Contacts of the helix formed by residues 508 - 520 (chain 2) in PDB entry 5U8T
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 508 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5062 TYR 3.4 2.8 + - - -
5072 GLY* 1.3 81.8 - - - -
5092 ARG* 1.3 62.2 + - - +
5102 ASP* 2.9 25.2 + - + -
5112 ILE* 3.2 27.9 - - + +
5122 LYS* 3.2 15.9 - - - +
5472 THR* 5.9 5.1 - - + +
6832 VAL* 6.1 3.6 - - + +
6842 ARG* 4.6 17.8 - - - +
6852 ASP* 6.1 0.8 - - - -
6952 LEU* 5.6 4.5 - - + -
9012 ANP 6.3 0.4 - - - -
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Residues in contact with ARG 509 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4952 ASP* 2.6 48.5 + - - -
4962 LYS* 5.2 0.4 - - - +
4982 ILE* 3.4 26.7 - - + +
4992 SER* 3.4 29.9 - - - +
5072 GLY 4.1 1.4 + - - -
5082 HIS* 1.3 69.8 - - - +
5102 ASP* 1.3 54.2 + - - +
5122 LYS* 3.7 16.7 - - + +
5132 THR* 2.5 33.7 + - - +
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Residues in contact with ASP 510 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5082 HIS* 2.9 20.6 - - + +
5092 ARG* 1.3 76.3 - - - +
5112 ILE* 1.3 60.1 + - + +
5132 THR* 3.0 20.5 + - - -
5142 ALA* 4.3 1.9 + - - +
6822 VAL 4.9 8.7 - - - +
8432 ASP* 4.7 13.2 - - - +
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Residues in contact with ILE 511 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5082 HIS* 3.2 31.4 - - + +
5102 ASP* 1.3 72.6 - - + +
5122 LYS* 1.3 60.1 + - + +
5132 THR 3.0 2.9 - - - -
5142 ALA* 2.7 32.1 + - + +
5152 VAL* 2.9 27.6 + - + -
5412 LEU* 3.4 34.3 - - + -
5522 ILE* 4.7 18.8 - - + -
6812 CYS* 4.5 20.9 - - + -
6832 VAL* 5.3 12.3 - - + -
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Residues in contact with LYS 512 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4982 ILE* 3.6 28.9 + - + +
4992 SER* 4.9 8.7 + - - +
5012 MET* 4.2 11.0 - - + +
5022 ALA* 3.3 30.9 + - + +
5062 TYR* 2.7 41.9 + - - +
5072 GLY 4.8 0.2 - - - -
5082 HIS 3.2 26.7 - - - +
5092 ARG* 3.7 12.3 + - + +
5102 ASP 3.6 0.2 - - - -
5112 ILE* 1.3 77.7 - - + +
5132 THR* 1.3 63.7 + - - +
5152 VAL* 3.3 13.3 - - + +
5162 ALA* 2.9 27.4 + - - +
5522 ILE* 5.9 3.8 - - + -
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Residues in contact with THR 513 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4982 ILE* 4.4 26.5 - - + +
5092 ARG* 2.5 27.6 + - - +
5102 ASP* 3.0 11.1 + - - -
5122 LYS* 1.3 79.1 - - - +
5142 ALA* 1.3 57.4 + - - +
5162 ALA* 3.9 1.8 - - - +
5172 CYS* 2.9 25.8 + - - +
8202 PHE* 4.5 18.0 - - + -
8362 ARG* 5.3 5.8 - - - -
8402 VAL* 4.2 23.1 - - + -
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Residues in contact with ALA 514 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5102 ASP 5.1 1.3 - - - +
5112 ILE* 2.7 16.4 + - - +
5132 THR* 1.3 77.0 - - - +
5152 VAL* 1.3 56.4 + - + +
5172 CYS* 3.4 9.0 - - - +
5182 SER* 2.9 29.1 + - - -
5392 VAL* 4.3 3.8 - - + +
6792 ILE* 3.6 39.3 - - + +
6812 CYS* 4.8 7.6 - - - -
8402 VAL* 4.9 11.2 - - + +
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Residues in contact with VAL 515 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5012 MET* 4.7 11.4 - - + +
5112 ILE* 2.9 41.1 + - + +
5122 LYS* 2.9 15.5 + - + +
5142 ALA* 1.3 75.2 - - - +
5162 ALA* 1.3 63.7 + - - +
5172 CYS 3.0 0.9 - - - -
5182 SER* 3.2 6.1 + - - -
5192 LEU* 2.9 30.4 + - + +
5392 VAL* 5.5 4.0 - - + -
5522 ILE* 4.4 17.7 - - + -
5552 TYR* 5.8 3.8 - - + -
5562 VAL* 4.4 23.1 - - + -
6472 ILE* 5.0 9.0 - - + +
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Residues in contact with ALA 516 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4972 ILE 4.8 6.5 - - - +
4982 ILE* 6.2 0.4 - - - -
5012 MET* 3.6 36.8 - - + -
5122 LYS 2.9 12.9 + - - +
5132 THR 4.5 1.1 - - - +
5152 VAL* 1.3 72.4 - - - +
5172 CYS* 1.3 59.8 + - - +
5192 LEU* 3.6 12.6 - - + +
5202 PHE* 2.9 33.4 + - - +
7672 ILE* 5.8 0.2 - - + -
8232 MET* 4.5 16.9 - - + +
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Residues in contact with CYS 517 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5132 THR 2.9 21.7 + - - +
5142 ALA* 3.4 10.3 - - - +
5162 ALA* 1.3 79.3 - - - +
5182 SER* 1.3 63.3 + - - +
5202 PHE* 3.2 14.2 + - - +
5372 ILE* 3.8 7.7 - - - +
6792 ILE* 4.5 10.8 - - - -
8162 ILE* 3.5 31.0 - - - -
8192 SER* 3.4 31.3 - - - -
8202 PHE* 3.8 17.9 - - + -
8232 MET* 5.3 3.1 - - - -
8402 VAL* 6.1 0.7 - - - -
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Residues in contact with SER 518 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5142 ALA 2.9 18.3 + - - -
5152 VAL* 3.6 3.4 - - - -
5172 CYS* 1.3 76.1 - - - +
5192 LEU* 1.3 62.0 + - - +
5202 PHE 3.1 0.2 - - - -
5212 GLY* 3.1 12.1 + - - -
5372 ILE* 3.2 42.2 + - - +
5392 VAL* 3.4 25.8 - - - +
6032 VAL* 4.9 2.1 - - - +
6452 SER* 4.2 14.4 + - - -
6462 ILE 4.9 0.3 + - - -
6472 ILE* 4.5 9.8 - - - +
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Residues in contact with LEU 519 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5012 MET* 3.5 28.3 - - + -
5152 VAL* 2.9 18.7 + - + +
5162 ALA* 3.7 10.5 - - + +
5172 CYS 3.2 0.2 - - - -
5182 SER* 1.3 78.5 - - - +
5202 PHE* 1.3 56.8 + - - +
5212 GLY 3.3 0.2 - - - -
5552 TYR* 5.7 1.1 - - + -
5562 VAL* 3.6 32.1 - - + -
5592 THR* 3.5 33.9 - - + -
5602 ALA* 4.1 12.1 - - + +
6032 VAL* 5.0 8.3 - - + -
6472 ILE* 5.9 2.0 - - + -
7672 ILE* 3.5 22.9 - - + +
7712 ARG* 2.8 25.2 + - - +
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Residues in contact with PHE 520 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5162 ALA 2.9 12.8 + - - +
5172 CYS 3.6 7.2 - - - +
5182 SER 3.1 0.8 - - - -
5192 LEU* 1.3 79.4 - - - +
5212 GLY* 1.3 63.6 + - - +
7662 TYR* 3.3 29.4 - + - -
7672 ILE* 3.5 28.5 - - + -
7702 ALA* 3.3 30.3 - - + -
7712 ARG* 3.1 22.8 - - + +
8192 SER* 4.0 6.7 - - - -
8222 LYS* 3.2 47.0 + - + +
8232 MET* 3.4 29.8 - - + -
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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