Contacts of the helix formed by residues 418 - 428 (chain r) 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 r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379r HIS* 2.6 36.5 + - - -
412r GLN* 3.9 2.7 - - - -
416r LYS 4.4 0.2 + - - -
417r LEU* 1.3 75.5 - - - +
419r GLU* 1.3 59.5 + - - +
420r LYS* 3.5 4.9 + - - +
421r GLN* 3.0 25.0 + - - +
422r ALA* 3.0 27.9 + - - +
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Residues in contact with GLU 419 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408r MET* 3.3 24.8 - - + +
412r GLN* 3.7 23.8 + - - +
418r SER* 1.3 71.3 - - - +
420r LYS* 1.3 59.3 + - + +
422r ALA 3.3 0.5 + - - -
423r GLN* 3.0 32.0 + - + +
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Residues in contact with LYS 420 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376r ASP* 5.9 8.1 - - + -
379r HIS* 4.6 8.7 - - + -
380r ILE* 3.4 25.4 - - + +
418r SER* 3.3 8.2 + - - +
419r GLU* 1.3 80.4 - - + +
421r GLN* 1.3 55.4 + - - +
423r GLN* 3.6 6.4 + - - +
424r ALA* 3.2 20.4 + - - +
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Residues in contact with GLN 421 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379r HIS* 2.8 56.7 + - + +
380r ILE* 4.3 3.6 - - - +
382r GLU* 3.9 9.7 + - - +
383r GLY* 3.5 27.7 - - - +
386r ILE* 5.5 2.2 - - - +
416r LYS 4.7 1.2 - - - +
417r LEU* 3.6 15.7 - - + +
418r SER* 3.0 36.6 + - - +
420r LYS* 1.3 72.9 - - - +
422r ALA* 1.3 60.4 + - - +
424r ALA* 3.3 7.4 + - - +
425r ILE* 3.1 33.7 + - - +
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Residues in contact with ALA 422 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408r MET* 3.7 37.2 - - + +
411r LEU* 4.2 14.4 - - + +
412r GLN* 4.1 5.4 - - + -
417r LEU* 4.6 4.0 - - + +
418r SER 3.0 17.2 + - - +
419r GLU 3.7 2.0 - - - +
421r GLN* 1.3 71.2 - - - +
423r GLN* 1.3 64.4 + - - +
425r ILE* 3.3 12.0 + - - +
426r LEU* 3.1 27.9 + - - +
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Residues in contact with GLN 423 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408r MET* 3.4 25.0 - - + +
419r GLU* 3.0 18.4 + - + +
420r LYS* 3.7 7.9 - - - +
422r ALA* 1.3 75.4 - - - +
424r ALA* 1.3 55.6 + - - +
426r LEU* 3.2 3.1 + - - +
427r ASP* 3.0 49.0 + - - +
431t ARG* 2.1 36.8 + - - +
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Residues in contact with ALA 424 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380r ILE* 3.7 32.5 - - + +
384r LEU* 4.1 12.5 - - + +
420r LYS 3.2 15.0 + - - +
421r GLN* 3.4 9.9 - - - +
422r ALA 3.3 0.2 - - - -
423r GLN* 1.3 75.5 - - - +
425r ILE* 1.3 56.6 + - - +
427r ASP* 3.3 8.7 + - - +
428r MET* 3.0 25.3 + - - +
432r ARG* 5.1 2.6 + - - -
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Residues in contact with ILE 425 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383r GLY 3.5 24.0 - - - +
384r LEU* 4.2 9.0 - - + -
387r ALA* 3.7 22.4 - - + -
394r ILE* 3.9 20.4 - - + -
398r ILE* 4.6 0.9 - - + -
411r LEU* 4.5 11.0 - - + -
417r LEU* 3.6 29.6 - - + -
421r GLN 3.1 21.3 + - - +
422r ALA* 3.8 5.2 - - - +
423r GLN 3.3 0.4 - - - -
424r ALA* 1.3 72.4 - - - +
426r LEU* 1.3 66.5 + - - +
427r ASP 3.2 0.4 - - - -
428r MET* 3.3 15.5 - - + +
430t LEU* 3.2 33.4 - - + +
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Residues in contact with LEU 426 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398r ILE* 4.0 31.0 - - + -
404r ASP* 4.0 10.8 - - + +
407r ALA* 4.2 7.6 - - + -
408r MET* 3.6 45.1 - - + +
411r LEU* 4.1 5.8 - - + -
422r ALA 3.1 10.7 + - - +
423r GLN 3.2 4.0 + - - +
425r ILE* 1.3 75.5 - - - +
427r ASP* 1.3 57.6 + - - +
429t ARG* 3.4 2.9 - - - +
430t LEU* 3.3 7.9 + - - -
431t ARG* 2.9 78.6 + - + +
434t THR* 5.1 1.1 - - + -
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Residues in contact with ASP 427 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423r GLN* 3.0 35.1 + - - +
424r ALA* 3.6 8.9 + - - +
425r ILE 3.2 0.2 - - - -
426r LEU* 1.3 72.5 - - - +
428r MET* 1.3 66.5 + - - +
429r ARG* 3.5 2.8 + - - +
432r ARG* 5.5 0.8 + - - -
429t ARG* 3.2 35.9 + - - +
431t ARG* 3.1 22.5 + - - -
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Residues in contact with MET 428 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384r LEU* 3.8 29.4 - - + -
387r ALA* 3.9 24.2 - - + -
388r LEU* 4.1 25.4 - - + -
391r ILE* 5.5 2.9 - - + -
424r ALA 3.0 10.2 + - - +
425r ILE* 3.3 21.2 + - + +
427r ASP* 1.3 76.2 - - - +
429r ARG* 1.3 71.8 + - - +
432r ARG* 3.9 33.2 - - + +
433r LEU* 4.6 6.7 - - + -
441r ILE* 5.2 1.6 - - - -
429t ARG* 3.2 2.3 - - - -
430t LEU* 3.0 38.5 + - + +
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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
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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