Contacts of the helix formed by residues 441 - 456 (chain B) in PDB entry 5DKG
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 GLN 441 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B TRP* 3.8 2.0 - - - -
439B ASN* 2.9 44.0 + - - +
440B LEU* 1.3 78.1 + - - +
442B GLY* 1.3 62.1 + - - +
443B GLU* 3.2 15.2 - - + +
444B GLU* 3.0 30.3 + - + +
445B PHE* 2.8 27.7 + - - +
493B ALA* 6.5 0.7 - - + -
503B ARG* 5.0 1.3 - - - +
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Residues in contact with GLY 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU* 4.6 6.1 - - - -
393B TRP* 3.5 27.8 - - - -
441B GLN* 1.3 72.8 + - - +
443B GLU* 1.3 66.5 + - - +
445B PHE* 3.2 3.7 + - - +
446B VAL* 3.1 31.6 + - - +
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Residues in contact with GLU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B VAL* 3.6 24.1 - - + +
320B LEU* 4.2 15.9 - - + +
441B GLN* 3.7 14.1 - - + +
442B GLY* 1.3 82.7 + - - +
444B GLU* 1.3 58.8 + - + +
446B VAL* 3.2 22.5 - - - +
447B CYS* 3.3 17.3 - - - -
489B LEU* 3.6 29.1 - - + +
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Residues in contact with GLU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B LEU* 3.7 11.2 - - + +
441B GLN* 3.0 33.8 + - + +
443B GLU* 1.3 78.9 - - + +
445B PHE* 1.3 58.3 + - - +
447B CYS* 3.2 3.8 + - - +
448B LEU* 3.0 33.5 + - - +
486B LEU* 4.1 16.8 - - + +
489B LEU* 4.4 16.8 - - + +
490B MET* 3.8 19.2 - - - +
503B ARG* 2.9 46.3 + - - -
507B LEU* 4.3 7.2 - - + -
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Residues in contact with PHE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B GLU* 3.6 22.7 - - - -
389B ILE* 3.5 44.9 - - + -
390B GLY* 4.0 9.6 - - - -
393B TRP* 3.5 56.1 - + + -
435B PHE* 5.4 0.2 - + - -
440B LEU* 3.9 13.0 - - + +
441B GLN 2.8 13.0 + - - +
442B GLY* 3.2 6.7 + - - +
444B GLU* 1.3 77.8 - - - +
446B VAL* 1.3 66.7 + - + +
448B LEU* 3.3 5.7 + - - +
449B LYS* 2.9 50.3 + - + +
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Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B VAL* 4.9 2.9 - - + +
319B LEU* 3.8 32.6 - - + +
320B LEU* 4.0 17.7 - - + -
323B GLU* 3.8 35.4 - - + +
360B TRP* 5.4 0.9 - - - -
442B GLY 3.1 13.9 + - - +
443B GLU* 3.2 23.6 - - - +
445B PHE* 1.3 82.0 - - + +
447B CYS* 1.3 62.3 + - - +
449B LYS* 3.6 8.5 + - - +
450B SER* 3.0 26.3 + - - -
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Residues in contact with CYS 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B MET* 5.3 0.2 - - - -
316B VAL* 5.1 2.0 - - - -
319B LEU* 4.1 12.8 - - - -
443B GLU 3.3 17.5 - - - -
444B GLU 3.2 9.3 + - - +
446B VAL* 1.3 82.8 - - - +
448B LEU* 1.3 56.8 + - - +
450B SER* 2.9 19.7 + - - -
451B ILE* 3.0 22.4 + - - +
482B ILE* 3.7 18.2 - - + +
485B THR* 3.8 30.1 - - - -
486B LEU* 3.6 23.3 - - + -
489B LEU* 4.2 3.4 - - - -
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Residues in contact with LEU 448 (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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389B ILE* 4.0 10.8 - - + -
435B PHE* 4.4 18.6 - - + -
440B LEU* 4.1 13.9 - - + -
444B GLU 3.0 16.8 + - - +
445B PHE* 3.5 7.6 - - - +
447B CYS* 1.3 77.4 - - - +
449B LYS* 1.3 63.1 + - - +
451B ILE* 3.2 10.5 + - + +
452B ILE* 3.1 28.1 + - - +
486B LEU* 4.7 4.9 - - + -
507B LEU* 4.0 49.1 - - + +
508B LEU* 4.1 16.8 - - + -
511B LEU* 4.0 20.2 - - + +
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Residues in contact with LYS 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B GLU* 2.7 39.0 + - - -
324B PRO* 3.8 17.2 - - - +
360B TRP* 3.8 25.9 - - + +
386B ILE* 3.8 33.9 - - + +
389B ILE* 4.0 17.7 - - + +
390B GLY* 5.2 1.7 - - - +
445B PHE* 2.9 38.7 + - + +
446B VAL* 4.0 6.1 - - - +
447B CYS 3.3 0.2 - - - -
448B LEU* 1.3 76.6 - - - +
450B SER* 1.3 60.6 + - - +
452B ILE* 3.5 12.2 + - - +
453B LEU 3.3 15.2 + - - -
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Residues in contact with SER 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.7 13.3 - - - +
360B TRP* 4.3 11.9 - - - -
364B VAL* 3.8 24.5 - - - -
446B VAL 3.0 12.9 + - - -
447B CYS* 2.9 18.5 + - - -
449B LYS* 1.3 76.3 - - - +
451B ILE* 1.3 64.9 + - - +
453B LEU* 3.4 4.9 + - - +
454B LEU* 3.2 28.2 + - - +
482B ILE* 3.6 15.9 - - - +
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Residues in contact with ILE 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A LEU* 3.7 27.4 - - + -
447B CYS 3.0 20.5 + - - +
448B LEU* 3.2 10.7 + - - +
450B SER* 1.3 77.2 - - - +
452B ILE* 1.3 52.5 + - - +
454B LEU* 3.2 1.0 + - - -
455B ASN* 2.7 40.0 + - + +
479B LEU* 4.0 14.4 - - + +
482B ILE* 3.6 29.4 - - + -
483B THR* 5.2 5.4 - - - +
486B LEU* 3.8 22.0 - - + -
508B LEU* 4.0 14.4 - - + -
511B LEU* 3.7 21.1 - - + -
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Residues in contact with ILE 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ALA* 3.9 2.6 - - + +
385B GLU* 3.7 26.7 - - + +
386B ILE* 4.0 12.8 - - + -
389B ILE* 3.8 40.2 - - + -
448B LEU 3.1 11.1 + - - +
449B LYS* 3.5 8.1 - - - +
450B SER 3.3 0.2 - - - -
451B ILE* 1.3 77.2 - - - +
453B LEU* 1.3 63.4 + - - +
455B ASN* 4.7 1.3 - - - +
456B SER* 3.0 46.2 + - - +
511B LEU* 3.8 26.2 - - + -
514B ILE* 4.3 16.8 - - + -
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B TRP* 3.7 18.8 - - + -
361B ALA* 3.7 28.5 - - + -
364B VAL* 4.1 13.7 - - + -
367B PHE* 3.8 28.7 - - + -
378B LEU* 3.6 30.6 - - - +
379B LEU* 3.7 30.3 - - + -
382B ALA* 4.2 5.6 - - - -
386B ILE* 4.0 8.7 - - + +
449B LYS 3.3 10.8 + - - +
450B SER 3.6 7.9 - - - +
452B ILE* 1.3 81.2 - - - +
454B LEU* 1.3 61.6 + - + +
456B SER 4.5 0.7 + - - -
457B GLY 4.9 0.3 + - - -
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Residues in contact with LEU 454 (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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364B VAL* 4.7 6.7 - - + -
365B PRO 4.5 4.5 - - - +
366B GLY 5.3 1.6 - - - -
367B PHE* 4.2 33.7 - - + +
370B LEU* 4.6 7.0 - - + -
378B LEU* 4.0 16.3 - - + +
450B SER 3.2 17.7 + - - +
453B LEU* 1.3 78.4 - - + +
455B ASN* 1.3 62.8 + - - +
458B VAL* 3.6 10.4 - - - +
475B ILE* 3.3 32.0 - - + +
478B VAL* 3.6 35.0 - - + -
479B LEU* 3.8 16.6 - - + -
482B ILE* 4.1 12.8 - - + -
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Residues in contact with ASN 455 (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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509A LEU* 3.5 43.7 + - - +
512A SER* 4.1 14.8 + - - -
513A HIS 5.5 0.2 - - - +
451B ILE* 2.7 31.6 + - + +
452B ILE* 4.4 2.2 - - - +
454B LEU* 1.3 72.6 - - - +
456B SER* 1.3 63.0 + - - +
457B GLY 2.8 10.7 + - - -
458B VAL* 3.0 25.0 + - - +
459B TYR* 3.5 29.4 + - - -
479B LEU* 4.3 12.0 - - + +
511B LEU* 5.5 2.0 - - - +
515B ARG* 4.8 1.2 + - - +
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Residues in contact with SER 456 (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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512A SER* 4.9 1.4 + - - -
513A HIS* 5.6 2.3 + - - -
381B CYS* 4.1 9.7 - - - +
382B ALA* 4.0 15.3 - - - -
385B GLU* 2.6 36.2 + - - -
452B ILE* 3.0 25.4 + - - +
455B ASN* 1.3 77.7 + - - +
457B GLY* 1.3 56.5 + - - +
459B TYR* 5.4 1.9 + - - -
460B THR* 5.1 3.1 - - - +
515B ARG* 3.1 35.5 + - - +
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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
------------------------------------------------------------
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