA* 1.3 54.1 + - - +
364B LYS* 4.6 2.7 - - - +
365B PHE* 2.7 60.7 + - + +
416B VAL* 4.4 9.6 - - - -
421B PRO* 3.1 37.5 - - + -
422B TRP* 3.2 36.3 - - + +
437B LEU* 3.9 13.0 - - + -
440B LEU* 5.1 1.6 - - - -
34D C 3.5 28.5 - - - +
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Residues in contact with ALA 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B VAL 2.9 12.8 + - - +
359B VAL* 3.2 5.4 - - - +
361B MET* 1.3 78.4 - - - +
363B HIS* 1.3 56.1 + - - +
366B LEU* 3.1 26.0 + - - +
367B GLY 3.2 6.2 + - - -
368B GLY* 3.4 5.8 + - - +
370B VAL* 4.1 14.6 - - + -
437B LEU* 3.9 13.0 - - + +
441B VAL* 4.8 4.5 - - + -
485B LEU* 3.1 35.2 - - + -
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Residues in contact with HIS 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A LYS* 5.9 3.6 + - - -
359B VAL* 2.9 26.8 + - + +
360B ASN* 2.7 18.3 + - - +
362B ALA* 1.3 73.4 - - + +
364B LYS* 1.3 57.6 + - + +
367B GLY* 3.3 19.2 - - - -
368B GLY* 3.7 21.1 + - - +
485B LEU* 3.7 20.3 - - + +
486B GLY 2.7 30.3 + - - -
487B GLU* 4.4 2.6 - - - -
488B ARG* 4.9 10.1 - - + -
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Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B ASN* 2.9 27.2 + - - +
361B MET* 4.3 0.9 - - - +
363B HIS* 1.3 78.7 - - + +
365B PHE* 1.3 85.7 + - + +
367B GLY 4.7 0.2 - - - -
425B ASN* 5.0 0.8 - - - +
426B LYS* 5.7 6.8 - - - +
34D C 4.4 23.7 + - - +
35D A 6.1 0.7 - - - +
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Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B MET* 2.7 49.7 + - + +
364B LYS* 1.3 113.4 - - + +
366B LEU* 1.3 65.9 + - - +
367B GLY 3.5 1.3 + - - -
422B TRP* 3.4 40.6 - - + -
425B ASN* 3.1 34.8 + - + +
426B LYS* 5.4 3.8 - - - -
433B LEU* 3.9 28.8 - - + +
437B LEU* 4.4 5.2 - - + -
34D C 4.4 13.0 - - - -
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B ALA 3.1 11.1 + - - +
365B PHE* 1.3 85.1 - - - +
367B GLY* 1.3 70.8 + - - +
369B GLU* 3.1 26.6 - - - +
370B VAL* 4.4 14.4 - - + -
430B LYS* 5.3 3.1 - - + +
433B LEU* 3.6 23.6 - - + +
434B GLN* 4.1 39.0 - - + +
437B LEU* 4.2 28.3 - - + -
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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