Contacts of the helix formed by residues 437 - 452 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413B HIS* 3.8 38.1 - - + +
414B PHE* 5.7 2.2 - - + -
435B ALA 4.3 2.7 - - - +
436B LEU* 1.3 85.5 - - + +
438B LEU* 1.3 64.7 + - - +
439B GLU 3.2 4.0 + - - +
440B GLY* 4.5 10.5 - - - +
441B VAL* 3.2 23.2 + - + +
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Residues in contact with LEU 438 (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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436B LEU* 2.7 28.3 + - + +
437B PRO* 1.3 72.2 - - - +
439B GLU* 1.3 61.0 + - - +
441B VAL* 3.2 9.9 - - - +
442B ILE* 3.2 26.4 - - - +
510B GLU* 5.0 5.4 - - + +
511B ALA* 3.9 23.8 - - + -
514B SER* 5.2 6.5 - - - -
518B ILE* 4.4 7.6 - - + +
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Residues in contact with GLU 439 (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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437B PRO* 3.2 0.8 - - - +
438B LEU* 1.3 77.7 - - - +
440B GLY* 1.3 59.7 + - - +
442B ILE* 3.4 8.1 + - - +
443B LEU* 2.9 30.4 + - - +
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Residues in contact with GLY 440 (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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43B GLY 3.8 9.8 - - - +
44B ASN* 5.0 7.5 + - - -
410B LEU* 6.4 0.2 - - - -
437B PRO* 3.4 14.2 + - - +
439B GLU* 1.3 79.3 - - - +
441B VAL* 1.3 56.8 + - - +
443B LEU* 3.3 8.1 + - - +
444B SER* 2.9 29.0 + - - -
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 5.7 9.0 - - + +
411B TYR* 4.9 10.3 - - + -
414B PHE* 4.3 36.1 - - + -
437B PRO* 3.2 16.4 + - + +
438B LEU* 3.2 20.9 - - - +
440B GLY* 1.3 75.5 - - - +
442B ILE* 1.3 70.6 + - + +
444B SER* 2.5 22.8 + - - +
445B LEU* 2.9 36.0 + - + +
518B ILE* 4.8 6.7 - - + -
522B LEU* 5.6 2.9 - - + -
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Residues in contact with ILE 442 (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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438B LEU 3.2 19.7 + - - +
439B GLU* 3.4 6.2 + - - +
440B GLY 3.3 0.4 - - - -
441B VAL* 1.3 77.4 - - + +
443B LEU* 1.3 58.9 + - - +
445B LEU* 3.3 9.8 + - + +
446B GLN* 2.9 54.5 + - + +
514B SER* 4.3 18.4 - - - +
517B GLU* 4.7 11.7 - - + +
518B ILE* 3.6 34.5 - - + -
521B LEU* 5.2 6.5 - - + -
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Residues in contact with LEU 443 (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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43B GLY 3.4 21.8 - - - +
44B ASN* 4.7 0.2 - - - -
45B ARG* 4.4 20.9 - - + +
439B GLU 2.9 18.1 + - - +
440B GLY* 3.6 6.3 - - - +
442B ILE* 1.3 78.5 - - - +
444B SER* 1.3 56.8 + - - +
446B GLN* 3.3 12.3 + - + +
447B ASP* 2.9 63.4 + - - +
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Residues in contact with SER 444 (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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42B PHE 5.3 0.4 - - - -
43B GLY* 3.6 23.3 - - - +
407B THR* 5.8 7.9 - - - -
410B LEU* 4.8 13.5 - - - +
411B TYR* 5.6 1.4 - - - -
440B GLY 2.9 15.4 + - - -
441B VAL* 2.5 29.8 + - - +
443B LEU* 1.3 77.0 - - - +
445B LEU* 1.3 59.2 + - - +
447B ASP* 3.3 2.3 + - - +
448B LEU* 2.9 31.8 + - - +
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Residues in contact with LEU 445 (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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407B THR* 5.7 0.2 - - - +
411B TYR* 3.2 41.1 - - + +
441B VAL* 2.9 33.3 + - + +
442B ILE* 3.8 7.4 - - + +
444B SER* 1.3 80.1 + - - +
446B GLN* 1.3 58.6 + - - +
448B LEU* 3.8 4.6 - - + +
449B ILE* 2.9 35.6 + - + +
518B ILE* 4.6 3.4 - - + +
521B LEU* 3.6 32.8 - - + +
522B LEU* 3.5 32.5 - - + +
525B ILE* 4.6 10.8 - - + -
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Residues in contact with GLN 446 (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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442B ILE* 2.9 39.2 + - - +
443B LEU* 3.8 12.4 - - + +
445B LEU* 1.3 76.7 - - - +
447B ASP* 1.3 65.1 + - - +
449B ILE* 4.4 3.8 - - - +
450B GLY* 3.8 13.3 + - - -
521B LEU* 3.8 28.3 - - + +
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Residues in contact with ASP 447 (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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41B GLY 5.0 1.4 - - - +
42B PHE* 4.9 18.9 - - + -
43B GLY 3.8 19.2 + - - +
443B LEU* 2.9 43.1 + - - +
444B SER 3.9 2.9 - - - +
445B LEU 3.2 0.2 - - - -
446B GLN* 1.3 81.3 - - - +
448B LEU* 1.3 61.5 + - - +
449B ILE 3.4 0.2 - - - -
450B GLY* 3.8 2.3 + - - -
451B TYR* 3.6 17.0 + - - +
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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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42B PHE* 5.9 0.9 - - - -
403B MET* 5.3 8.1 - - + -
407B THR* 5.9 6.1 - - - +
444B SER 2.9 18.0 + - - +
445B LEU* 3.2 3.5 + - + +
447B ASP* 1.3 77.0 - - - +
449B ILE* 1.3 64.3 + - - +
451B TYR* 3.3 13.3 + - - +
452B PHE* 3.4 28.5 - - + -
478B PHE* 6.2 2.5 - - + -
525B ILE* 4.4 19.3 - - + -
529B LEU* 5.6 0.2 - - - +
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Residues in contact with ILE 449 (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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445B LEU 2.9 17.5 + - - +
446B GLN* 4.4 4.9 - - - +
447B ASP 3.4 0.2 - - - -
448B LEU* 1.3 76.8 - - - +
450B GLY* 1.3 61.0 + - - +
452B PHE* 3.0 28.1 + - - +
453B GLU* 4.1 2.3 + - - +
521B LEU* 3.7 29.8 - - + +
524B GLU* 3.8 13.7 - - + -
525B ILE* 3.7 42.6 - - + +
528B SER* 4.6 10.3 - - - +
529B LEU* 6.1 0.9 - - - -
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Residues in contact with GLY 450 (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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446B GLN 3.8 10.6 + - - -
447B ASP 3.8 3.5 + - - -
448B LEU 3.3 0.4 - - - -
449B ILE* 1.3 81.5 - - - +
451B TYR* 1.3 60.9 + - - +
453B GLU* 3.9 16.5 - - - +
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Residues in contact with TYR 451 (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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42B PHE* 4.7 11.9 - + + -
396B GLU* 5.3 5.4 + - - +
399B GLN* 5.8 2.4 - - - +
400B ALA* 5.1 10.6 + - + +
403B MET* 3.6 35.4 - - + -
447B ASP 3.6 12.5 + - - +
448B LEU 3.3 9.1 + - - +
449B ILE 3.2 0.8 - - - -
450B GLY* 1.3 78.4 - - - +
452B PHE* 1.3 86.3 + + - +
453B GLU* 3.5 3.8 + - - +
474B ARG* 3.3 60.3 + - + +
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Residues in contact with PHE 452 (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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403B MET* 4.6 9.0 - - + -
448B LEU* 3.4 26.9 - - + +
449B ILE* 3.0 16.8 + - - +
451B TYR* 1.3 99.6 - + - +
453B GLU* 1.3 57.8 + - - +
454B PRO* 4.4 2.8 - - - +
471B LEU* 4.4 21.5 - - + -
474B ARG* 3.6 36.1 - - + -
475B GLN* 5.0 2.9 - - + +
478B PHE* 3.5 41.3 - + - -
525B ILE* 6.4 0.4 - - + -
528B SER* 4.4 18.2 - - - +
529B 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