Contacts of the helix formed by residues 391 - 396 (chain 0) in PDB entry 5OA3
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 MET 391 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3870 VAL* 4.6 0.2 - - - -
3880 PRO* 3.4 20.3 + - + +
3890 ALA 2.9 1.2 + - - -
3900 SER* 1.3 83.1 + - - +
3920 THR* 1.3 64.6 + - - +
3930 LEU* 3.2 3.1 - - - -
3940 LEU* 2.9 49.5 + - + +
3950 PHE* 3.4 20.5 + - + -
4420 CYS* 4.1 14.8 - - + -
4430 ILE* 3.8 21.8 - - + -
4640 CYS* 3.8 18.8 - - + +
4670 LYS* 3.6 24.0 - - + -
4680 LEU* 3.7 26.7 - - - -
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Residues in contact with THR 392 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3870 VAL* 4.5 8.5 - - - -
3880 PRO 3.7 5.9 + - - -
3890 ALA* 2.9 22.2 + - + +
3900 SER 3.5 0.8 - - - +
3910 MET* 1.3 75.0 - - - +
3930 LEU* 1.3 83.6 + - + +
3950 PHE* 2.9 15.7 + - - +
3960 GLN* 3.0 13.1 + - - +
4000 HIS 4.4 1.9 + - - +
4010 LYS* 3.0 46.6 + - - +
4020 LYS 4.8 3.8 - - - -
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Residues in contact with LEU 393 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3900 SER 5.0 3.8 + - - +
3910 MET 3.2 1.3 - - - -
3920 THR* 1.3 88.5 - - + +
3940 LEU* 1.3 63.9 + - - +
3960 GLN* 2.9 41.1 + - - +
3970 GLU 4.6 0.3 + - - -
4180 TYR* 4.9 3.6 - - - -
4380 ILE* 3.8 39.9 - - + +
4410 ASP* 6.1 1.6 - - + +
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Residues in contact with LEU 394 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3910 MET* 2.9 47.2 + - + +
3930 LEU* 1.3 74.3 - - - +
3950 PHE* 1.3 65.7 + - + +
3960 GLN 3.4 0.4 + - - -
3970 GLU* 4.8 2.4 + - - +
4140 ILE* 4.5 9.2 - - + +
4150 VAL* 4.6 11.9 - - + -
4180 TYR* 3.7 50.6 - - + -
4380 ILE* 3.7 17.6 - - + +
4390 LEU* 3.8 15.3 - - + -
4420 CYS* 3.8 15.5 - - - -
4640 CYS* 3.9 17.7 - - - -
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Residues in contact with PHE 395 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3870 VAL* 3.8 16.2 - - + -
3910 MET* 3.4 30.6 + - + -
3920 THR 2.9 7.9 + - - +
3940 LEU* 1.3 84.8 - - + +
3960 GLN* 1.3 65.4 + - - +
3970 GLU 3.2 3.1 - - - -
3980 SER* 2.6 31.4 + - - +
3990 GLY 3.4 4.9 + - - -
4000 HIS* 3.4 23.1 - - + +
4060 LEU* 3.4 27.6 - - + -
4110 VAL* 4.4 12.6 - - + -
4140 ILE* 3.6 33.7 - - + -
4150 VAL* 5.4 2.5 - - + -
4680 LEU* 3.9 36.8 - - + -
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Residues in contact with GLN 396 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3920 THR 3.0 9.0 + - - +
3930 LEU* 2.9 38.3 + - - +
3940 LEU 3.4 0.2 - - - -
3950 PHE* 1.3 76.6 - - - +
3970 GLU* 1.3 61.9 + - + +
3980 SER 3.5 0.2 + - - -
3990 GLY* 3.7 9.4 + - - -
4000 HIS 4.7 3.1 - - - -
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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