Contacts of the helix formed by residues 907 - 915 (chain B) in PDB entry 3HIL
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 THR 907 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905B TYR* 4.2 0.9 - - - +
906B ARG* 1.3 87.2 - - + +
908B VAL* 1.3 55.4 + - - +
909B SER* 3.6 10.9 + - - -
910B GLU* 3.1 27.9 + - - +
911B TRP* 3.0 19.4 + - - +
931B THR* 6.2 0.4 - - - +
932B MET* 2.7 22.1 - - - +
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Residues in contact with VAL 908 (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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907B THR* 1.3 71.9 - - - +
909B SER* 1.3 58.5 + - - +
911B TRP* 3.4 8.5 + - + +
912B LEU* 2.9 47.7 + - + +
921B ILE* 4.7 7.4 - - + -
924B PHE* 4.1 21.8 - - + -
929B LEU 4.0 6.3 - - - +
930B ASP* 3.8 19.7 + - - +
931B THR* 3.6 30.0 - - - +
932B MET* 2.7 19.2 - - + +
935B VAL* 4.6 5.6 - - + -
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Residues in contact with SER 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B THR* 3.2 10.0 + - - -
908B VAL* 1.3 79.8 - - - +
910B GLU* 1.3 57.0 + - - +
912B LEU* 3.9 2.7 - - - +
913B GLU* 2.9 32.0 + - - +
918B LYS* 4.1 17.1 - - - +
921B ILE* 3.0 33.6 - - - +
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Residues in contact with GLU 910 (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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916A ARG* 3.0 31.6 + - - +
904B PRO 4.3 0.5 - - - +
905B TYR* 3.4 8.4 - - + -
906B ARG* 3.1 53.2 + - - +
907B THR* 3.1 20.7 + - - +
909B SER* 1.3 71.8 - - - +
911B TRP* 1.3 60.0 + - - +
913B GLU* 3.4 8.7 + - - +
914B SER* 2.8 33.7 + - - +
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Residues in contact with TRP 911 (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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905B TYR* 3.5 43.9 - + + +
907B THR 3.0 6.0 + - - +
908B VAL* 3.9 8.3 - - + -
910B GLU* 1.3 75.3 - - - +
912B LEU* 1.3 84.2 + - + +
914B SER* 3.1 12.8 + - - -
915B ILE* 3.1 25.4 + - + +
924B PHE* 3.7 37.5 - + - -
932B MET* 3.0 42.2 - - + -
935B VAL* 4.0 12.3 - - + -
957B ILE* 4.0 17.0 - - + -
960B SER* 3.6 17.8 - - - -
961B ILE* 3.7 25.8 - - + -
964B PHE* 3.5 15.0 - + - -
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Residues in contact with LEU 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B VAL* 2.9 36.6 + - + +
909B SER 4.0 1.6 - - - +
911B TRP* 1.3 104.8 - - + +
913B GLU* 1.3 56.6 + - - +
915B ILE* 3.2 8.4 + - + -
916B ARG 2.8 9.4 + - - -
917B MET* 2.7 57.1 + - + +
918B LYS* 3.8 5.2 - - + +
920B TYR 4.1 0.2 - - - -
921B ILE* 3.6 39.5 - - + +
924B PHE* 4.0 18.4 - - + -
957B ILE* 4.8 2.9 - - + -
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Residues in contact with GLU 913 (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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909B SER 2.9 18.4 + - - +
910B GLU* 3.7 8.3 - - - +
912B LEU* 1.3 76.2 - - - +
914B SER* 1.3 52.7 + - - +
916B ARG* 2.8 41.7 + - - +
918B LYS* 3.3 42.6 + - + +
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Residues in contact with SER 914 (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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905A TYR* 2.6 37.2 + - - -
914A SER* 3.4 26.9 + - - -
916A ARG* 3.7 15.4 + - - -
905B TYR* 3.4 21.4 - - - -
910B GLU* 2.8 16.3 + - - +
911B TRP 3.1 9.6 + - - -
913B GLU* 1.3 77.6 - - - +
915B ILE* 1.3 52.8 + - - +
916B ARG* 3.8 5.6 - - - +
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Residues in contact with ILE 915 (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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905A TYR* 3.7 10.1 - - - +
915A ILE* 5.7 4.3 - - + -
905B TYR* 4.7 9.6 - - - +
911B TRP* 3.1 38.5 + - + +
912B LEU* 3.2 16.1 + - + +
914B SER* 1.3 78.2 - - - +
916B ARG* 1.3 66.1 + - - +
917B MET* 3.4 9.3 + - + -
956B ARG* 2.9 40.2 + - + +
957B ILE* 3.9 26.5 - - + -
960B SER* 2.7 39.5 - - - +
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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