Contacts of the helix formed by residues 504 - 512 (chain A) in PDB entry 4S15
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 PRO 504 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A GLN* 4.8 4.7 - - - +
324A ALA* 3.9 23.6 - - + +
325A ILE* 4.1 16.6 - - + +
328A THR* 3.5 38.4 - - + +
502A HIS 4.4 2.5 - - - +
503A PHE* 1.3 89.6 - - + +
505A PRO* 1.3 73.9 - - + +
507A TYR* 3.0 7.9 + - + +
508A LYS* 3.0 20.1 + - - +
325B ILE* 4.6 4.7 - - + -
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Residues in contact with PRO 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A PHE 3.5 4.7 - - - +
504A PRO* 1.3 84.1 - - + +
506A LEU* 1.3 57.8 + - - +
508A LYS* 3.4 18.9 + - - +
509A GLU* 2.9 31.3 + - - +
325B ILE* 4.2 19.3 - - + +
329B GLU* 3.7 44.9 - - + +
332B GLN* 4.7 9.6 - - - +
499C LEU* 3.8 14.8 - - + -
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Residues in contact with LEU 506 (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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328A THR* 3.9 14.4 - - + -
331A ILE* 4.0 18.4 - - + -
332A GLN* 3.7 33.7 - - + +
335A VAL* 4.8 2.9 - - + -
504A PRO* 3.3 1.0 - - - +
505A PRO* 1.3 79.4 - - - +
507A TYR* 1.3 56.9 + - - +
509A GLU* 3.6 5.6 - - + +
510A LEU* 2.9 51.0 + - + +
332B GLN* 5.9 0.4 - - - +
499C LEU* 3.8 14.8 - - + +
500C LEU* 4.2 29.6 - - + +
503C LEU* 4.2 20.2 - - + -
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Residues in contact with TYR 507 (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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320A TRP* 3.4 18.5 + - - -
324A ALA* 3.9 21.3 - - + -
327A ILE* 4.0 17.7 - - + -
328A THR* 3.2 27.6 + - - +
331A ILE* 5.2 1.3 - - + -
484A HIS* 2.7 32.8 + - - -
488A LEU* 3.5 24.6 - - + +
499A VAL* 6.4 0.2 - - + -
503A PHE* 3.6 33.0 - + + -
504A PRO* 3.0 13.9 + - + +
506A LEU* 1.3 76.1 - - - +
508A LYS* 1.3 66.8 + - + +
510A LEU* 5.4 0.7 - - - -
511A PHE* 3.1 53.1 + + - +
601A 4D8 4.3 2.8 - - - +
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Residues in contact with LYS 508 (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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499A VAL* 3.1 42.0 - - + +
500A ARG* 2.9 33.6 + - - +
503A PHE* 3.8 20.2 + - + +
504A PRO 3.0 10.5 + - - +
505A PRO* 3.7 20.9 - - - +
507A TYR* 1.3 79.5 - - + +
509A GLU* 1.3 58.3 + - - +
512A THR* 2.4 48.1 + - - +
325B ILE* 6.2 1.2 - - - +
326B LYS* 5.4 2.6 - - - +
329B GLU* 5.7 1.8 + - - -
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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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357A LYS* 3.5 26.2 + - - +
505A PRO* 2.9 18.3 + - - +
506A LEU* 3.6 7.4 - - + +
507A TYR 3.2 0.2 - - - -
508A LYS* 1.3 79.5 - - - +
510A LEU* 1.3 62.1 + - + +
512A THR 4.0 7.5 - - - +
498C THR* 3.1 21.9 + - - +
499C LEU* 3.2 25.8 + - - +
500C LEU* 2.5 40.0 + - + +
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Residues in contact with LEU 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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331A ILE* 3.4 42.6 - - + -
335A VAL* 5.5 0.4 - - + -
356A LEU 3.9 7.2 - - - +
357A LYS* 3.7 47.7 - - + +
360A SER* 4.6 6.7 - - - +
506A LEU* 2.9 34.5 + - + +
509A GLU* 1.3 78.9 - - + +
511A PHE* 1.3 80.5 + - + +
500C LEU* 3.7 32.5 - - + -
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Residues in contact with PHE 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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327A ILE* 4.7 0.9 - - + -
331A ILE* 3.4 34.8 - - + -
357A LYS 4.4 13.0 - - - -
360A SER* 5.4 1.1 - - - -
361A LEU* 3.8 36.6 - - + -
484A HIS* 3.9 16.6 - + + -
485A THR* 4.8 20.5 + - - +
488A LEU* 3.6 20.0 - - + +
489A MET* 3.9 12.0 - - - +
507A TYR* 3.1 45.6 + + - +
510A LEU* 1.3 97.8 - - + +
512A THR* 1.3 61.9 + - - +
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Residues in contact with THR 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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357A LYS* 5.8 1.4 - - - -
488A LEU* 3.6 31.4 - - + -
489A MET* 3.9 16.6 - - - -
492A LYS* 3.9 41.5 + - + +
499A VAL* 4.9 7.4 - - + +
507A TYR* 6.1 0.2 - - + -
508A LYS* 2.4 45.7 + - - +
509A GLU* 4.0 8.7 - - - +
510A LEU 5.1 0.2 - - - -
511A PHE* 1.3 83.2 - - - +
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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