Contacts of the helix formed by residues 426 - 435 (chain A) in PDB entry 4OSV
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 THR 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A CYS* 3.9 0.7 - - - -
424A GLY 5.2 2.9 - - - +
425A LEU* 1.3 75.2 - - - +
427A PRO* 1.3 74.3 - - - +
428A GLN* 3.4 10.7 + - - +
429A GLN* 2.9 45.4 + - - +
430A VAL* 3.2 12.0 + - - +
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Residues in contact with PRO 427 (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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389A HIS 5.4 6.3 - - - +
390A GLY 5.7 3.6 - - - +
391A LEU* 4.4 19.4 - - + +
395A GLN* 4.9 3.8 - - - +
416A LEU* 4.2 8.7 - - + -
420A CYS* 3.8 19.5 - - - -
425A LEU 4.3 0.2 - - - +
426A THR* 1.3 87.2 - - - +
428A GLN* 1.3 56.7 + - - +
430A VAL* 3.2 2.4 + - - +
431A VAL* 2.9 34.3 + - - +
390B GLY 6.1 1.1 - - - +
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Residues in contact with GLN 428 (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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395A GLN* 4.4 16.9 - - - +
426A THR* 3.1 9.5 + - - +
427A PRO* 1.3 81.2 - - - +
429A GLN* 1.3 62.5 + - - +
431A VAL* 3.4 3.3 + - + +
432A ALA* 3.0 30.0 + - + +
-10J A 4.5 14.1 + - - -
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Residues in contact with GLN 429 (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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424A GLY 4.4 1.6 - - - +
425A LEU* 3.4 18.9 - - + +
426A THR* 2.9 45.9 + - - +
428A GLN* 1.3 82.1 - - - +
430A VAL* 1.3 63.3 + - - +
432A ALA* 3.2 8.5 + - - +
433A ILE* 3.1 27.8 + - - +
461A PRO* 5.6 1.0 - - - +
462A GLN* 4.6 18.2 - - - +
465A VAL* 3.9 36.5 - - + +
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Residues in contact with VAL 430 (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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412A VAL* 4.4 16.8 - - + -
415A LEU* 6.3 0.2 - - + -
416A LEU* 3.6 34.3 - - + +
419A LEU* 4.0 30.7 - - + -
420A CYS* 4.1 4.9 - - - -
425A LEU* 4.3 10.1 - - + -
426A THR 3.2 12.7 + - - +
427A PRO 3.2 6.9 + - - +
429A GLN* 1.3 76.4 - - - +
431A VAL* 1.3 58.4 + - + +
433A ILE* 3.1 10.9 + - - +
434A ALA* 2.9 26.3 + - - +
443A LEU* 3.8 16.8 - - + +
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Residues in contact with VAL 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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391A LEU* 3.8 25.6 - - + -
395A GLN* 4.0 39.3 - - + +
398A ALA* 4.9 6.3 - - + -
399A ILE* 4.1 27.5 - - + +
416A LEU* 5.8 0.2 - - + -
427A PRO 2.9 20.8 + - - +
428A GLN* 3.7 6.7 - - + +
430A VAL* 1.3 76.7 - - + +
432A ALA* 1.3 58.2 + - - +
434A ALA* 3.2 1.0 + - - +
435A SER* 2.9 36.0 + - - +
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Residues in contact with ALA 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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428A GLN* 3.0 18.7 + - + +
429A GLN* 3.4 11.9 - - - +
430A VAL 3.2 0.2 - - - -
431A VAL* 1.3 78.7 - - - +
433A ILE* 1.3 61.7 + - - +
435A SER* 3.4 11.6 + - - -
436A ASN* 3.0 17.5 + - - -
465A VAL* 5.5 2.2 - - + -
469A SER* 3.6 20.3 - - - +
-10J A 4.8 15.7 - - - +
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Residues in contact with ILE 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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419A LEU* 5.5 0.4 - - + -
425A LEU* 4.3 22.0 - - + -
429A GLN 3.1 17.8 + - - +
430A VAL* 3.1 9.4 + - + +
432A ALA* 1.3 76.5 - - - +
434A ALA* 1.3 62.1 + - - +
436A ASN* 3.2 13.7 + - - +
439A GLY* 4.2 3.3 - - - -
442A ALA* 3.7 39.2 - - + +
443A LEU* 3.8 17.3 - - + -
446A VAL* 4.1 20.0 - - + -
465A VAL* 4.2 14.1 - - + +
468A ALA* 3.8 20.6 - - + +
469A SER* 3.9 14.8 - - - +
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Residues in contact with ALA 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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399A ILE* 4.0 16.0 - - + +
408A ALA* 3.7 11.5 - - + +
412A VAL* 3.3 33.9 - - + -
430A VAL 2.9 14.1 + - - +
431A VAL 3.2 4.2 + - - +
433A ILE* 1.3 79.1 - - - +
435A SER* 1.3 56.4 + - - +
436A ASN 2.9 15.5 + - - +
439A GLY* 3.6 9.2 - - - -
443A LEU* 3.8 14.6 - - + -
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Residues in contact with SER 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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398A ALA* 3.5 31.9 - - - -
399A ILE* 4.1 4.9 - - - +
402A ASN* 3.4 18.6 + - - -
431A VAL* 2.9 19.1 + - - +
432A ALA* 3.4 11.3 + - - -
433A ILE 3.4 1.2 - - - -
434A ALA* 1.3 72.2 - - - +
436A ASN* 1.3 66.9 + - - +
-9J G 3.6 23.2 + - - -
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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