Contacts of the helix formed by residues 414 - 424 (chain A) in PDB entry 3SPZ
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 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413A THR* 1.3 69.0 - - - +
415A ALA* 1.3 57.9 + - - +
416A TYR 3.6 1.6 - - - -
417A PRO* 3.2 26.4 - - - +
418A SER* 2.6 36.7 + - - -
479A PHE* 3.6 27.4 - - - -
482A ARG* 4.5 5.4 - - - -
560A LYS* 5.8 1.4 - - - +
563A ILE* 3.6 12.6 - - - +
564A ASN* 4.7 0.2 + - - -
904A UPC 2.6 34.0 + - - -
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Residues in contact with ALA 415 (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 LEU* 4.0 15.7 - - + -
413A THR 3.4 5.1 - - - -
414A SER* 1.3 70.4 - - - +
416A TYR* 1.3 72.2 + - + +
418A SER* 3.2 4.2 + - - -
419A ILE* 2.9 29.6 + - + +
623A ASP* 3.5 37.5 - - + +
681A MET* 4.6 0.2 - - - +
904A UPC 2.9 19.6 + - - +
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Residues in contact with TYR 416 (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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393A GLY* 4.9 0.5 - - - -
394A ALA* 3.8 27.5 + - - +
415A ALA* 1.3 84.5 - - + +
417A PRO* 1.4 72.2 - - + +
419A ILE* 3.0 15.6 + - + +
420A ILE* 3.0 26.3 + - - +
564A ASN* 4.7 0.2 - - - +
567A ALA* 4.0 20.9 - - + -
586A ILE* 3.5 25.9 - - + +
587A THR* 4.0 35.5 + - + +
590A GLY* 5.0 6.7 - - - -
622A THR* 4.0 19.1 - - + +
623A ASP* 6.2 0.2 - - + -
904A UPC 3.1 39.5 + - + -
5T G 5.2 8.2 + - - -
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Residues in contact with PRO 417 (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 SER* 3.2 27.1 - - - +
416A TYR* 1.4 91.4 - - + +
418A SER* 1.3 60.1 + - - +
420A ILE* 3.2 6.2 + - + +
421A ARG* 3.0 32.4 + - - +
475A ILE* 3.7 27.5 - - + +
479A PHE* 5.4 3.6 - - + -
563A ILE* 3.7 27.4 - - + +
564A ASN* 3.2 27.1 - - - +
567A ALA* 5.3 0.4 - - + -
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Residues in contact with SER 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 6.3 0.2 - - - -
413A THR* 2.8 17.7 + - - +
414A SER* 2.6 29.2 + - - -
415A ALA* 3.5 4.7 - - - -
417A PRO* 1.3 76.0 - - - +
419A ILE* 1.3 57.7 + - - +
421A ARG* 3.3 19.4 + - - +
422A GLN* 2.8 30.8 + - - +
479A PHE* 5.3 1.6 - - - -
680A LEU* 3.8 26.2 + - - +
681A MET* 3.8 7.9 - - - +
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 5.5 3.4 - - + -
415A ALA* 2.9 21.4 + - + +
416A TYR* 3.0 21.5 + - + +
418A SER* 1.3 73.6 - - - +
420A ILE* 1.3 67.0 + - - +
422A GLN* 4.3 1.6 - - - -
423A VAL* 2.9 26.8 + - + +
425A ILE* 4.2 7.6 - - + -
586A ILE* 3.7 31.9 - - + +
589A PHE* 3.6 44.4 - - + -
590A GLY* 3.8 15.9 - - - -
593A ALA* 5.5 0.2 - - + -
681A MET* 3.8 17.5 - - + -
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Residues in contact with ILE 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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416A TYR 3.0 15.0 + - - +
417A PRO* 3.3 8.5 - - + +
419A ILE* 1.3 75.8 - - - +
421A ARG* 1.3 56.4 + - - +
424A ASN* 2.8 25.6 + - - -
425A ILE* 3.0 38.5 + - + +
471A VAL* 3.7 20.6 - - + -
472A PRO* 4.0 13.8 - - + +
475A ILE* 3.7 26.7 - - + -
566A LEU* 5.0 0.7 - - + -
567A ALA* 4.1 18.6 - - + +
570A LEU* 4.6 4.0 - - + -
586A ILE* 3.6 33.0 - - + -
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Residues in contact with ARG 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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417A PRO* 3.0 22.9 + - - +
418A SER* 3.7 11.9 + - - +
420A ILE* 1.3 74.0 - - - +
422A GLN* 1.3 66.8 + - - +
423A VAL 3.6 0.2 + - - -
424A ASN* 3.6 9.0 + - - +
472A PRO* 4.3 12.8 - - + +
475A ILE* 3.9 17.5 - - + -
476A THR* 2.8 42.4 + - - +
479A PHE* 3.5 38.3 - - - -
480A ASN* 5.4 1.6 + - - +
677A LYS* 4.4 9.5 + - - +
678A GLN* 4.7 10.8 + - - +
680A LEU* 3.5 47.9 - - + +
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Residues in contact with GLN 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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418A SER 2.8 17.1 + - - +
419A ILE* 3.7 3.8 - - - +
421A ARG* 1.3 78.0 - - - +
423A VAL* 1.3 64.0 + - + +
589A PHE* 3.7 11.9 - - + -
667A PHE 5.1 0.8 + - - -
670A MET* 4.8 1.4 - - - +
671A CYS* 3.8 20.4 - - - +
676A ASN* 2.9 32.5 + - + +
677A LYS* 3.0 27.7 + - - +
678A GLN 3.2 23.2 + - - +
679A HIS* 3.6 2.7 + - - +
680A LEU* 2.7 33.1 + - - +
681A MET* 3.4 29.3 + - + +
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Residues in contact with VAL 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ILE* 2.9 21.7 + - + +
422A GLN* 1.3 76.0 - - + +
424A ASN* 1.3 70.4 + - - +
425A ILE* 3.8 15.5 - - + -
455A SER* 2.8 30.5 + - - +
456A CYS 4.0 15.5 - - - +
457A SER* 4.4 2.2 - - - +
463A TYR* 3.5 29.1 - - + +
589A PHE* 3.9 30.5 - - + -
676A ASN* 3.7 13.9 - - - +
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Residues in contact with ASN 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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420A ILE 2.8 12.5 + - - -
421A ARG 3.6 4.0 + - - +
422A GLN 3.4 2.8 - - - -
423A VAL* 1.3 80.8 - - - +
425A ILE* 1.3 53.1 + - - +
429A THR* 2.5 41.8 + - - +
463A TYR* 3.5 5.2 - - - -
464A TYR 2.7 24.2 + - - +
467A ARG 2.6 26.9 + - - -
468A ASP* 3.5 20.6 - - - +
469A GLY 3.5 3.5 + - - -
472A PRO* 3.5 15.2 - - - +
677A LYS* 3.5 25.1 - - + +
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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