Contacts of the helix formed by residues 430 - 443 (chain A) in PDB entry 5FHH
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 ASP 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A HIS* 3.6 4.0 + - + -
429A GLN* 1.3 86.6 + - - +
431A ASP* 1.3 61.8 + - - +
432A VAL 3.3 1.1 - - - +
433A ALA* 3.4 9.0 - - - +
434A LEU* 2.6 37.1 + - - +
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Residues in contact with ASP 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A CYS* 3.9 21.9 - - + -
427A THR 5.9 0.5 + - - -
428A HIS* 4.0 21.0 + - - +
429A GLN 3.8 0.4 - - - -
430A ASP* 1.3 79.0 - - - +
432A VAL* 1.3 53.2 + - - +
434A LEU* 3.0 4.9 + - - +
435A THR* 2.4 43.2 + - - -
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A CYS* 3.4 21.3 - - + -
428A HIS 3.7 1.8 - - - +
429A GLN* 3.0 53.2 - - - +
431A ASP* 1.3 75.6 - - - +
433A ALA* 1.3 55.1 + - - +
436A ASN* 2.9 35.7 + - - +
551A ALA* 3.1 36.1 - - + +
552A MET 3.3 21.1 - - - +
553A SER* 3.7 7.9 - - - +
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A GLN* 3.2 22.9 + - - +
430A ASP* 3.3 12.3 + - - +
431A ASP 3.2 0.2 - - - -
432A VAL* 1.3 78.4 - - - +
434A LEU* 1.3 62.8 + - - +
436A ASN* 4.1 2.1 - - - +
437A GLU* 3.4 20.1 + - - +
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A ASP 2.6 21.2 + - - +
431A ASP* 3.7 4.7 - - - +
433A ALA* 1.3 71.9 - - - +
435A THR* 1.3 57.3 + - - +
437A GLU* 2.9 6.3 + - - +
438A ARG* 2.7 38.0 + - + +
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Residues in contact with THR 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A CYS* 5.4 3.6 - - - -
431A ASP* 2.4 36.3 + - - -
434A LEU* 1.3 68.5 - - - +
436A ASN* 1.3 62.1 + - - +
438A ARG* 4.3 5.7 - - - +
439A ARG* 3.4 21.7 + - - +
550A TRP* 4.7 3.4 - - - +
551A ALA* 4.3 16.8 - - - -
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Residues in contact with ASN 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A VAL 2.9 20.5 + - - +
433A ALA* 4.1 3.1 - - - +
435A THR* 1.3 78.9 - - - +
437A GLU* 1.3 60.6 + - - +
439A ARG* 3.7 4.7 - - - +
440A LEU* 3.4 17.5 + - - +
548A LEU* 2.7 40.2 + - + +
549A ALA 2.5 26.5 + - - +
550A TRP* 3.9 12.3 - - - +
551A ALA* 2.6 35.6 + - - +
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Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A ALA 3.4 16.3 + - - +
434A LEU* 2.9 4.3 + - - +
436A ASN* 1.3 76.7 - - - +
438A ARG* 1.3 58.2 + - - +
439A ARG 3.2 1.8 - - - -
440A LEU* 2.6 32.0 + - + +
441A GLN* 2.9 14.8 + - - +
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Residues in contact with ARG 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A LEU* 2.7 21.4 + - + +
435A THR* 4.3 5.6 - - - +
437A GLU* 1.3 70.5 - - - +
439A ARG* 1.3 64.3 + - - +
441A GLN* 3.5 5.1 + - - +
442A GLU* 3.0 38.4 + - + +
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Residues in contact with ARG 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A THR 3.4 13.0 + - - +
436A ASN 3.7 3.1 - - - +
437A GLU 3.2 0.4 - - - -
438A ARG* 1.3 78.9 - - - +
440A LEU* 1.3 62.5 + - - +
442A GLU* 3.4 13.0 + - - +
443A LEU* 3.0 22.9 + - - +
550A TRP* 3.3 58.5 - - + -
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A ASN 3.4 10.2 + - - +
437A GLU* 2.6 23.3 + - + +
439A ARG* 1.3 70.9 - - - +
441A GLN* 1.3 65.4 + - - +
443A LEU* 3.1 25.3 + - + +
447A VAL 6.1 0.4 - - - +
474A GLN* 2.9 42.0 - - + +
476A LYS* 3.4 33.6 - - + +
479A ALA* 3.6 23.6 - - + -
550A TRP* 5.4 0.2 - - - -
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Residues in contact with GLN 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A GLU 2.9 11.4 + - - +
438A ARG* 4.1 5.6 - - - +
440A LEU* 1.3 78.2 - - - +
442A GLU* 1.3 63.1 + - - +
443A LEU 3.4 6.4 + - - +
444A PRO* 5.2 0.7 - - - +
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Residues in contact with GLU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A ARG* 3.0 37.7 + - + +
439A ARG* 3.5 10.1 + - - +
441A GLN* 1.3 78.9 - - - +
443A LEU* 1.3 62.7 + - - +
444A PRO* 3.1 12.3 - - - +
550A TRP* 6.0 1.2 - - - -
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Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A ARG 3.0 13.1 + - - +
440A LEU* 3.1 18.4 + - - +
441A GLN 3.6 4.7 - - - +
442A GLU* 1.3 74.4 - - - +
444A PRO* 1.3 84.5 - - + +
445A GLY* 3.7 3.4 + - - +
476A LYS* 4.1 13.9 - - + +
477A LEU* 4.5 3.1 - - + +
478A GLY* 3.4 20.9 - - - +
479A ALA* 3.1 40.4 - - + +
550A TRP* 6.0 4.0 - - + -
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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