Contacts of the helix formed by residues 840 - 849 (chain Z) in PDB entry 5WTI
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 SER 840 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294Z ARG* 3.6 5.6 - - - +
328Z ARG* 3.3 32.1 - - - +
329Z GLU* 3.9 16.8 + - - -
839Z ARG* 1.3 78.9 - - - +
841Z ARG* 1.3 61.1 + - - +
842Z PHE* 3.6 7.9 + - - +
843Z GLU* 3.0 26.5 + - - +
844Z ASN* 2.8 34.2 + - - -
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Residues in contact with ARG 841 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B U 3.5 24.2 - - - +
114B C 3.3 44.2 + - - +
115B A 5.2 6.5 + - - -
2E T 2.9 50.7 + - - +
3E T 3.3 42.1 + - - +
291Z ARG* 4.4 9.4 - - - +
294Z ARG* 4.2 1.8 - - - +
328Z ARG 4.9 0.6 + - - -
840Z SER* 1.3 74.5 - - - +
842Z PHE* 1.3 58.3 + - - +
844Z ASN* 3.8 0.7 - - - +
845Z SER* 2.8 34.7 + - - -
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Residues in contact with PHE 842 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E T 5.0 3.0 + - - +
328Z ARG* 3.8 50.7 - - - +
840Z SER* 3.1 6.1 + - - +
841Z ARG* 1.3 78.1 - - - +
843Z GLU* 1.3 66.0 + - + +
845Z SER* 3.3 8.4 + - - -
846Z LYS* 3.1 30.1 + - + +
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Residues in contact with GLU 843 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329Z GLU* 4.2 13.8 - - - +
833Z TYR* 2.7 31.8 + - - +
839Z ARG* 4.0 23.5 + - + +
840Z SER* 3.0 19.4 + - - +
842Z PHE* 1.3 78.3 - - + +
844Z ASN* 1.3 65.3 + - - +
846Z LYS* 3.2 32.4 + - + +
847Z LEU* 3.1 28.2 + - + +
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Residues in contact with ASN 844 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B G 3.3 19.4 + - - +
113B U 2.8 34.0 + - - +
291Z ARG* 3.8 3.8 - - - +
835Z PRO* 3.2 21.2 - - + +
836Z TYR 2.8 22.0 + - - -
839Z ARG* 3.2 26.1 - - - +
840Z SER 2.8 25.1 + - - +
843Z GLU* 1.3 70.3 - - - +
845Z SER* 1.3 65.1 + - - +
847Z LEU* 3.5 4.1 + - - +
848Z MET* 3.2 22.9 + - - +
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Residues in contact with SER 845 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B U 3.0 33.0 + - - -
114B C 4.1 4.0 + - - -
841Z ARG 2.8 23.0 + - - -
842Z PHE* 3.5 8.3 - - - -
843Z GLU 3.3 0.2 - - - -
844Z ASN* 1.3 77.2 - - - +
846Z LYS* 1.3 61.2 + - - +
848Z MET* 3.8 5.4 - - - +
849Z LYS* 3.2 45.7 + - - +
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Residues in contact with LYS 846 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577Z GLN* 5.0 13.2 - - + +
833Z TYR* 3.5 27.3 + - - -
842Z PHE* 3.1 21.6 + - + +
843Z GLU* 3.2 29.8 + - + +
845Z SER* 1.3 75.7 - - - +
847Z LEU* 1.3 63.6 + - + +
849Z LYS* 3.7 4.3 + - - +
850Z TRP* 3.0 53.8 + - + +
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Residues in contact with LEU 847 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E T 4.6 2.9 - - - +
833Z TYR* 3.6 69.3 - - + +
835Z PRO* 4.0 25.6 - - + +
839Z ARG* 4.3 20.9 - - - +
843Z GLU* 3.1 20.3 + - + +
844Z ASN* 3.5 1.1 + - - +
845Z SER 3.4 0.2 - - - -
846Z LYS* 1.3 79.5 - - + +
848Z MET* 1.3 65.2 + - - +
850Z TRP* 3.5 29.7 + - + +
851Z SER 3.7 5.2 + - - -
852Z ARG* 4.0 18.3 + - - +
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Residues in contact with MET 848 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B G 3.7 31.0 - - - +
113B U 3.9 33.4 - - - +
10E C 5.3 1.6 - - + +
11E T 3.8 38.1 - - + +
12E T 3.2 34.2 - - - +
748Z ASP* 5.6 4.3 - - - +
835Z PRO* 4.8 5.1 - - + +
844Z ASN 3.2 16.9 + - - +
845Z SER* 3.8 6.1 - - - +
846Z LYS 3.3 0.2 - - - -
847Z LEU* 1.3 75.0 - - - +
849Z LYS* 1.3 76.6 + - + +
850Z TRP 3.1 5.3 + - - -
851Z SER 3.8 1.2 + - - -
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Residues in contact with LYS 849 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741Z LEU* 3.6 16.3 - - + +
744Z ILE* 4.1 24.4 - - + +
745Z ASP* 3.7 29.1 + - - +
748Z ASP* 3.9 29.8 + - - +
752Z LYS* 5.5 3.0 - - - +
784Z LEU* 6.0 0.9 - - + -
788Z LYS* 3.4 21.5 - - - +
845Z SER* 3.2 31.7 + - - +
846Z LYS* 3.9 3.8 - - - +
848Z MET* 1.3 89.6 - - + +
850Z TRP* 1.3 60.5 + - - +
851Z SER 3.6 0.2 - - - -
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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