Contacts of the helix formed by residues 821 - 834 (chain 4) 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 ASP 821 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8054 ALA* 3.6 12.6 - - - +
8084 HIS* 3.2 35.6 + - + +
8174 VAL* 2.9 31.9 - - - +
8184 GLU 2.9 17.1 - - - +
8194 LEU 3.2 1.4 - - - +
8204 GLU* 1.3 71.3 - - - +
8224 VAL* 1.3 78.8 + - - +
8234 GLN* 2.7 16.4 + - - -
8244 GLU* 2.7 37.4 + - - +
8254 ALA* 3.2 5.8 + - - +
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Residues in contact with VAL 822 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7664 ALA* 5.4 8.5 - - + +
7694 GLU* 5.0 9.9 - - + -
7704 LEU* 4.3 27.6 - - + +
8014 MET* 4.0 24.7 - - + +
8054 ALA* 3.6 15.9 - - + -
8194 LEU 4.3 7.4 - - - +
8214 ASP* 1.3 93.4 + - - +
8234 GLN* 1.3 57.6 + - - +
8254 ALA* 3.5 13.2 - - + -
8264 VAL* 2.8 44.7 + - + +
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Residues in contact with GLN 823 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7694 GLU* 2.5 43.4 + - - +
8194 LEU* 3.8 3.1 - - - +
8204 GLU* 3.1 39.5 - - + +
8214 ASP 2.7 22.9 + - - +
8224 VAL* 1.3 69.5 + - - +
8244 GLU* 1.3 63.3 + - - +
8264 VAL* 3.6 5.7 + - - +
8274 ARG* 2.9 24.5 + - - +
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Residues in contact with GLU 824 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5194 TYR* 3.6 28.2 + - + +
5384 LYS* 5.2 6.0 - - - +
5424 LEU* 6.4 0.2 - - - -
8084 HIS* 2.9 33.9 + - + -
8204 GLU* 4.7 4.3 - - - +
8214 ASP* 2.7 31.4 + - - +
8234 GLN* 1.3 78.7 - - + +
8254 ALA* 1.3 60.7 + - + +
8274 ARG* 3.3 26.0 - - - +
8284 LEU* 2.9 30.5 + - - +
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Residues in contact with ALA 825 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5424 LEU* 6.3 0.2 - - - -
8014 MET 4.7 2.0 - - - +
8044 LEU* 3.6 28.0 - - + +
8054 ALA* 3.9 20.4 - - + +
8084 HIS* 5.8 2.0 - - + -
8214 ASP 3.2 5.8 + - - +
8224 VAL* 3.5 22.2 - - + +
8244 GLU* 1.3 75.5 - - - +
8264 VAL* 1.3 61.3 + - - +
8274 ARG 3.1 0.9 - - - -
8284 LEU* 2.9 18.7 + - - +
8294 ILE* 3.0 19.7 + - + +
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Residues in contact with VAL 826 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7694 GLU* 6.2 1.3 - - + -
7734 ALA* 4.3 16.6 - - + -
7774 MET* 4.0 7.4 - - + -
8014 MET* 3.9 23.3 - - + -
8224 VAL* 2.8 37.2 + - + +
8234 GLN* 3.7 4.9 - - - +
8254 ALA* 1.3 75.5 - - - +
8274 ARG* 1.3 50.9 + - - +
8294 ILE* 2.9 15.1 + - + +
8304 ARG* 2.8 71.1 + - + +
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Residues in contact with ARG 827 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5384 LYS* 4.4 18.1 - - - +
8234 GLN 2.9 19.0 + - - +
8244 GLU* 3.3 24.0 - - - +
8264 VAL* 1.3 79.0 - - - +
8284 LEU* 1.3 58.2 + - + +
8304 ARG* 3.3 12.7 + - + +
8314 SER* 2.9 26.5 + - - -
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Residues in contact with LEU 828 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5194 TYR* 4.4 2.5 - - - +
5354 ASP* 4.2 12.1 - - + +
5384 LYS* 4.0 22.9 - - + -
5394 GLY* 3.8 16.6 - - - +
5424 LEU* 3.6 22.4 - - + -
7044 LEU* 3.1 15.4 - - + +
7064 TYR* 3.7 17.7 - - - +
8044 LEU* 3.5 33.7 - - + -
8244 GLU 2.9 16.2 + - - +
8254 ALA 2.9 12.1 + - - +
8274 ARG* 1.3 79.2 - - + +
8294 ILE* 1.3 57.1 + - - +
8314 SER* 2.2 28.9 + - - +
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Residues in contact with ILE 829 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7034 ASP 5.7 3.1 - - - +
7044 LEU* 3.9 8.7 - - + -
7774 MET* 3.9 9.9 - - + -
7974 GLN* 4.2 36.1 - - + +
8004 SER* 5.3 1.6 - - - +
8014 MET* 3.6 41.7 - - + -
8044 LEU* 4.5 11.7 - - + -
8254 ALA* 3.2 15.9 - - + +
8264 VAL* 2.9 14.1 + - + +
8284 LEU* 1.3 75.8 - - - +
8304 ARG* 1.3 63.7 + - - +
8314 SER 3.0 1.8 - - - -
8324 ALA* 3.1 9.7 + - - +
8334 ILE* 3.0 37.7 + - + +
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Residues in contact with ARG 830 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7734 ALA* 4.8 10.3 + - - +
7764 GLY* 5.7 1.6 - - - -
7774 MET* 2.8 42.0 - - - +
8264 VAL* 2.8 43.3 + - + +
8274 ARG* 3.5 13.0 - - + +
8294 ILE* 1.3 72.4 - - - +
8314 SER* 1.3 51.9 + - - +
8334 ILE* 3.2 14.8 - - - +
8344 LYS* 2.2 76.8 + - + +
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Residues in contact with SER 831 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5354 ASP* 5.4 8.3 - - - -
7044 LEU* 3.9 1.9 - - - +
7054 VAL 4.2 0.7 - - - -
7064 TYR* 3.6 28.0 - - - -
8274 ARG 2.9 13.0 + - - -
8284 LEU* 2.2 32.8 + - - -
8294 ILE 3.0 0.4 - - - -
8304 ARG* 1.3 76.9 - - - +
8324 ALA* 1.3 59.5 + - - +
8344 LYS* 3.6 7.5 + - - +
8354 ASP* 2.9 31.5 + - - +
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Residues in contact with ALA 832 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7044 LEU* 3.5 14.1 - - + -
7054 VAL* 3.1 47.1 + - + +
7974 GLN* 5.7 4.3 - - - +
8294 ILE 3.1 4.6 + - - +
8314 SER* 1.3 80.8 + - - +
8334 ILE* 1.3 59.9 + - + +
8354 ASP* 3.1 21.3 + - - +
8364 TYR* 3.2 24.6 - - + +
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Residues in contact with ILE 833 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7774 MET* 3.5 35.2 - - + +
7934 ALA* 5.6 6.7 - - + -
7974 GLN* 5.3 6.3 - - + +
8294 ILE* 3.2 24.9 - - + +
8304 ARG* 2.8 18.5 + - + +
8324 ALA* 1.3 75.1 - - + +
8344 LYS* 1.3 59.6 + - + +
8354 ASP 3.0 4.7 - - - -
8364 TYR* 2.9 40.5 + - + +
8374 ALA* 3.5 5.5 + - - +
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Residues in contact with LYS 834 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8304 ARG* 2.2 71.3 + - + +
8314 SER* 4.0 8.1 - - - +
8334 ILE* 1.3 71.7 - - + +
8354 ASP* 1.3 63.7 + - - +
8364 TYR 3.2 0.6 + - - -
8374 ALA* 3.8 20.3 - - + +
8384 THR 4.9 0.5 + - - -
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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
------------------------------------------------------------
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