Contacts of the helix formed by residues 455 - 466 (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 THR 455 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B ASP* 3.4 39.3 - - + +
320B TYR* 4.0 10.1 - - + -
451B LEU* 2.8 26.3 + - + +
452B TYR 3.4 2.5 - - - -
454B ILE* 1.3 94.9 - - + +
456B PRO* 1.3 65.2 - - - +
457B ASN 3.4 0.3 + - - -
458B LYS* 3.6 1.8 + - - -
459B MET* 3.1 30.5 + - - +
492B PHE* 4.5 19.3 - - + -
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Residues in contact with PRO 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 3.7 40.2 - - - +
88B LYS* 5.9 0.4 - - + +
316B ASP* 3.5 6.7 - - - +
319B ARG* 3.7 17.3 - - - +
452B TYR* 2.9 34.0 - - + +
453B PRO 3.5 4.7 - - - +
454B ILE 3.3 9.0 - - - +
455B THR* 1.3 87.6 - - - +
457B ASN* 1.3 74.5 + - - +
459B MET* 3.3 1.7 + - - +
460B LYS* 2.9 28.3 + - - +
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Residues in contact with ASN 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 5.8 1.2 + - - -
88B LYS* 3.1 31.6 - - - +
315B LEU* 3.1 29.4 - - - +
316B ASP* 2.9 31.2 + - - +
319B ARG* 4.8 2.0 - - - +
456B PRO* 1.3 83.8 - - - +
458B LYS* 1.3 61.1 + - + +
460B LYS* 3.2 22.8 + - - +
461B GLU* 3.2 18.1 + - - +
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Residues in contact with LYS 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 6.0 0.2 - - - +
308A GLU* 4.9 9.9 - - - +
311A GLN* 3.2 23.6 - - - +
316B ASP* 3.0 30.6 + - + +
317B GLU* 3.6 26.9 + - - -
455B THR* 3.6 5.3 + - - +
456B PRO 3.4 0.2 - - - -
457B ASN* 1.3 75.9 - - + +
459B MET* 1.3 62.2 + - - +
461B GLU* 3.0 26.6 + - - +
462B ALA* 2.9 24.9 + - - +
491B LEU* 3.0 37.1 + - + +
492B PHE* 3.9 23.6 - - + -
493B PRO* 3.8 8.5 - - - +
495B ARG* 4.9 7.5 - - - +
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Residues in contact with MET 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B TYR* 2.9 31.9 - - - +
447B LEU 3.6 1.6 - - - +
448B THR* 2.9 43.6 - - + +
451B LEU* 3.4 39.3 - - + -
452B TYR* 3.6 21.1 - - + +
455B THR* 3.1 22.7 + - - +
456B PRO 3.9 2.0 - - - +
458B LYS* 1.3 78.3 - - - +
460B LYS* 1.3 60.5 + - - +
462B ALA* 3.6 6.7 - - - -
463B LEU* 3.0 24.6 + - - +
471B PHE* 3.8 3.8 - - + -
491B LEU* 5.2 3.4 - - - -
492B PHE* 5.8 3.6 - - - -
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Residues in contact with LYS 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 4.5 3.3 - - - +
90B GLU* 3.9 19.4 + - - -
452B TYR* 4.0 26.1 + - - -
456B PRO* 2.9 13.7 + - - +
457B ASN* 3.4 16.4 + - - +
458B LYS 3.1 0.4 - - - -
459B MET* 1.3 77.2 - - - +
461B GLU* 1.3 64.1 + - + +
463B LEU* 3.7 14.1 - - + +
464B GLN* 3.7 8.7 + - - +
471B PHE* 4.2 20.0 - - + -
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Residues in contact with GLU 461 (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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311A GLN* 2.9 63.6 - - - +
312A GLU* 4.9 5.9 - - + +
457B ASN* 3.2 15.6 + - - +
458B LYS* 3.0 24.4 + - - +
460B LYS* 1.3 75.8 - - - +
462B ALA* 1.3 66.5 + - - +
464B GLN* 3.0 20.3 + - - +
465B MET* 3.1 11.8 + - - +
489B LYS* 4.2 12.4 + - + +
491B LEU* 3.7 16.9 - - + +
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Residues in contact with ALA 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B TYR* 3.9 26.7 - - + -
448B THR* 4.0 9.6 - - + +
458B LYS 2.9 12.2 + - - +
459B MET* 3.6 13.2 - - - +
461B GLU* 1.3 76.4 - - - +
463B LEU* 1.3 56.4 + - - +
465B MET* 2.6 37.1 + - - +
466B LEU* 2.8 14.8 + - - +
491B LEU* 4.0 12.3 - - + +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B PHE* 3.9 31.0 - - + -
448B THR* 4.1 7.7 - - + +
449B HIS* 5.0 0.4 - - - +
459B MET 3.0 14.5 + - - +
460B LYS* 3.7 9.6 - - + +
462B ALA* 1.3 78.2 - - - +
464B GLN* 1.3 59.9 + - - +
466B LEU* 3.4 6.7 + - - +
467B GLY 3.2 3.1 + - - -
468B GLU* 2.9 37.9 + - + +
469B LYS 3.9 8.3 - - - +
470B GLU 3.8 24.9 - - - +
471B PHE* 3.6 48.0 - - + -
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Residues in contact with GLN 464 (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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312A GLU 5.4 2.2 + - - -
493A PRO* 4.7 9.6 - - + +
495A ARG* 3.6 48.4 + - - +
497A GLY* 6.1 1.8 - - - +
460B LYS 3.7 7.6 + - - +
461B GLU* 3.0 12.8 + - - +
462B ALA 2.9 1.4 - - - -
463B LEU* 1.3 77.5 - - - +
465B MET* 1.3 59.5 + - - +
466B LEU 3.0 1.6 - - - -
467B GLY* 2.7 22.5 + - - -
468B GLU 3.9 8.7 - - - +
486B GLY* 4.0 7.7 - - - -
489B LYS* 5.3 5.5 - - - +
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Residues in contact with MET 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B TYR* 4.4 15.0 - - + -
359B VAL* 3.8 27.8 - - + +
461B GLU 3.1 7.7 + - - +
462B ALA* 2.6 16.8 + - - +
464B GLN* 1.3 72.9 - - - +
466B LEU* 1.3 55.8 + - + +
485B LEU* 3.6 6.4 - - - +
486B GLY* 2.6 27.7 + - - +
487B GLU 3.1 27.6 - - - +
488B ARG* 4.2 5.6 - - - -
489B LYS* 3.5 44.4 - - + +
491B LEU* 3.8 33.2 - - + -
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B TYR* 4.8 6.7 - - + -
359B VAL* 4.9 3.4 - - + -
441B VAL* 4.4 7.9 - - + +
444B LEU* 3.9 30.1 - - + -
445B PHE* 3.4 47.1 - - + +
448B THR* 3.7 16.2 - - - +
462B ALA 2.8 13.3 + - - +
463B LEU* 3.5 12.6 - - - +
465B MET* 1.3 79.5 - - + +
467B GLY* 1.3 59.4 + - - +
468B GLU* 3.3 11.9 + - + +
483B TYR* 4.5 7.9 - - + -
484B LYS 3.4 13.0 + - - +
485B LEU* 3.6 27.1 - - + +
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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