Contacts of the helix formed by residues 436 - 443 (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 ASP 436 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4180 TYR* 2.9 28.4 + - - -
4220 ASN* 4.7 5.7 - - - +
4240 LEU* 3.3 35.3 - - + +
4340 ARG* 3.6 10.6 + - - +
4350 LEU* 1.3 74.2 - - - +
4370 PRO* 1.3 78.7 - - + +
4380 ILE* 3.2 6.6 + - - +
4390 LEU* 3.6 16.8 + - - +
4400 CYS* 3.1 22.2 + - - +
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Residues in contact with PRO 437 (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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4340 ARG* 5.9 0.9 - - - +
4350 LEU 4.8 0.4 - - - +
4360 ASP* 1.3 89.1 - - + +
4380 ILE* 1.3 58.9 + - + +
4400 CYS* 3.6 6.9 - - + +
4410 ASP* 2.9 40.7 + - - +
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Residues in contact with ILE 438 (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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3930 LEU* 3.8 42.8 - - + +
3940 LEU* 3.7 33.2 - - + +
3960 GLN* 6.0 0.7 - - - +
4180 TYR* 3.2 31.6 - - + +
4360 ASP* 3.2 4.7 - - - +
4370 PRO* 1.3 75.5 - - + +
4390 LEU* 1.3 61.6 + - - +
4410 ASP* 3.3 6.8 + - - +
4420 CYS* 2.9 31.0 + - + +
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Residues in contact with LEU 439 (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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3940 LEU* 3.8 32.1 - - + -
4150 VAL* 5.3 2.7 - - + -
4180 TYR* 4.3 10.3 - - + -
4190 ALA* 5.8 1.1 - - + -
4240 LEU* 4.0 16.2 - - + -
4330 VAL* 4.2 9.0 - - + -
4350 LEU* 3.6 31.6 - - + -
4360 ASP* 3.5 22.4 + - - +
4380 ILE* 1.3 77.5 - - - +
4400 CYS* 1.3 58.8 + - - +
4420 CYS* 3.9 2.7 - - - -
4430 ILE* 2.9 44.3 + - + +
4440 LEU 3.7 1.0 + - - -
4600 LEU* 3.9 26.0 - - + -
4640 CYS* 4.5 2.9 - - - -
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Residues in contact with CYS 440 (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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4350 LEU* 3.7 26.4 - - - +
4360 ASP 3.1 22.1 + - - +
4370 PRO* 3.6 8.1 - - + +
4390 LEU* 1.3 76.1 - - - +
4410 ASP* 1.3 60.9 + - - +
4440 LEU* 3.4 32.6 - - + +
4490 GLN* 3.3 38.4 - - - +
4520 VAL 4.8 4.9 - - - -
4530 MET* 6.1 3.8 - - - -
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Residues in contact with ASP 441 (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 6.1 0.4 - - - +
3930 LEU* 6.1 1.7 - - + +
4370 PRO* 2.9 28.6 + - - +
4380 ILE* 3.6 6.3 - - - +
4390 LEU 3.2 0.4 - - - -
4400 CYS* 1.3 78.8 - - - +
4420 CYS* 1.3 63.7 + - + +
4440 LEU 4.2 7.1 - - - +
4490 GLN* 3.5 17.7 + - - +
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Residues in contact with CYS 442 (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* 3.8 28.0 + - - +
3910 MET* 4.1 15.9 - - + +
3940 LEU* 3.8 29.2 - - - -
4380 ILE* 2.9 29.2 + - + +
4390 LEU* 3.9 8.1 - - - -
4410 ASP* 1.3 77.1 - - + +
4430 ILE* 1.3 85.1 + - - +
4440 LEU 3.7 1.9 + - - +
4670 LYS* 3.8 20.5 + - - +
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Residues in contact with ILE 443 (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* 3.8 11.9 - - + -
4350 LEU* 4.4 4.9 - - + -
4390 LEU* 2.9 39.0 + - + +
4420 CYS* 1.3 84.7 - - - +
4440 LEU* 1.3 64.8 + - + +
4450 GLU* 5.0 1.0 - - - +
4550 LEU* 3.6 31.0 - - + -
4600 LEU* 3.7 15.5 - - + -
4630 ARG* 3.8 31.1 + - + +
4640 CYS* 3.4 36.3 - - - +
4670 LYS* 4.1 15.0 - - + -
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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