Contacts of the helix formed by residues 430 - 440 (chain B) in PDB entry 5Y7G
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 ARG 430 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B ALA* 2.7 29.9 + - + +
402B ILE 3.9 3.2 + - - -
404B ALA* 3.5 15.7 + - + +
406B ILE* 3.3 40.0 - - + +
409B ALA* 3.7 15.8 - - - +
418B PRO* 3.8 10.9 - - - +
420B ASP* 3.0 28.5 + - - -
426B PHE* 3.1 36.8 + - - +
427B ARG 3.3 2.0 + - - -
428B GLN 3.1 0.6 - - - -
429B ARG* 1.3 80.1 - - - +
431B ALA* 1.3 51.2 + - - +
432B ALA* 2.6 5.7 + - - -
433B LEU* 2.5 47.2 + - + +
434B PHE* 3.2 22.6 + - + -
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Residues in contact with ALA 431 (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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427B ARG* 3.0 33.7 + - - +
428B GLN* 3.0 24.7 + - + +
429B ARG 3.5 0.4 + - - -
430B ARG* 1.3 74.0 - - - +
432B ALA* 1.3 57.4 + - - +
434B PHE* 3.9 3.1 - - - -
435B GLU* 2.9 29.6 + - - +
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Residues in contact with ALA 432 (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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430B ARG 2.6 6.1 + - - +
431B ALA* 1.3 73.2 - - - +
433B LEU* 1.3 67.4 + - + +
435B GLU* 2.9 8.1 + - - +
436B ALA* 2.9 27.8 + - - +
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Residues in contact with LEU 433 (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 GLU* 3.3 32.8 - - + +
401B ALA* 3.9 14.4 - - + +
404B ALA* 3.9 17.3 - - + -
406B ILE* 5.7 3.1 - - + -
430B ARG* 2.5 27.4 + - + +
432B ALA* 1.3 83.9 - - + +
434B PHE* 1.3 54.6 + - - +
436B ALA* 3.9 6.4 - - - +
437B CYS* 2.9 36.6 + - - +
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Residues in contact with PHE 434 (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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394B PHE* 3.7 26.9 - + - -
398B CYS* 3.8 17.0 - - + -
401B ALA* 3.5 27.1 - - + -
402B ILE* 4.5 5.6 - - + -
426B PHE* 3.9 30.1 - + - -
427B ARG* 3.9 32.3 - - - +
430B ARG* 3.2 37.0 + - + +
431B ALA* 4.0 2.9 - - - +
432B ALA 3.1 0.6 - - - -
433B LEU* 1.3 75.8 - - - +
435B GLU* 1.3 59.5 + - - +
437B CYS* 4.8 0.9 - - - -
438B LEU* 3.0 39.2 + - + +
495B LEU* 3.7 23.3 - - + -
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Residues in contact with GLU 435 (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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427B ARG* 3.7 24.9 + - - -
431B ALA 2.9 18.7 + - - +
432B ALA* 2.9 7.4 + - - +
434B PHE* 1.3 78.1 - - - +
436B ALA* 1.3 56.0 + - - +
438B LEU* 4.7 2.2 - - - -
439B GLY* 2.9 22.5 + - - -
488B ARG* 3.6 23.1 + - - -
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Residues in contact with ALA 436 (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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432B ALA 2.9 14.1 + - - +
433B LEU* 3.9 7.2 - - - +
434B PHE 3.2 0.2 - - - -
435B GLU* 1.3 75.9 - - - +
437B CYS* 1.3 61.8 + - - +
439B GLY* 2.9 15.3 + - - -
440B ARG* 3.0 21.1 + - - +
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Residues in contact with CYS 437 (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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397B LEU* 3.1 48.9 - - - +
398B CYS* 3.7 28.9 - - + -
400B GLU* 4.3 7.0 - - - -
401B ALA 4.3 9.4 - - - -
433B LEU* 2.9 21.5 + - - +
434B PHE* 4.4 0.7 - - - +
436B ALA* 1.3 76.1 - - - +
438B LEU* 1.3 62.9 + - - +
440B ARG* 3.2 16.1 + - - +
453B ARG* 4.2 14.1 - - - -
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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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394B PHE* 5.0 2.2 - - + -
397B LEU* 4.5 3.6 - - + -
398B CYS* 4.1 17.0 - - - -
427B ARG* 3.6 26.7 - - - +
434B PHE* 3.0 27.1 + - + +
435B GLU* 4.2 4.5 - - - +
437B CYS* 1.3 74.6 - - - +
439B GLY* 1.3 61.7 + - - +
441B LEU* 3.1 20.2 + - + +
488B ARG* 3.0 41.1 + - - +
491B PHE* 3.9 38.1 - - + +
492B GLU* 4.3 8.5 - - - +
495B LEU* 4.0 15.3 - - + -
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Residues in contact with GLY 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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435B GLU 2.9 16.2 + - - -
436B ALA* 2.9 10.9 + - - -
438B LEU* 1.3 72.5 - - - +
440B ARG* 1.3 61.2 + - - +
441B LEU 2.8 11.6 + - - -
442B GLU* 3.1 17.5 + - - +
443B ASP* 3.1 13.0 - - - +
488B ARG* 4.7 5.1 - - - -
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Residues in contact with ARG 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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397B LEU* 4.2 7.9 - - + -
436B ALA* 3.0 20.1 + - - +
437B CYS* 3.2 15.3 + - - +
439B GLY* 1.3 76.9 - - - +
441B LEU* 1.3 57.7 + - - +
442B GLU 3.5 0.2 - - - -
443B ASP* 3.5 16.7 + - - +
445B SER* 3.1 46.8 + - - +
446B TYR* 2.6 32.5 + - - +
449B ALA* 4.7 9.2 - - + -
453B ARG* 6.3 0.9 - - - +
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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