Contacts of the helix formed by residues 506 - 515 (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 LEU 506 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5014 ILE* 3.6 23.6 - - + +
5024 THR 3.4 17.5 - - - +
5034 ASP* 3.0 29.7 + - - +
5054 ASP* 1.3 80.0 + - - +
5074 ALA* 1.3 55.2 + - - +
5084 LYS 3.1 4.3 - - - -
5094 ILE* 3.0 39.2 + - + +
5104 ARG* 3.1 32.2 + - - +
7534 TYR* 3.7 34.7 - - + -
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Residues in contact with ALA 507 (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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5034 ASP 3.9 4.8 + - - +
5044 GLN* 3.9 6.9 + - - +
5054 ASP 3.4 0.2 - - - -
5064 LEU* 1.3 74.7 - - - +
5084 LYS* 1.3 59.9 + - - +
5094 ILE 3.2 0.9 - - - -
5104 ARG* 3.1 26.4 - - + +
5114 GLU* 3.0 23.9 + - - +
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Residues in contact with LYS 508 (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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5044 GLN 3.6 6.4 + - - +
5054 ASP* 3.4 26.4 + - + +
5064 LEU 3.1 0.4 - - - -
5074 ALA* 1.3 77.8 - - - +
5094 ILE* 1.3 58.2 + - - +
5114 GLU* 3.4 15.1 + - + +
5124 VAL* 3.0 39.3 + - - +
5154 ARG* 5.8 1.2 - - - +
7434 PRO* 6.1 1.0 - - - +
7464 PHE* 3.2 44.1 - - + +
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Residues in contact with ILE 509 (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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5054 ASP 3.0 12.7 + - - +
5064 LEU* 3.0 31.4 - - + +
5084 LYS* 1.3 76.4 - - - +
5104 ARG* 1.3 59.0 + - - +
5124 VAL* 3.0 6.6 + - + +
5134 ALA* 2.8 23.4 + - - +
5184 LEU* 5.3 0.9 - - - +
7464 PHE* 3.4 21.3 - - + -
7494 MET* 3.6 26.7 - - + -
7504 TYR* 3.4 54.2 - - + -
7534 TYR* 4.5 7.0 - - + -
8134 LEU* 4.1 13.9 - - + -
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Residues in contact with ARG 510 (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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5034 ASP* 5.2 1.4 + - - -
5064 LEU* 3.1 27.5 + - - +
5074 ALA* 3.1 42.2 + - - +
5094 ILE* 1.3 72.4 - - - +
5114 GLU* 1.3 59.6 + - - +
5134 ALA* 3.0 12.2 + - + +
5144 ALA* 2.9 27.4 + - - +
7534 TYR* 3.6 27.5 + - - -
8134 LEU* 3.6 23.7 - - + +
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Residues in contact with GLU 511 (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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5074 ALA 3.0 20.1 + - - +
5084 LYS* 3.4 16.8 + - + +
5104 ARG* 1.3 78.4 - - - +
5124 VAL* 1.3 76.2 + - - +
5134 ALA 3.3 0.3 + - - -
5144 ALA* 3.5 7.8 + - - +
5154 ARG* 3.4 29.8 + - - +
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Residues in contact with VAL 512 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5084 LYS* 3.0 20.8 + - - +
5094 ILE* 3.0 10.6 + - - +
5114 GLU* 1.3 85.0 - - - +
5134 ALA* 1.3 59.0 + - - +
5154 ARG* 3.2 54.5 - - - +
5184 LEU* 3.2 28.6 - - + +
5224 LEU* 4.5 10.8 - - + -
7434 PRO* 5.7 1.3 - - + -
7464 PHE* 3.5 26.2 - - + -
7504 TYR* 5.9 2.5 - - + -
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Residues in contact with ALA 513 (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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5094 ILE* 2.8 11.5 + - + +
5104 ARG* 3.0 19.7 + - + +
5124 VAL* 1.3 75.7 - - - +
5144 ALA* 1.3 62.0 + - - +
5154 ARG 3.1 9.9 - - - +
5184 LEU* 4.3 9.8 - - + +
7504 TYR* 5.4 2.0 - - + +
8124 LYS* 4.4 25.9 - - - +
8134 LEU* 4.8 7.2 - - + -
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Residues in contact with ALA 514 (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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5104 ARG 2.9 13.3 + - - +
5114 GLU* 3.5 7.6 + - - +
5134 ALA* 1.3 73.8 - - - +
5154 ARG* 1.3 64.8 + - - +
5164 GLU* 3.3 5.9 + - - +
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Residues in contact with ARG 515 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5084 LYS* 5.8 1.2 - - - +
5114 GLU* 3.4 23.6 + - - +
5124 VAL* 3.2 58.6 - - - +
5134 ALA 3.1 12.5 - - - +
5144 ALA* 1.3 75.2 - - - +
5164 GLU* 1.3 65.5 + - - +
5174 ASP* 3.1 23.0 + - - +
5184 LEU* 3.7 9.8 + - - +
5214 LEU* 3.2 31.9 - - - +
7414 VAL* 4.7 17.8 - - - +
7434 PRO* 4.7 8.1 - - - +
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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