Contacts of the helix formed by residues 868 - 876 (chain B) in PDB entry 5WRZ
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 868 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767B ASN* 3.0 54.1 + - - +
770B ASP* 3.5 26.1 + - - +
864B SER* 2.8 25.8 + - - +
865B ARG* 3.0 23.4 + - - +
867B THR* 1.3 81.4 + - - +
869B PHE* 1.3 60.0 + - - +
870B ALA 3.3 2.5 - - - -
871B GLY* 3.2 6.9 + - - -
872B ILE* 2.8 30.3 + - + +
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Residues in contact with PHE 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676B ILE* 3.8 20.2 - - + -
862B HIS 4.7 0.7 - - - -
864B SER* 3.2 39.3 - - - -
865B ARG 3.3 16.6 - - - -
866B THR* 3.3 12.3 + - - +
867B THR 3.5 0.2 - - - -
868B ASN* 1.3 77.6 - - - +
870B ALA* 1.3 59.9 - - - +
872B ILE* 4.1 12.3 - - + +
873B LEU* 2.8 40.8 + - + +
918B LEU* 3.4 38.8 - - + -
919B ILE* 4.3 1.6 - - - -
920B LEU* 3.7 28.0 - - + -
1002B LEU* 3.4 32.3 - - + -
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Residues in contact with ALA 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B ILE* 4.2 20.0 + - + +
677B PHE* 4.2 25.4 - - + -
773B VAL* 5.2 0.2 - - - -
774B ALA* 3.7 28.0 - - + -
777B LEU* 4.2 3.8 - - + +
797B LEU* 3.8 13.1 - - + +
867B THR 5.1 0.8 + - - +
868B ASN 3.3 0.4 - - - -
869B PHE* 1.3 77.4 - - - +
871B GLY* 1.3 58.1 + - - +
874B SER* 2.9 32.6 + - - -
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Residues in contact with GLY 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770B ASP* 4.3 18.9 + - - -
773B VAL* 3.8 26.4 - - - +
774B ALA* 4.9 0.2 - - - +
868B ASN 3.2 7.6 + - - -
869B PHE 3.2 0.2 - - - -
870B ALA* 1.3 79.4 - - - +
872B ILE* 1.3 59.7 + - - +
874B SER* 3.8 0.2 - - - -
875B GLN* 3.0 33.6 + - - +
876B GLY 3.9 1.4 + - - +
878B ARG* 4.7 1.7 + - - -
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Residues in contact with ILE 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770B ASP* 4.8 7.0 - - - +
841B ARG* 3.6 2.4 - - - -
862B HIS* 5.0 0.7 - - + +
864B SER* 3.8 31.9 - - - +
868B ASN* 2.8 27.5 + - + +
869B PHE* 3.2 21.3 + - + +
871B GLY* 1.3 77.8 - - - +
873B LEU* 1.3 60.5 + - + +
876B GLY* 2.7 38.7 + - - +
877B LEU* 3.8 34.1 - - + -
920B LEU* 3.9 17.5 - - + -
999B LEU* 4.1 10.9 - - + +
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Residues in contact with LEU 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672B LEU* 5.4 0.4 - - + -
676B ILE* 4.0 22.2 - - + -
797B LEU* 3.4 21.3 - - + +
798B LYS* 4.9 0.7 - - - +
799B THR* 3.2 26.2 + - + +
801B ILE* 4.5 13.5 - - + -
839B ILE* 4.2 26.5 - - + -
841B ARG* 2.8 25.7 + - + +
869B PHE* 2.8 28.6 + - + +
872B ILE* 1.3 81.6 - - + +
874B SER* 1.3 61.8 + - - +
920B LEU* 4.8 3.8 - - + -
999B LEU* 4.9 4.0 - - + -
1002B LEU* 4.3 22.2 - - + -
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Residues in contact with SER 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773B VAL* 4.1 2.3 - - - +
777B LEU* 3.7 24.9 - - - +
796B LYS 4.3 8.5 - - - -
797B LEU* 3.6 15.7 + - - +
798B LYS* 5.3 9.3 - - - +
841B ARG* 3.1 12.5 + - - -
870B ALA 2.9 19.9 + - - -
871B GLY* 3.5 6.1 + - - -
873B LEU* 1.3 78.4 - - - +
875B GLN* 1.3 80.6 + - - +
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Residues in contact with GLN 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773B VAL* 4.3 16.1 - - + +
777B LEU* 5.7 4.4 - - - +
841B ARG* 3.3 11.0 + - - +
847B ARG* 4.8 5.7 + - - -
871B GLY 3.0 13.3 + - - +
874B SER* 1.3 99.1 + - - +
876B GLY* 1.3 60.4 + - - +
877B LEU 4.8 0.2 - - - +
878B ARG* 3.8 38.7 + - - +
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Residues in contact with GLY 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B ARG* 3.3 26.5 - - - +
844B GLU* 4.6 2.7 - - - -
847B ARG* 5.1 1.3 - - - -
872B ILE* 2.7 37.2 + - - +
875B GLN* 1.3 75.6 - - - +
877B LEU* 1.3 65.7 + - - -
878B ARG* 3.4 10.4 + - - +
999B LEU* 4.8 1.8 - - - -
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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