Contacts of the helix formed by residues 508 - 519 (chain A) in PDB entry 3I5Y
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 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A GLU* 4.8 7.2 + - - -
505A TYR* 4.8 0.2 + - - -
506A GLU 3.6 3.4 + - - -
507A PRO* 1.3 74.9 - - - +
509A GLU* 1.3 62.8 + - - +
510A GLU* 3.6 15.0 + - - +
511A ILE* 3.1 40.7 + - - +
512A LYS* 3.3 8.9 + - - +
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Residues in contact with GLU 509 (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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507A PRO 5.2 2.1 - - - +
508A SER* 1.3 74.7 - - - +
510A GLU* 1.3 61.8 + - - +
512A LYS* 3.4 30.4 + - - +
513A SER* 2.7 39.1 + - - +
564A ASN* 5.7 0.9 - - - +
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Residues in contact with GLU 510 (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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508A SER* 3.2 13.0 - - - +
509A GLU* 1.3 86.3 + - - +
511A ILE* 1.3 60.5 + - - +
513A SER* 3.2 7.3 + - - -
514A GLU* 2.8 32.7 + - - +
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Residues in contact with ILE 511 (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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357A PHE* 4.2 12.3 - - + +
360A VAL* 4.1 13.9 - - + -
361A GLU* 3.8 31.6 - - + +
364A LYS* 4.7 6.1 - - - +
396A GLU* 4.5 5.2 - - - +
505A TYR* 4.1 7.0 - - - +
507A PRO* 3.9 13.2 - - + -
508A SER* 3.1 37.1 + - - +
510A GLU* 1.3 74.3 - - - +
512A LYS* 1.3 66.2 + - - +
514A GLU* 4.3 14.4 - - - +
515A VAL* 2.9 54.1 + - + +
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Residues in contact with LYS 512 (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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354A ASN* 5.3 2.6 + - - -
357A PHE* 4.0 29.8 - - + -
507A PRO* 4.0 26.8 - - + +
508A SER 3.3 15.5 + - - +
509A GLU* 3.6 33.9 + - - +
511A ILE* 1.3 82.2 - - - +
513A SER* 1.3 56.3 + - - +
516A LEU* 2.9 43.5 + - + +
561A VAL* 4.7 14.0 - - - +
564A ASN* 5.2 11.4 + - - +
566A PRO* 6.4 0.4 - - - +
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Residues in contact with SER 513 (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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509A GLU* 2.7 21.9 + - - +
510A GLU* 3.2 9.7 + - - -
512A LYS* 1.3 74.4 - - - +
514A GLU* 1.3 67.0 + - - +
516A LEU* 5.0 1.1 - - - -
517A GLU* 3.0 53.5 + - - +
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Residues in contact with GLU 514 (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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364A LYS* 2.7 32.2 + - - -
396A GLU* 2.8 27.6 - - - +
510A GLU* 2.8 21.2 + - - +
511A ILE* 3.7 12.2 - - - +
513A SER* 1.3 76.0 - - - +
515A VAL* 1.3 61.3 + - - +
517A GLU* 4.8 1.6 - - - +
518A ALA* 3.8 17.5 + - - +
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Residues in contact with VAL 515 (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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356A ILE* 4.5 2.5 - - + -
357A PHE* 3.7 31.2 - - + -
360A VAL* 4.3 13.0 - - + -
392A ILE* 3.9 38.2 - - + +
396A GLU* 3.8 17.9 - - - +
511A ILE* 2.9 31.4 + - + +
514A GLU* 1.3 77.5 - - - +
516A LEU* 1.3 67.9 + - + +
517A GLU 3.4 0.5 + - - -
518A ALA* 3.4 13.1 + - - +
519A VAL* 3.5 12.7 + - + +
562A LEU* 6.1 0.4 - - + -
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Residues in contact with LEU 516 (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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357A PHE* 4.2 19.7 - - + -
512A LYS* 2.9 39.0 + - + +
513A SER* 4.5 2.0 - - - +
515A VAL* 1.3 78.8 - - + +
517A GLU* 1.3 62.5 + - + +
519A VAL* 3.5 23.3 - - + +
561A VAL 3.4 20.4 - - - +
562A LEU* 3.6 50.5 - - + +
564A ASN* 4.2 22.0 - - + +
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Residues in contact with GLU 517 (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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513A SER* 3.0 40.5 + - - +
514A GLU* 4.8 2.6 - - - +
516A LEU* 1.3 78.5 - - + +
518A ALA* 1.3 60.7 + - - +
519A VAL 3.9 5.2 - - - +
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Residues in contact with ALA 518 (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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392A ILE* 6.5 0.2 - - - -
395A ASN* 3.5 38.9 + - + +
396A GLU* 6.5 0.4 - - + -
514A GLU 3.8 16.8 + - - +
515A VAL* 3.4 5.5 + - - +
516A LEU 3.3 0.4 - - - -
517A GLU* 1.3 78.8 - - - +
519A VAL* 1.3 63.8 + - - +
520A THR* 3.3 14.0 + - - +
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Residues in contact with VAL 519 (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 PHE* 4.0 28.3 - - + -
391A SER* 6.5 0.9 - - - -
392A ILE* 4.7 12.1 - - + -
395A ASN* 5.0 2.7 - - - +
515A VAL 3.5 14.5 + - - +
516A LEU* 3.5 25.0 - - + +
517A GLU 3.3 7.5 - - - +
518A ALA* 1.3 78.0 - - - +
520A THR* 1.3 61.7 + - - +
521A GLU* 3.5 32.4 - - + +
526A ILE* 4.5 6.5 - - + -
562A LEU* 5.5 4.9 - - + +
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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