Contacts of the helix formed by residues 415 - 425 (chain B) in PDB entry 5KJH
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 415 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414B PRO* 1.4 65.1 + - - -
416B GLN* 1.3 59.3 + - + +
417B LYS 3.3 2.0 - - - -
418B SER* 3.2 17.6 + - - -
419B ASN* 2.9 62.9 + - - +
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Residues in contact with GLN 416 (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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413B THR* 2.9 49.2 + - - +
415B GLN* 1.3 72.4 - - + +
417B LYS* 1.4 60.3 + - - +
419B ASN* 3.4 11.9 + - - +
420B LEU* 3.2 17.3 + - - +
464B MET* 6.4 1.8 - - - +
473B PHE* 3.5 56.4 - - + +
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Residues in contact with LYS 417 (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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402B MET 4.2 6.1 - - - -
403B ALA* 3.4 29.0 - - + +
405B GLN 2.8 29.5 + - - -
406B PRO* 3.6 4.6 - - - +
407B GLU* 3.1 36.3 + - - +
413B THR 4.7 6.5 - - - +
414B PRO* 3.9 30.4 - - + +
415B GLN 3.3 0.4 - - - -
416B GLN* 1.4 75.1 - - + +
418B SER* 1.3 58.9 + - - +
420B LEU* 3.7 9.1 + - + +
421B LEU* 3.2 37.3 + - + +
460B ARG* 4.3 2.9 - - - +
473B PHE* 5.4 1.6 - - + -
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Residues in contact with SER 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B PRO* 4.8 4.5 - - - +
415B GLN* 3.2 27.3 + - - +
417B LYS* 1.3 76.3 - - - +
419B ASN* 1.3 54.9 + - - +
421B LEU* 3.3 7.9 + - - +
422B ASP* 2.9 50.2 + - - -
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Residues in contact with ASN 419 (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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415B GLN* 2.9 54.4 + - - +
416B GLN* 3.5 14.4 - - - +
418B SER* 1.3 76.7 - - - +
420B LEU* 1.3 60.5 + - - +
422B ASP* 3.5 23.5 + - - +
423B THR* 3.6 15.2 + - - +
472B ILE* 3.9 26.5 - - + +
473B PHE* 5.8 0.9 - - - -
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Residues in contact with LEU 420 (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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399B ILE* 3.8 25.1 - - + -
402B MET* 3.9 18.6 - - + -
403B ALA* 3.9 19.1 - - + -
416B GLN 3.2 11.9 + - - +
417B LYS* 3.8 8.7 - - + +
418B SER 3.3 0.4 - - - -
419B ASN* 1.3 75.6 - - - +
421B LEU* 1.4 59.6 + - - +
423B THR* 3.2 8.5 + - - -
424B TYR* 2.9 53.3 + - + -
464B MET* 5.8 0.2 - - - -
469B VAL* 4.3 19.1 - - + +
472B ILE* 4.3 16.7 + - + +
473B PHE* 4.3 16.6 - - + -
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Residues in contact with LEU 421 (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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400B ARG* 4.4 4.5 - - + +
403B ALA* 3.9 31.6 - - + +
404B SER* 4.0 11.7 - - - +
417B LYS* 3.2 23.5 + - + +
418B SER* 3.9 5.8 - - - +
420B LEU* 1.4 75.0 - - - +
422B ASP* 1.4 58.1 + - - +
424B TYR* 4.5 1.8 - - + -
425B SER* 2.8 42.7 + - - +
426B ASP* 3.4 26.0 - - - +
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Residues in contact with ASP 422 (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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418B SER* 2.9 39.5 + - - +
419B ASN* 3.5 17.7 + - - +
420B LEU 3.2 0.2 - - - -
421B LEU* 1.4 77.8 - - - +
423B THR* 1.4 62.4 + - + +
425B SER* 4.8 0.9 + - - -
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Residues in contact with THR 423 (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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419B ASN 3.6 13.5 + - - +
420B LEU 3.2 8.1 + - - -
422B ASP* 1.4 81.5 - - + +
424B TYR* 1.3 73.7 + - - +
425B SER* 5.4 0.3 - - - -
472B ILE* 3.7 28.5 - - + +
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Residues in contact with TYR 424 (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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396B SER* 3.6 42.7 + - - -
399B ILE* 3.5 26.1 - - + +
400B ARG* 2.8 44.4 + - + -
403B ALA* 6.5 0.4 - - + -
420B LEU* 2.9 37.9 + - + +
421B LEU* 4.5 1.1 - - + -
423B THR* 1.3 93.5 - - - +
425B SER* 1.4 71.4 + - - +
468B ASN* 2.7 45.5 + - + +
472B ILE* 4.2 1.6 - - + -
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Residues in contact with SER 425 (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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400B ARG* 3.4 13.5 + - - +
421B LEU* 2.8 39.3 + - - +
422B ASP 4.7 1.0 + - - -
423B THR 3.7 1.4 - - - -
424B TYR* 1.4 80.2 + - - +
426B ASP* 1.3 70.6 + - - +
427B ASP* 3.4 16.6 + - - +
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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