Contacts of the helix formed by residues 418 - 428 (chain A) in PDB entry 3RAW
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 SER 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A ASP* 3.0 34.3 + - - +
417A ASN* 1.3 81.6 - - - +
419A SER* 1.3 59.3 + - - +
420A ASP* 3.3 10.0 + - - +
421A GLY 2.6 27.2 + - - -
422A ARG* 2.8 27.8 + - - +
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Residues in contact with SER 419 (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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417A ASN 3.9 0.4 + - - -
418A SER* 1.3 73.1 - - - +
420A ASP* 1.3 63.8 + - - +
422A ARG* 4.1 5.4 - - - +
423A TYR* 3.0 29.5 + - - +
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Residues in contact with ASP 420 (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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377A HIS* 3.0 33.9 + - - -
378A GLU* 4.2 13.0 - - - +
381A GLU* 3.3 32.3 - - + +
418A SER* 3.1 8.9 + - - +
419A SER* 1.3 81.9 + - - +
421A GLY* 1.3 64.9 + - - +
423A TYR* 3.3 4.6 + - - +
424A VAL* 3.1 30.0 + - - +
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Residues in contact with GLY 421 (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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414A TRP* 3.8 17.0 - - - -
415A ASP 3.4 20.6 - - - -
416A GLU 3.6 6.5 - - - -
418A SER* 2.6 14.9 + - - -
420A ASP* 1.3 73.5 - - - +
422A ARG* 1.3 62.8 + - - +
424A VAL* 3.2 4.2 + - - +
425A LYS* 3.0 27.5 + - - +
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Residues in contact with ARG 422 (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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416A GLU* 3.2 17.0 + - - +
417A ASN* 2.8 42.3 + - - +
418A SER 2.8 23.4 + - - +
419A SER* 4.1 5.4 - - - +
421A GLY* 1.3 72.2 - - - +
423A TYR* 1.3 57.7 + - - +
425A LYS* 3.3 25.0 + - - +
426A GLU* 2.9 33.1 + - - +
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Residues in contact with TYR 423 (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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375A GLN* 3.7 33.3 - - + +
381A GLU* 4.5 6.7 - - - +
385A MET* 3.8 28.9 - - + -
419A SER 3.0 20.5 + - - +
420A ASP* 3.5 6.5 - - - +
421A GLY 3.2 0.2 - - - -
422A ARG* 1.3 76.7 - - - +
424A VAL* 1.3 61.1 + - + +
426A GLU* 4.7 1.1 - - - -
427A ASN* 2.8 68.6 + - + +
428A CYS* 5.2 1.8 - - - -
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Residues in contact with VAL 424 (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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381A GLU* 3.6 29.8 - - + +
384A VAL* 3.7 28.0 - - + -
385A MET* 3.7 23.6 - - + -
388A LYS* 4.1 9.8 - - + +
414A TRP* 5.0 1.6 - - + -
420A ASP 3.1 17.1 + - - +
421A GLY* 3.8 5.4 - - - +
423A TYR* 1.3 75.8 - - + +
425A LYS* 1.3 61.3 + - - +
428A CYS* 3.0 51.1 + - + +
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Residues in contact with LYS 425 (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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388A LYS* 4.5 11.8 - - - +
414A TRP* 3.7 17.3 - - + -
416A GLU* 3.1 52.6 + - + +
421A GLY 3.0 17.8 + - - +
422A ARG* 3.9 21.0 - - - +
424A VAL* 1.3 78.9 - - - +
426A GLU* 1.3 58.0 + - - +
428A CYS 4.8 0.9 - - - +
429A LYS* 3.0 18.5 + - - -
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Residues in contact with GLU 426 (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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422A ARG 2.9 17.9 + - - +
423A TYR* 4.7 0.9 - - - -
425A LYS* 1.3 79.1 - - - +
427A ASN* 1.3 72.6 + - - +
429A LYS* 2.6 22.8 + - - +
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Residues in contact with ASN 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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423A TYR* 2.8 65.3 + - + +
426A GLU* 1.3 95.3 - - - +
428A CYS* 1.3 61.1 + - - +
429A LYS* 3.7 7.4 + - - +
434A TYR* 3.1 15.9 + - - -
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Residues in contact with CYS 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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373A LEU 5.4 2.7 - - - -
385A MET* 3.6 37.9 - - - -
388A LYS* 4.1 20.5 - - + +
389A ILE* 4.1 20.4 - - + -
423A TYR* 5.2 1.3 - - - -
424A VAL* 3.0 37.7 + - + +
425A LYS 4.8 1.2 - - - +
426A GLU 4.0 0.2 - - - -
427A ASN* 1.3 77.2 - - - +
429A LYS* 1.3 68.0 + - - +
434A TYR* 3.8 3.4 - - - -
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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