Contacts of the helix formed by residues 418 - 428 (chain t) in PDB entry 6QX2
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 SER 418 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379t HIS* 2.6 36.6 + - - -
412t GLN* 3.9 3.4 - - - +
416t LYS 4.4 0.4 + - - -
417t LEU* 1.3 74.6 - - - +
419t GLU* 1.3 58.6 + - - +
420t LYS* 3.5 5.1 + - - +
421t GLN* 3.0 25.4 + - - +
422t ALA* 3.0 27.4 + - - +
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Residues in contact with GLU 419 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408t MET* 3.4 25.2 - - + +
412t GLN* 3.7 23.8 - - - +
418t SER* 1.3 71.5 - - - +
420t LYS* 1.3 58.9 + - + +
422t ALA 3.3 0.7 + - - -
423t GLN* 3.0 44.2 + - - +
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Residues in contact with LYS 420 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376t ASP* 5.9 8.5 - - + +
379t HIS* 4.6 9.9 - - + +
380t ILE* 3.4 24.7 - - + +
418t SER* 3.3 8.4 + - - +
419t GLU* 1.3 79.7 - - + +
421t GLN* 1.3 55.5 + - - +
423t GLN* 3.6 7.2 + - - +
424t ALA* 3.2 20.6 + - - +
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Residues in contact with GLN 421 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379t HIS* 2.8 58.8 + - + +
380t ILE* 4.3 6.7 - - - -
382t GLU* 3.9 9.1 + - - +
383t GLY* 3.5 27.7 - - - +
386t ILE* 5.4 2.6 - - - +
416t LYS 4.7 1.4 - - - +
417t LEU* 3.5 16.1 - - + +
418t SER* 3.0 35.9 + - - +
420t LYS* 1.3 72.4 - - - +
422t ALA* 1.3 64.7 + - - +
424t ALA* 3.3 5.0 + - - +
425t ILE* 3.1 28.9 + - - +
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Residues in contact with ALA 422 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408t MET* 3.7 37.2 - - + +
411t LEU* 4.2 15.0 - - + +
412t GLN* 4.1 5.6 - - + -
417t LEU* 4.6 4.0 - - + +
418t SER 3.0 16.9 + - - +
419t GLU 3.7 2.0 - - - +
421t GLN* 1.3 73.9 - - - +
423t GLN* 1.3 65.3 + - - +
425t ILE* 3.3 10.6 + - - +
426t LEU* 3.1 27.9 + - - +
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Residues in contact with GLN 423 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431r ARG* 2.7 32.7 + - - +
408t MET* 3.2 29.6 - - + +
419t GLU* 3.0 30.0 + - - +
420t LYS* 3.7 6.7 - - - +
421t GLN 3.3 0.2 - - - -
422t ALA* 1.3 76.7 - - - +
424t ALA* 1.3 55.8 + - - +
426t LEU* 3.2 5.2 + - - +
427t ASP* 3.0 39.0 + - - +
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Residues in contact with ALA 424 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380t ILE* 3.7 32.5 - - + +
384t LEU* 4.1 11.5 - - + +
420t LYS 3.2 12.1 + - - +
421t GLN* 3.4 10.8 - - - +
422t ALA 3.3 0.2 - - - -
423t GLN* 1.3 78.3 - - - +
425t ILE* 1.3 54.8 + - - +
427t ASP* 3.4 8.2 + - - +
428t MET* 3.0 25.1 + - - +
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Residues in contact with ILE 425 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430r LEU* 3.2 23.4 - - + +
383t GLY 3.5 25.8 - - - +
384t LEU* 4.2 9.6 - - + -
387t ALA* 3.6 21.8 - - + -
394t ILE* 3.9 29.4 - - + -
398t ILE* 4.7 0.2 - - + -
411t LEU* 4.5 11.4 - - + -
417t LEU* 3.5 29.8 - - + -
421t GLN 3.1 21.8 + - - +
422t ALA* 3.7 5.6 - - - +
423t GLN 3.3 0.4 - - - -
424t ALA* 1.3 72.1 - - - +
426t LEU* 1.3 65.3 + - - +
427t ASP 3.2 0.2 - - - -
428t MET* 3.3 15.9 - - + +
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Residues in contact with LEU 426 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429r ARG* 3.6 2.6 - - - +
430r LEU* 3.3 9.7 + - - -
431r ARG* 2.9 68.9 + - + +
434r THR* 5.1 0.7 - - + -
398t ILE* 4.0 28.5 - - + -
404t ASP* 4.0 9.9 - - + +
407t ALA* 4.2 10.3 - - + -
408t MET* 3.6 44.9 - - + +
411t LEU* 4.1 5.8 - - + -
422t ALA 3.1 11.4 + - - +
423t GLN* 3.2 11.9 + - - +
425t ILE* 1.3 76.0 - - - +
427t ASP* 1.3 57.9 + - - +
428t MET 3.4 0.2 - - - -
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Residues in contact with ASP 427 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429r ARG* 2.7 42.6 + - - +
431r ARG* 3.3 28.1 + - - -
423t GLN* 3.0 25.6 + - - +
424t ALA* 3.6 8.1 - - - +
425t ILE 3.2 0.2 - - - -
426t LEU* 1.3 73.5 - - - +
428t MET* 1.3 66.5 + - - +
429t ARG* 3.5 6.2 + - - +
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Residues in contact with MET 428 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429r ARG* 3.2 1.0 - - - -
430r LEU* 3.0 38.3 + - + +
384t LEU* 3.8 35.9 - - + +
387t ALA* 3.9 26.5 - - + -
388t LEU* 5.2 3.8 - - - +
391t ILE* 5.3 1.3 - - + -
424t ALA 3.0 10.2 + - - +
425t ILE* 3.3 21.0 + - + +
427t ASP* 1.3 77.0 - - - +
429t ARG* 1.3 72.3 + - - +
432t ARG* 3.8 20.9 - - + +
433t LEU* 5.0 15.7 - - + -
441t ILE* 5.4 5.6 - - - -
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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