Contacts of the helix formed by residues 823 - 833 (chain A) in PDB entry 3BWT
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 GLY 823 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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790A ILE* 3.8 24.9 - - - +
818A GLU 3.4 7.5 + - - -
819A ILE 3.3 9.9 - - - -
821A ASN 3.3 0.4 - - - -
822A ASN* 1.3 80.8 - - - +
824A GLY* 1.3 61.0 + - - +
826A THR* 3.8 5.7 + - - +
827A GLY* 2.8 25.4 + - - -
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Residues in contact with GLY 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819A ILE 3.4 8.1 + - - -
820A LEU 3.5 16.1 + - - -
821A ASN 4.1 4.2 + - - -
822A ASN 3.8 0.8 - - - -
823A GLY* 1.3 76.4 - - - +
825A GLU* 1.3 57.8 + - - -
828A ILE* 2.8 38.0 + - - +
862A ILE* 4.6 5.4 - - - -
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Residues in contact with GLU 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A GLY* 1.3 71.0 - - - -
826A THR* 1.3 56.9 + - - +
829A GLN* 2.8 35.3 + - + +
862A ILE* 3.4 42.7 - - + +
865A PRO* 4.2 16.1 - - - +
866A LEU* 4.0 20.0 - - + +
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Residues in contact with THR 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823A GLY 4.2 4.5 - - - +
824A GLY 3.2 0.6 - - - -
825A GLU* 1.3 78.3 - - - +
827A GLY* 1.3 61.1 + - - +
829A GLN* 3.3 13.9 + - - +
830A SER* 2.9 36.2 + - - +
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Residues in contact with GLY 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A ILE* 3.9 22.7 - - - -
823A GLY* 2.8 27.9 + - - -
826A THR* 1.3 75.8 - - - +
828A ILE* 1.3 56.7 + - - +
830A SER* 3.0 11.6 + - - -
831A LEU* 2.9 30.5 + - - +
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Residues in contact with ILE 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A ILE* 4.6 0.2 - - - +
819A ILE* 4.2 28.7 - - + +
820A LEU* 4.4 13.9 - - + -
824A GLY 2.8 23.0 + - - +
825A GLU 4.1 1.3 - - - +
827A GLY* 1.3 75.3 - - - +
829A GLN* 1.3 59.0 + - - +
831A LEU* 3.1 8.1 + - + +
832A LEU* 2.8 27.9 + - + +
841A LEU* 3.9 14.1 - - + +
859A LEU* 4.6 9.9 - - + +
862A ILE* 3.8 38.6 - - + -
863A VAL* 3.9 25.6 - - + -
866A LEU* 4.3 8.3 - - + -
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Residues in contact with GLN 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A GLU* 2.8 25.0 + - - +
826A THR* 3.6 11.2 + - - +
828A ILE* 1.3 73.7 - - - +
830A SER* 1.3 63.0 + - - +
832A LEU* 3.5 3.7 + - + +
833A ASN* 3.2 45.9 + - - +
866A LEU* 3.6 36.8 - - + +
871A ILE* 6.2 0.2 - - + -
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Residues in contact with SER 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A ILE* 4.9 7.6 - - - +
794A ILE* 4.6 10.0 - - - +
826A THR* 2.9 23.5 + - - +
827A GLY* 3.1 15.4 - - - -
829A GLN* 1.3 77.6 - - - +
831A LEU* 1.3 63.6 + - - +
833A ASN* 3.2 4.0 + - - +
834A ASP* 3.1 26.2 + - - +
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Residues in contact with LEU 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A ILE* 4.0 17.3 - - + -
793A SER* 3.9 26.7 - - - +
794A ILE* 3.9 14.8 - - + -
819A ILE* 4.1 31.4 - - + -
827A GLY 2.9 17.4 + - - +
828A ILE* 3.1 9.4 + - - +
830A SER* 1.3 71.3 - - - +
832A LEU* 1.3 67.5 + - - +
833A ASN 2.8 3.9 + - - -
834A ASP* 3.0 6.1 + - - -
837A GLY* 3.6 25.6 - - - +
838A ASN* 2.9 23.2 + - - -
840A VAL* 4.8 0.9 - - + -
841A LEU* 4.0 24.2 - - + +
844A ALA* 6.2 0.4 - - + -
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Residues in contact with LEU 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A ILE* 2.8 20.9 + - + +
829A GLN* 3.7 6.1 - - - +
831A LEU* 1.3 72.8 - - - +
833A ASN* 1.3 61.2 + - - +
834A ASP 3.8 0.2 + - - -
838A ASN* 3.0 23.5 - - - +
841A LEU* 3.6 13.1 - - + +
863A VAL* 5.0 3.4 - - + +
866A LEU* 3.6 34.1 - - + -
867A LEU* 3.8 23.3 - - + -
871A ILE* 3.7 33.0 - - + -
876A HIS* 3.6 9.9 - - - -
877A GLY* 4.9 1.8 - - - -
880A ILE* 3.7 29.8 - - + -
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Residues in contact with ASN 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A GLN* 3.2 40.0 + - - +
830A SER* 3.2 4.5 + - - +
831A LEU 2.9 1.6 - - - -
832A LEU* 1.3 79.8 - - - +
834A ASP* 1.3 59.8 + - - +
835A SER 4.1 0.5 + - - -
871A ILE* 3.8 32.2 - - - +
876A HIS* 4.4 14.7 + - - -
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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