Contacts of the helix formed by residues 820 - 825 (chain I) in PDB entry 6XAV
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 GLU 820 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33H ARG* 2.7 44.1 + - - -
819I SER* 1.3 76.2 + - - +
821I ARG* 1.3 57.5 + - - +
822I VAL 3.2 2.5 - - - -
823I VAL* 2.9 16.7 + - + +
824I GLN* 2.9 53.4 + - + +
1079I ILE* 4.2 10.8 - - + -
1080I ASN 2.8 12.0 + - - +
1081I PRO* 4.0 7.9 - - + +
1082I ILE* 3.7 19.4 - - + +
152K TYR* 4.2 16.1 - - + +
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Residues in contact with ARG 821 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819I SER* 3.4 10.9 + - - +
820I GLU* 1.3 78.8 - - - +
822I VAL* 1.3 61.2 + - + +
824I GLN* 4.1 17.6 + - - +
825I GLU* 3.1 60.1 + - - +
1082I ILE* 3.6 38.4 - - + +
1093I PRO* 4.9 10.2 - - + +
1095I ASP* 4.5 16.4 - - - +
48K LEU* 4.4 5.1 - - - +
180K VAL 4.3 5.3 + - - -
181K GLU* 2.6 52.8 + - - +
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Residues in contact with VAL 822 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800I MET* 3.8 22.0 - - + -
818I VAL* 4.0 26.5 - - + -
819I SER* 3.9 3.1 + - - +
820I GLU 3.2 0.4 - - - -
821I ARG* 1.3 75.9 - - + +
823I VAL* 1.3 61.0 + - - +
825I GLU* 5.1 0.9 - - - +
826I ASP* 3.5 2.8 + - - -
827I ARG* 3.4 49.9 + - + +
828I PHE* 4.0 10.2 + - + +
1060I ILE* 4.8 8.2 - - + +
1095I ASP* 3.8 37.5 - - + +
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Residues in contact with VAL 823 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819I SER 3.5 18.6 - - - +
820I GLU* 2.9 16.7 + - + +
822I VAL* 1.3 77.6 - - - +
824I GLN* 1.3 64.2 + - - +
826I ASP* 3.2 17.5 + - - +
1059I ARG* 3.4 27.3 + - + +
1060I ILE* 3.6 39.0 - - + -
1079I ILE* 3.9 18.4 - - + -
152K TYR* 3.8 11.2 + - + -
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Residues in contact with GLN 824 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820I GLU* 2.9 33.5 + - + +
821I ARG* 4.1 21.0 + - - +
823I VAL* 1.3 76.2 - - - +
825I GLU* 1.3 60.4 + - + +
826I ASP* 3.1 13.4 - - - +
1082I ILE* 3.7 23.3 - - - +
86K LYS* 3.7 18.1 - - - -
151K GLY* 5.3 1.6 - - - -
152K TYR* 3.6 50.6 - - + +
176K CYS* 4.1 9.7 - - + +
178K SER* 5.2 11.2 + - - -
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Residues in contact with GLU 825 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694I ARG* 3.2 23.8 + - - +
821I ARG* 3.1 45.7 + - - +
822I VAL* 5.1 0.3 - - - -
824I GLN* 1.3 75.6 - - + +
826I ASP* 1.3 68.7 + - - +
827I ARG* 3.3 38.6 + - + +
86K LYS* 4.8 12.3 - - - +
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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