Contacts of the helix formed by residues 463 - 465 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLY* 4.2 1.7 - - - -
69C ASN* 3.4 35.9 - - + +
70C VAL* 4.0 20.0 - - + +
105C ARG* 5.9 4.3 - - + -
106C PRO* 2.5 38.0 + - + +
108C ALA 4.7 0.7 - - - -
357C CYS* 3.4 13.4 - - - -
459C ALA 3.8 11.7 - - - -
460C ARG* 3.7 19.1 - - - +
461C GLN 3.3 1.0 - - - -
462C ALA* 1.3 76.2 - - - +
464C LEU* 1.3 57.5 + - - +
465C TYR 3.1 3.4 - - - +
468C ILE 4.9 0.2 - - - -
469C PHE* 6.3 0.4 - + - -
470C PRO* 3.8 23.6 - - + +
535C GOL 2.7 41.1 + - - +
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Residues in contact with LEU 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ILE* 5.0 3.4 - - + -
70C VAL* 5.6 2.5 - - + -
238C MET* 3.7 42.4 - - + -
265C LYS* 4.3 20.0 - - + -
267C ILE* 3.9 29.2 - - + -
322C PRO* 3.1 34.9 - - + +
324C ILE* 4.1 19.7 - - + -
356C ASP* 3.3 13.9 - - - +
357C CYS* 3.5 13.3 - - - -
461C GLN 3.6 15.9 + - - +
462C ALA 3.1 0.4 - - - -
463C HIS* 1.3 78.5 - - - +
465C TYR* 1.3 60.3 + - + +
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Residues in contact with TYR 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C LYS* 3.7 17.5 + - - +
287C ASP* 5.2 0.9 + - - +
320C GLY 3.8 13.7 - - - -
321C LYS 5.6 0.2 - - - -
322C PRO* 3.6 35.1 - - + +
356C ASP* 3.6 8.1 - - - +
438C HIS* 3.2 66.7 + + + -
441C ALA* 4.2 6.7 - - + -
442C ARG* 6.1 0.4 - - + -
461C GLN 3.6 19.1 - - - -
462C ALA 3.4 7.6 + - - +
463C HIS 3.1 1.2 - - - -
464C LEU* 1.3 85.2 - - + +
466C ARG* 1.3 64.6 + - - +
467C GLY 3.4 0.7 + - - -
468C ILE* 3.5 22.1 + - + -
535C GOL 3.2 19.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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