Contacts of the helix formed by residues 463 - 465 (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 HIS 463 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45F GLY* 4.3 1.7 - - - -
69F ASN* 3.2 52.9 + - + +
70F VAL* 4.3 13.9 - - + +
105F ARG* 4.3 9.3 + - - +
106F PRO* 2.6 34.2 + - - +
108F ALA 4.6 0.9 - - - -
238F MET* 6.1 0.2 - - + -
357F CYS* 3.3 15.8 - - - -
459F ALA 4.1 1.8 - - - -
460F ARG 3.5 18.1 + - - +
461F GLN 3.1 1.0 - - - -
462F ALA* 1.3 75.9 - - - +
464F LEU* 1.3 62.3 + - - +
465F TYR 3.1 0.8 + - - -
468F ILE 5.0 0.2 - - - -
470F PRO* 3.5 33.0 - - + +
536F GOL 3.3 29.5 + - - -
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Residues in contact with LEU 464 (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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47F ILE* 5.4 1.8 - - + -
70F VAL* 5.7 1.6 - - + -
238F MET* 3.6 39.3 - - + -
265F LYS* 4.3 23.6 - - + -
267F ILE* 3.8 28.9 - - + -
287F ASP* 6.3 0.2 - - + -
322F PRO* 3.3 21.1 - - + +
324F ILE* 4.0 19.7 - - + +
356F ASP* 3.2 23.4 - - - +
357F CYS* 3.6 10.6 - - - -
461F GLN* 3.3 18.2 + - - +
462F ALA 3.1 0.6 - - - -
463F HIS* 1.3 77.6 - - - +
465F TYR* 1.3 68.8 + - + +
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Residues in contact with TYR 465 (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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265F LYS* 3.7 24.9 + - - +
287F ASP 4.8 2.3 + - - -
320F GLY 4.2 12.3 - - - -
321F LYS 5.4 0.4 - - - -
322F PRO* 3.4 37.0 - - + +
356F ASP* 3.5 9.6 - - - +
438F HIS* 3.4 58.3 + + + +
441F ALA* 4.4 5.6 - - + -
442F ARG* 6.5 0.4 - - + -
461F GLN 3.8 15.7 - - - -
462F ALA 3.2 9.2 + - - +
463F HIS 3.1 0.6 - - - -
464F LEU* 1.3 87.7 - - + +
466F ARG* 1.3 66.1 + - - +
467F GLY 3.4 2.3 + - - -
468F ILE* 3.5 26.8 + - + -
536F GOL 3.4 14.3 + - - -
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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