Contacts of the helix formed by residues 437 - 452 (chain F) in PDB entry 6X34
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 PRO 437 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413F HIS* 3.8 38.1 - - + +
414F PHE* 5.7 2.4 - - + -
435F ALA 4.3 3.1 - - - +
436F LEU* 1.3 83.6 - - + +
438F LEU* 1.3 64.1 + - - +
439F GLU 3.2 2.7 - - - +
440F GLY* 4.5 9.2 - - - +
441F VAL* 3.2 23.6 + - + +
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Residues in contact with LEU 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436F LEU* 2.7 28.6 + - + +
437F PRO* 1.3 72.5 - - - +
439F GLU* 1.3 60.1 + - - +
441F VAL* 3.2 10.9 - - - +
442F ILE* 3.2 26.5 - - - +
510F GLU* 5.0 5.2 - - + +
511F ALA* 3.9 23.8 - - + -
514F SER* 5.2 6.3 - - - -
518F ILE* 4.4 7.6 - - + -
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Residues in contact with GLU 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437F PRO 3.2 0.8 - - - -
438F LEU* 1.3 78.0 - - - +
440F GLY* 1.3 60.7 + - - +
442F ILE* 3.4 6.7 + - - +
443F LEU* 2.9 30.1 + - - +
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Residues in contact with GLY 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F GLY 3.8 10.0 - - - +
44F ASN* 5.0 7.8 + - - -
410F LEU* 6.4 0.2 - - - -
437F PRO* 3.4 14.8 + - - +
439F GLU* 1.3 79.6 - - - +
441F VAL* 1.3 56.2 + - - +
443F LEU* 3.3 8.6 + - - +
444F SER* 2.9 28.8 + - - -
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Residues in contact with VAL 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410F LEU* 5.7 8.5 - - + +
411F TYR* 4.9 10.5 - - + -
414F PHE* 4.3 37.5 - - + -
437F PRO* 3.2 15.9 + - + +
438F LEU* 3.2 20.2 - - - +
440F GLY* 1.3 75.1 - - - +
442F ILE* 1.3 67.8 + - + +
444F SER* 2.5 23.3 + - - +
445F LEU* 2.9 35.6 + - + +
518F ILE* 4.8 6.5 - - + -
522F LEU* 5.6 3.8 - - + -
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Residues in contact with ILE 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438F LEU 3.2 19.5 - - - +
439F GLU* 3.4 6.9 + - - +
440F GLY 3.3 0.6 - - - -
441F VAL* 1.3 78.1 - - + +
443F LEU* 1.3 58.9 + - - +
445F LEU* 3.3 10.3 + - + +
446F GLN* 2.9 55.4 + - + +
514F SER* 4.3 18.8 - - - +
517F GLU* 4.7 13.0 - - + -
518F ILE* 3.6 33.0 - - + -
521F LEU* 5.0 6.7 - - + +
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Residues in contact with LEU 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F GLY 3.4 20.9 - - - +
44F ASN* 4.7 0.7 - - - -
45F ARG* 4.4 20.6 - - + +
439F GLU 2.9 17.7 + - - +
440F GLY* 3.6 6.7 - - - +
442F ILE* 1.3 79.5 - - - +
444F SER* 1.3 56.5 + - - +
446F GLN* 3.3 12.1 + - + +
447F ASP* 2.9 61.1 + - - +
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Residues in contact with SER 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F PHE 5.3 0.4 - - - -
43F GLY* 3.6 23.5 - - - +
407F THR* 5.8 7.9 - - - -
410F LEU* 4.8 14.2 - - - +
411F TYR* 5.6 1.5 - - - -
440F GLY 2.9 15.0 + - - -
441F VAL* 2.5 29.6 + - - +
443F LEU* 1.3 76.6 - - - +
445F LEU* 1.3 58.7 + - - +
447F ASP* 3.3 2.1 + - - +
448F LEU* 2.9 31.4 + - - +
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Residues in contact with LEU 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411F TYR* 3.2 40.4 - - + +
441F VAL* 2.9 33.7 + - + +
442F ILE* 3.8 7.2 - - + +
444F SER* 1.3 78.6 + - - +
446F GLN* 1.3 59.0 + - - +
448F LEU* 3.2 4.6 + - - +
449F ILE* 2.9 35.8 + - + +
518F ILE* 4.6 3.1 - - + +
521F LEU* 3.6 33.4 - - + +
522F LEU* 3.5 33.7 - - + +
525F ILE* 4.6 10.5 - - + -
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Residues in contact with GLN 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442F ILE* 2.9 39.4 + - - +
443F LEU* 3.8 12.4 - - + +
444F SER 3.3 0.2 - - - -
445F LEU* 1.3 76.5 - - - +
447F ASP* 1.3 63.4 + - - +
449F ILE* 4.0 3.6 + - - +
450F GLY* 3.8 13.2 + - - -
521F LEU* 3.8 29.3 - - + +
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Residues in contact with ASP 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F GLY 5.0 1.9 - - - +
42F PHE* 4.9 19.7 - - + -
43F GLY 3.8 18.2 + - - +
443F LEU* 2.9 44.4 + - - +
444F SER 3.9 2.7 - - - +
446F GLN* 1.3 80.6 - - - +
448F LEU* 1.3 61.9 + - - +
449F ILE 3.4 0.2 - - - -
450F GLY* 3.8 2.5 + - - -
451F TYR* 3.6 17.7 + - - +
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Residues in contact with LEU 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F PHE* 6.0 0.4 - - - -
403F MET* 5.3 8.3 - - + -
407F THR* 5.9 6.3 - - - +
411F TYR* 6.0 0.4 - - - +
444F SER 2.9 18.4 + - - +
445F LEU* 3.9 3.1 - - - +
447F ASP* 1.3 77.2 - - - +
449F ILE* 1.3 65.1 + - - +
450F GLY 3.3 0.2 - - - -
451F TYR* 3.3 12.6 + - - +
452F PHE* 3.4 30.0 - - + -
478F PHE* 6.2 2.5 - - + -
525F ILE* 4.4 17.3 - - + -
529F LEU* 5.6 0.2 - - - +
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Residues in contact with ILE 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445F LEU 2.9 17.0 + - - +
446F GLN* 4.4 4.7 - - - +
448F LEU* 1.3 77.8 - - - +
450F GLY* 1.3 61.4 + - - +
452F PHE* 3.0 28.9 + - - +
453F GLU* 4.5 2.1 - - - +
521F LEU* 3.7 30.5 - - + +
524F GLU* 3.8 13.7 - - + -
525F ILE* 3.7 43.3 - - + +
528F SER* 4.6 10.3 - - - +
529F LEU* 6.1 0.4 - - - -
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Residues in contact with GLY 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446F GLN 3.8 11.0 + - - -
447F ASP 3.8 3.3 + - - -
448F LEU 3.3 0.4 - - - -
449F ILE* 1.3 81.1 - - - +
451F TYR* 1.3 60.9 + - - +
452F PHE 3.4 0.2 - - - -
453F GLU* 3.9 16.1 - - - +
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Residues in contact with TYR 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F PHE* 4.7 11.9 - + + -
396F GLU* 5.3 4.3 + - - +
399F GLN* 5.8 2.3 - - - +
400F ALA* 5.1 11.4 + - + +
403F MET* 3.6 35.7 - - + -
447F ASP 3.6 12.3 + - - +
448F LEU 3.3 9.5 + - - +
449F ILE 3.2 1.0 - - - -
450F GLY* 1.3 79.2 - - - +
452F PHE* 1.3 84.7 + + - +
453F GLU 3.5 3.5 + - - -
474F ARG* 3.3 61.1 + - + +
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Residues in contact with PHE 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403F MET* 4.6 8.3 - - + -
448F LEU* 3.4 26.9 + - + +
449F ILE* 3.0 15.9 + - - +
451F TYR* 1.3 102.8 - + - +
453F GLU* 1.3 58.7 + - - +
454F PRO* 4.4 2.3 - - - +
471F LEU* 4.4 20.9 - - + -
474F ARG* 3.6 36.3 - - + +
475F GLN* 5.0 3.4 - - + +
478F PHE* 3.5 41.5 - + - -
525F ILE* 6.4 0.2 - - + -
528F SER* 4.4 19.0 - - - +
529F LEU* 4.3 31.6 - - + -
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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