Contacts of the helix formed by residues 796 - 806 (chain Z) in PDB entry 5GJQ
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 796 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662Z MET* 6.5 1.1 - - - -
792Z ALA 4.0 5.6 - - - +
793Z VAL* 3.8 13.7 - - - +
794Z ALA 3.2 4.9 + - - -
795Z GLY* 1.3 75.8 - - - +
797Z LEU* 1.3 56.9 + - - +
798Z THR 2.9 2.9 - - - -
799Z VAL* 2.3 34.1 + - - +
800Z LEU* 2.9 7.7 + - - +
821Z LEU* 5.8 0.7 - - - +
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Residues in contact with LEU 797 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560Z LEU* 6.4 1.6 - - + -
659Z LEU* 5.8 8.7 - - + -
793Z VAL 4.4 5.0 + - - +
794Z ALA 5.2 0.2 - - - -
796Z LEU* 1.3 78.1 - - - +
798Z THR* 1.3 61.6 + - - +
800Z LEU* 2.9 23.5 + - + +
801Z VAL* 3.0 17.2 + - - +
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Residues in contact with THR 798 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520Z LEU* 5.4 18.6 - - - -
794Z ALA 3.5 23.1 + - - -
795Z GLY* 4.1 9.0 - - - -
796Z LEU 3.9 0.6 - - - +
797Z LEU* 1.3 76.2 - - - +
799Z VAL* 1.3 60.1 + - - -
801Z VAL* 4.3 2.5 - - - +
802Z SER* 3.2 26.3 + - - -
820Z GLY* 5.7 2.7 - - - -
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Residues in contact with VAL 799 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795Z GLY 4.1 9.6 - - - +
796Z LEU* 2.3 27.3 + - - +
798Z THR* 1.3 71.4 - - - +
800Z LEU* 1.3 59.9 + - - +
802Z SER* 4.1 7.6 - - - -
803Z PHE* 3.4 23.6 + - - +
817Z VAL 5.1 10.3 - - - +
818Z LEU 6.1 0.9 - - - +
820Z GLY* 5.1 4.2 - - - +
821Z LEU* 5.0 12.8 - - + +
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Residues in contact with LEU 800 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658Z ALA* 6.0 6.3 - - + -
659Z LEU* 6.0 4.7 - - - +
796Z LEU 2.9 3.9 + - - +
797Z LEU* 2.9 24.4 + - + +
799Z VAL* 1.3 77.6 - - - +
801Z VAL* 1.3 54.4 + - - +
803Z PHE* 3.7 0.5 - - - +
804Z LEU* 2.3 44.5 + - + +
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Residues in contact with VAL 801 (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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797Z LEU 3.0 13.1 + - - +
798Z THR* 4.5 2.2 - - - +
800Z LEU* 1.3 74.7 - - - +
802Z SER* 1.3 60.0 + - - +
804Z LEU* 3.9 5.6 - - - -
805Z ASP* 2.7 40.6 + - + +
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Residues in contact with SER 802 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798Z THR 3.2 19.9 + - - -
799Z VAL* 4.3 6.7 - - - -
801Z VAL* 1.3 80.7 - - - +
803Z PHE* 1.3 59.0 + - - +
805Z ASP* 4.5 0.6 - - - +
806Z VAL* 3.7 21.5 + - - +
817Z VAL* 3.9 28.2 - - - +
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Residues in contact with PHE 803 (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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799Z VAL 3.4 16.0 + - - +
800Z LEU 3.7 0.4 - - - +
802Z SER* 1.3 78.8 - - - +
804Z LEU* 1.3 59.4 + - - +
805Z ASP 3.6 0.2 - - - -
806Z VAL* 5.3 1.8 - - - -
807Z ARG* 2.9 26.5 + - - +
817Z VAL* 5.9 4.3 - - + +
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Residues in contact with LEU 804 (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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655Z LEU* 5.9 6.5 - - + -
689Z ALA* 6.2 3.8 - - + -
800Z LEU* 2.3 32.9 + - + +
801Z VAL* 3.9 3.8 - - - -
803Z PHE* 1.3 80.1 - - - +
805Z ASP* 1.3 62.8 + - - +
807Z ARG* 3.9 4.6 - - - +
808Z ASN* 3.4 20.8 + - - +
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Residues in contact with ASP 805 (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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801Z VAL* 2.7 27.1 + - + +
802Z SER* 4.5 1.3 - - - +
804Z LEU* 1.3 71.0 - - - +
806Z VAL* 1.3 60.5 + - - +
807Z ARG 3.1 4.6 + - - -
808Z ASN* 3.4 13.4 + - - +
809Z ILE* 3.6 11.6 + - - +
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Residues in contact with VAL 806 (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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802Z SER 3.7 16.2 + - - +
803Z PHE* 5.3 1.3 - - - -
805Z ASP* 1.3 78.5 - - - +
807Z ARG* 1.3 56.7 + - - +
808Z ASN 3.5 0.2 - - - -
809Z ILE* 2.7 26.6 - - - +
810Z ILE 3.0 8.0 - - - +
811Z LEU 3.4 6.2 - - - +
812Z GLY* 4.7 4.2 - - - -
813Z LYS* 4.5 23.1 - - + +
814Z SER 5.7 0.9 - - - +
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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