Contacts of the helix formed by residues 919 - 930 (chain B) in PDB entry 3H44
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 ASP 919 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547B TYR* 2.6 38.3 + - + -
917B ASN* 3.3 6.7 + - - +
918B PHE* 1.3 76.1 - - - +
920B ARG* 1.3 64.7 + - - +
921B ASP 3.2 4.0 + - - -
922B ASN* 2.7 32.8 + - - +
923B THR* 3.4 20.0 + - + +
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Residues in contact with ARG 920 (chain B).
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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800B GLN* 5.4 2.2 + - - -
805B ASN* 3.5 13.1 + - - -
893B ARG* 3.9 8.3 - - - +
910B GLU* 2.8 38.9 + - - +
913B SER* 5.4 0.2 + - - -
915B GLN* 2.6 37.8 + - - +
917B ASN* 3.1 39.5 + - - +
918B PHE 3.2 3.2 + - - +
919B ASP* 1.3 75.3 - - - +
921B ASP* 1.3 58.5 + - - +
923B THR* 3.1 7.4 + - - -
924B GLU* 2.8 78.8 + - - +
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Residues in contact with ASP 921 (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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893B ARG* 3.1 56.2 + - - +
894B LEU* 3.8 13.4 - - + -
896B LYS* 5.7 2.9 + - - +
906B LYS* 2.3 35.8 + - - -
918B PHE 5.3 0.5 + - - +
919B ASP 3.3 0.8 - - - -
920B ARG* 1.3 78.3 - - - +
922B ASN* 1.3 60.4 - - - +
925B VAL* 2.9 37.4 + - - +
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Residues in contact with ASN 922 (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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547B TYR* 3.4 8.8 + - - -
894B LEU* 3.4 23.2 - - - +
896B LYS* 4.9 6.5 - - - +
919B ASP* 2.7 34.4 + - - +
921B ASP* 1.3 78.4 - - - +
923B THR* 1.3 58.2 + - + +
925B VAL* 4.2 1.1 - - - +
926B ALA* 3.0 29.8 + - - +
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Residues in contact with THR 923 (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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802B THR* 4.8 8.9 + - - +
917B ASN* 4.6 6.4 + - - -
919B ASP* 3.4 21.2 + - + +
920B ARG* 3.1 17.2 + - - -
922B ASN* 1.3 79.1 - - - +
924B GLU* 1.3 59.0 + - - +
926B ALA* 3.3 6.3 + - - +
927B TYR* 2.9 30.4 + - - +
1011B HIS* 5.9 0.7 + - - -
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Residues in contact with GLU 924 (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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802B THR* 4.2 26.4 + - + +
805B ASN* 3.0 29.9 - - - +
806B MET* 3.5 29.5 - - + +
809B GLU* 4.4 2.4 - - - +
893B ARG* 2.6 39.6 + - - +
917B ASN* 5.1 1.9 + - - +
920B ARG* 2.8 44.9 + - + +
921B ASP 4.2 1.6 - - - +
923B THR* 1.3 72.6 - - - +
925B VAL* 1.3 54.0 + - - +
927B TYR 3.4 0.7 + - - -
928B LEU* 2.8 32.9 + - - +
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Residues in contact with VAL 925 (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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806B MET* 5.4 1.1 - - + -
890B ALA* 4.1 19.1 - - + +
893B ARG* 3.8 32.8 - - + +
894B LEU* 3.9 29.8 - - + -
921B ASP 2.9 22.1 + - - +
922B ASN* 4.3 1.6 - - - +
924B GLU* 1.3 73.4 - - - +
926B ALA* 1.3 65.7 + - - +
927B TYR 3.1 1.1 - - - -
928B LEU* 3.2 10.6 + - + +
929B LYS* 3.2 45.4 + - - +
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Residues in contact with ALA 926 (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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922B ASN 3.0 19.7 + - - +
923B THR* 3.6 6.3 - - - +
925B VAL* 1.3 79.5 - - - +
927B TYR* 1.3 61.7 + - - +
929B LYS* 3.4 17.7 + - - +
930B THR* 4.0 7.3 + - - +
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Residues in contact with TYR 927 (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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802B THR* 3.9 18.6 - - + -
803B SER* 3.1 40.5 - - - -
806B MET* 4.0 20.0 - - + -
807B PHE* 3.8 11.1 - - - -
923B THR 2.9 16.2 + - - +
924B GLU 3.8 2.7 - - - +
926B ALA* 1.3 74.5 - - - +
928B LEU* 1.3 67.1 + - - +
929B LYS 3.1 1.8 - - - -
930B THR* 3.1 25.5 + - - -
931B LEU* 3.5 33.3 + - + +
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Residues in contact with LEU 928 (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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806B MET* 3.5 21.5 - - + +
810B LEU* 3.6 35.4 - - + -
886B ILE* 3.5 42.3 - - + +
889B LEU* 3.7 15.7 - - + -
890B ALA* 3.9 15.9 - - + +
924B GLU 2.8 21.2 + - - +
925B VAL* 3.3 11.4 - - + +
927B TYR* 1.3 76.8 - - - +
929B LYS* 1.3 58.7 + - - +
931B LEU* 3.0 34.2 - - + +
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Residues in contact with LYS 929 (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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883B GLN* 4.4 18.3 + - - +
886B ILE* 3.9 21.2 - - + +
887B GLN* 5.0 8.6 + - - +
890B ALA* 4.6 13.0 - - - +
894B LEU* 5.6 2.6 - - - +
925B VAL* 3.2 37.1 + - - +
926B ALA* 3.4 11.6 + - - +
927B TYR 3.1 1.4 - - - -
928B LEU* 1.3 79.8 - - - +
930B THR* 1.3 59.8 + - - +
931B LEU 3.1 6.9 + - - +
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Residues in contact with THR 930 (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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926B ALA 4.0 4.9 + - - +
927B TYR* 3.1 27.6 + - - -
929B LYS* 1.3 75.0 - - - +
931B LEU* 1.3 62.9 + - - +
932B THR* 3.5 15.3 - - - +
935B ASP* 4.3 3.3 - - - +
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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