Contacts of the helix formed by residues 455 - 462 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432H GLU* 3.5 24.5 + - - +
453H THR* 3.0 14.4 + - - +
454H ARG* 1.3 76.9 - - - +
456H PRO* 1.3 68.7 - - - +
457H GLN* 3.1 26.2 + - - +
458H THR* 3.2 16.4 + - - +
459H ALA* 3.3 15.1 + - - +
472H LEU* 3.9 0.4 - - - -
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Residues in contact with PRO 456 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454H ARG 3.4 11.0 - - - +
455H ASN* 1.3 85.1 - - - +
457H GLN* 1.3 67.2 + - + +
459H ALA* 3.2 5.5 + - + +
460H ARG* 3.1 45.3 + - - +
472H LEU* 3.7 28.3 - - + -
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Residues in contact with GLN 457 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H ASP* 4.3 15.1 + - - +
236H VAL 4.9 7.9 + - - -
237H ASP* 4.1 12.1 + - - +
263H ASN* 3.4 35.8 + - - +
264H ILE* 5.1 4.2 - - - +
455H ASN* 3.1 10.9 + - - +
456H PRO* 1.3 76.9 - - + +
458H THR* 1.3 64.8 + - - +
460H ARG* 3.4 19.6 + - - +
461H GLN* 3.1 49.8 + - - +
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Residues in contact with THR 458 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431H THR* 4.7 4.3 - - + -
432H GLU 3.3 15.0 + - - -
433H SER* 3.4 35.0 + - - +
434H GLY* 3.5 11.7 - - - +
438H HIS* 5.5 1.9 + - - +
453H THR* 4.0 16.6 - - + +
455H ASN* 3.2 24.8 + - - -
457H GLN* 1.3 72.8 + - - +
459H ALA* 1.3 66.2 + - - +
461H GLN* 3.1 12.7 + - - +
462H ALA* 3.1 22.9 + - + +
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Residues in contact with ALA 459 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H PRO* 3.8 23.8 - - + -
453H THR* 3.7 22.4 - - + +
455H ASN 3.3 4.4 + - - +
456H PRO* 3.2 12.7 + - + +
458H THR* 1.3 78.3 - - - +
460H ARG* 1.3 61.8 + - - +
462H ALA* 3.4 6.2 + - - -
463H HIS* 3.9 2.9 - - - -
470H PRO* 3.2 36.3 - - + +
472H LEU* 4.7 9.4 - - + +
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Residues in contact with ARG 460 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H ARG* 5.9 3.6 - - - +
104H TYR* 5.9 3.0 + - - +
106H PRO* 4.2 17.7 - - + -
107H VAL 3.4 19.5 - - - +
108H ALA* 3.3 24.5 - - - +
109H VAL* 5.6 1.3 - - - +
235H ASP* 3.8 23.4 + - - -
237H ASP* 2.8 47.3 + - - +
238H MET* 4.5 1.0 - - - +
456H PRO* 3.1 35.5 + - - +
457H GLN* 3.8 23.1 - - - +
458H THR 3.2 0.2 - - - -
459H ALA* 1.3 77.5 - - - +
461H GLN* 1.3 60.6 + - - +
462H ALA 3.2 1.7 + - - -
463H HIS* 3.6 13.2 + - - +
472H LEU* 5.7 0.8 - - - +
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Residues in contact with GLN 461 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237H ASP* 3.7 28.4 + - + +
238H MET* 4.5 7.6 - - + -
263H ASN* 2.8 26.9 + - - +
264H ILE* 4.5 0.4 - - - +
265H LYS* 3.2 32.3 + - + +
433H SER 5.0 5.5 - - - +
438H HIS* 5.1 5.6 - - - +
457H GLN* 3.1 43.7 + - + +
458H THR* 3.1 10.7 + - - +
460H ARG* 1.3 73.4 - - - +
462H ALA* 1.3 62.1 + - - +
463H HIS 3.2 1.3 + - - -
464H LEU* 3.4 16.1 + - - +
465H TYR* 3.6 15.3 - - + -
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Residues in contact with ALA 462 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434H GLY* 6.5 0.4 - - - -
438H HIS* 4.7 7.4 - - + +
451H ALA* 5.4 2.0 - - + -
458H THR* 3.1 13.3 + - + +
459H ALA* 3.4 15.0 - - - +
460H ARG 3.2 0.8 - - - -
461H GLN* 1.3 77.6 - - - +
463H HIS* 1.3 62.2 + - - +
464H LEU 3.2 0.4 - - - -
465H TYR* 3.2 27.5 + - - +
468H ILE* 3.6 36.2 - - + +
470H PRO* 3.9 9.6 - - + -
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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