Contacts of the helix formed by residues 455 - 462 (chain F) in PDB entry 3SRF
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 ASN 455 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432F GLU* 3.7 10.5 + - + +
453F THR* 3.0 13.4 + - - +
454F ARG* 1.3 77.8 - - - +
456F PRO* 1.4 68.7 - - - +
457F GLN* 3.3 13.9 + - - +
458F THR* 3.1 32.5 + - - +
459F ALA* 3.1 18.7 + - - +
472F LEU* 4.0 2.2 - - - -
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Residues in contact with PRO 456 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F PRO* 5.5 0.2 - - - +
454F ARG 3.3 9.4 - - - +
455F ASN* 1.4 87.6 - - - +
457F GLN* 1.3 61.0 + - - +
459F ALA* 3.3 5.7 + - + +
460F ARG* 3.2 43.3 + - - +
472F LEU* 3.9 30.2 - - + +
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Residues in contact with GLN 457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F ASP* 4.5 13.8 + - - +
236F VAL 4.7 8.1 + - - -
237F ASP* 3.7 9.6 - - - +
263F ASN* 3.4 38.3 + - - +
264F ILE* 4.5 4.4 - - - +
455F ASN* 3.3 10.3 + - - +
456F PRO* 1.3 76.4 - - - +
458F THR* 1.3 65.8 + - - +
460F ARG* 3.5 25.5 - - - +
461F GLN* 3.1 48.4 + - - +
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Residues in contact with THR 458 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431F THR* 4.7 3.1 - - + +
432F GLU 2.9 28.2 + - - +
433F SER* 3.6 9.8 + - - +
434F GLY* 3.6 25.8 - - - +
438F HIS* 5.6 1.3 + - - +
453F THR* 3.6 15.0 - - + +
455F ASN* 3.1 23.8 + - - -
457F GLN* 1.3 74.7 + - - +
459F ALA* 1.3 65.4 + - - +
461F GLN* 3.6 6.6 + - - +
462F ALA* 3.1 25.1 + - + +
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Residues in contact with ALA 459 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F PRO* 4.2 23.1 - - + -
453F THR* 3.7 23.5 - - + +
455F ASN 3.1 8.5 + - - +
456F PRO* 3.4 13.2 - - + +
457F GLN 3.3 0.2 - - - -
458F THR* 1.3 76.5 - - - +
460F ARG* 1.3 62.5 + - - +
462F ALA* 3.4 6.2 + - - -
463F HIS* 4.1 1.4 + - - -
470F PRO* 3.2 31.9 - - + +
472F LEU* 4.5 11.4 - - + +
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Residues in contact with ARG 460 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ARG* 6.0 4.8 - - - +
104F TYR* 5.9 1.3 - - - +
106F PRO* 4.5 11.9 - - + -
107F VAL 3.4 22.0 - - - +
108F ALA* 3.3 25.0 - - - +
109F VAL* 5.9 1.6 - - - -
235F ASP* 4.7 17.5 + - - -
237F ASP* 2.8 47.6 + - - +
238F MET* 4.4 0.3 - - - +
456F PRO* 3.2 35.3 + - - +
457F GLN* 3.5 23.0 + - - +
459F ALA* 1.3 78.5 - - - +
461F GLN* 1.3 60.0 + - - +
462F ALA 3.4 0.5 + - - -
463F HIS* 3.5 17.9 + - - +
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Residues in contact with GLN 461 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F ASP* 3.0 35.6 + - + +
238F MET* 4.4 8.7 - - + -
263F ASN 2.6 30.9 + - - +
265F LYS* 3.6 30.9 - - + +
438F HIS* 5.3 3.1 - - + +
457F GLN* 3.1 40.3 + - + +
458F THR* 4.2 5.8 - - - +
459F ALA 3.4 0.2 - - - -
460F ARG* 1.3 72.0 - - - +
462F ALA* 1.3 59.4 + - - +
463F HIS 3.1 6.7 + - - -
464F LEU* 3.3 22.3 + - + +
465F TYR* 3.8 8.5 - - - -
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Residues in contact with ALA 462 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434F GLY* 6.4 0.7 - - - -
437F ALA* 6.2 1.1 - - + -
438F HIS* 4.7 8.7 + - - +
451F ALA* 5.6 2.0 - - + -
453F THR* 6.4 0.2 - - + -
458F THR* 3.1 20.1 + - + +
459F ALA* 3.4 9.6 - - - +
460F ARG 3.2 0.4 - - - -
461F GLN* 1.3 72.7 - - - +
463F HIS* 1.3 61.1 + - - +
464F LEU 3.1 6.1 + - - -
465F TYR* 3.2 26.2 + - - +
468F ILE* 3.8 33.3 - - + +
470F PRO* 3.9 10.3 - - + -
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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