Contacts of the helix formed by residues 810 - 819 (chain D) in PDB entry 5UH8
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 ASN 810 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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803D VAL* 4.2 4.2 - - - +
809D GLY* 1.3 82.8 + - - +
811D PHE* 1.3 64.5 + - - +
812D THR* 3.1 23.6 + - + +
813D GLN* 3.1 36.5 + - + +
814D THR* 3.4 7.3 + - - -
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Residues in contact with PHE 811 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786D GLY* 3.1 42.6 - - - -
789D LEU* 3.6 20.6 - - + -
790D ARG* 3.5 53.6 - - + +
800D ILE* 4.0 23.3 - - + -
803D VAL* 3.9 15.8 - - + +
804D ASP* 5.3 0.2 - - - -
810D ASN* 1.3 72.4 - - - +
812D THR* 1.3 56.2 + - + +
814D THR* 3.0 18.8 + - + -
815D ARG* 2.7 36.8 + - + +
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Residues in contact with THR 812 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810D ASN* 3.3 23.4 + - + +
811D PHE* 1.3 81.3 - - + +
813D GLN* 1.3 54.1 + - - +
815D ARG* 3.6 29.3 + - - +
816D THR* 2.6 35.1 + - - -
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Residues in contact with GLN 813 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923C PRO 4.0 11.0 - - - +
924C ARG* 3.7 35.0 + - - +
926C MET* 4.0 10.8 - - + +
809D GLY* 3.5 12.2 - - - -
810D ASN* 3.1 39.7 + - + +
812D THR* 1.3 76.7 + - - +
814D THR* 1.3 55.3 + - - +
816D THR* 2.9 10.6 + - - -
817D LEU* 2.8 35.4 + - - +
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Residues in contact with THR 814 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923C PRO* 6.1 0.3 - - - +
789D LEU* 3.7 12.1 - - + +
793D TYR* 4.4 6.5 - - + -
799D ILE* 3.7 27.1 - - + +
800D ILE* 4.1 17.5 - - + -
803D VAL* 3.5 27.2 - - - +
810D ASN 3.4 2.5 + - - -
811D PHE* 3.0 22.1 + - + -
813D GLN* 1.3 77.9 - - - +
815D ARG* 1.3 57.2 + - - +
817D LEU* 3.3 8.6 + - + +
818D ALA* 3.0 26.9 + - + -
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Residues in contact with ARG 815 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782D THR* 3.4 47.9 - - - +
783D ASP* 5.3 1.3 + - - +
785D VAL* 4.8 5.4 - - + -
786D GLY* 4.4 12.1 - - - +
789D LEU* 4.0 10.7 - - + +
811D PHE* 2.7 28.2 + - + +
812D THR* 3.6 33.2 + - - +
814D THR* 1.3 72.4 - - - +
816D THR* 1.3 57.0 + - - +
819D GLY* 2.8 9.9 + - - -
820D MET* 2.7 57.5 + - + +
821D LYS 3.2 19.4 + - - -
822D GLY* 4.4 0.2 - - - -
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Residues in contact with THR 816 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C ASP* 5.4 0.7 - - - +
926C MET* 4.1 11.0 - - + -
812D THR 2.6 22.0 + - - -
813D GLN* 2.9 11.5 + - - -
815D ARG* 1.3 84.7 + - - +
817D LEU* 1.3 60.7 + - - +
820D MET 3.4 10.8 + - - -
821D LYS* 3.7 29.6 + - + +
839D SER* 3.9 6.2 - - - -
840D PHE* 3.3 42.1 + - + -
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Residues in contact with LEU 817 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923C PRO* 4.3 27.8 - - + +
926C MET* 3.6 19.1 - - + -
928C ILE* 3.5 42.8 - - + -
736D VAL* 3.7 35.2 - - + -
799D ILE* 5.0 10.8 - - + -
813D GLN 2.8 14.8 + - - +
814D THR* 3.6 8.1 - - + +
816D THR* 1.3 78.2 - - - +
818D ALA* 1.3 59.7 + - + +
839D SER* 3.4 0.9 - - - -
840D PHE* 3.4 5.2 + - + +
841D ARG* 3.3 22.7 + - - +
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Residues in contact with ALA 818 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736D VAL* 4.1 11.2 - - + -
737D LEU 3.2 26.9 - - - +
738D VAL* 3.6 6.8 - - - +
739D PRO* 3.3 17.5 - - - +
742D LYS* 4.9 0.3 + - - -
789D LEU* 4.1 8.5 - - + -
793D TYR* 3.5 14.1 - - + +
814D THR* 3.0 13.5 + - + +
817D LEU* 1.3 75.7 - - + +
819D GLY* 1.3 64.4 + - - +
839D SER* 3.5 10.8 + - - -
841D ARG* 4.9 2.7 - - - -
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Residues in contact with GLY 819 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739D PRO* 4.2 7.4 - - - -
742D LYS* 3.2 19.4 + - - -
785D VAL* 3.5 23.3 - - - -
789D LEU* 4.1 5.4 - - - +
814D THR 4.0 0.6 + - - -
815D ARG 2.8 11.7 + - - -
818D ALA* 1.3 77.9 - - - +
820D MET* 1.3 64.5 + - - +
839D SER* 3.2 14.4 - - - -
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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