Contacts of the helix formed by residues 907 - 915 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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905A TYR* 4.1 1.0 - - - +
906A ARG* 1.3 85.7 - - + +
908A VAL* 1.3 63.4 + - - +
909A SER* 3.6 9.2 + - - -
910A GLU* 2.9 29.8 + - + +
911A TRP* 3.0 18.9 + - - +
930A ASP 5.8 1.3 - - - -
931A THR* 6.0 0.7 - - - +
932A MET* 3.5 11.4 - - - +
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Residues in contact with VAL 908 (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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907A THR* 1.3 70.6 - - - +
909A SER* 1.3 56.9 + - - +
911A TRP* 3.4 10.0 + - + +
912A LEU* 2.9 40.9 + - + +
921A ILE* 3.9 18.8 - - + -
924A PHE* 4.2 9.6 - - + -
925A HIS* 5.0 4.5 - - - +
929A LEU 3.7 15.9 - - - +
930A ASP* 3.7 9.8 + - - +
931A THR 3.5 41.5 - - - +
932A MET* 3.6 13.9 - - - +
935A VAL* 4.3 7.9 - - + -
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Residues in contact with SER 909 (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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907A THR* 3.1 8.9 + - - -
908A VAL* 1.3 79.2 - - - +
910A GLU* 1.3 56.2 + - - +
912A LEU* 4.0 1.5 - - - +
913A GLU* 3.0 32.7 + - - +
918A LYS* 3.4 24.9 + - - +
921A ILE* 3.9 21.9 - - - +
925A HIS* 5.6 3.5 + - - -
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Residues in contact with GLU 910 (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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904A PRO 3.9 1.0 - - - +
905A TYR* 3.5 13.0 - - - -
906A ARG* 3.0 31.9 + - - +
907A THR* 2.9 23.5 + - - +
909A SER* 1.3 72.5 + - - +
911A TRP* 1.3 57.1 + - - +
913A GLU* 3.4 9.0 + - - +
914A SER* 2.8 36.9 + - - +
916B ARG* 2.4 35.5 + - - +
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Residues in contact with TRP 911 (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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905A TYR* 3.6 40.6 - + + +
907A THR 3.0 15.7 + - - +
908A VAL* 3.6 19.5 - - + +
910A GLU* 1.3 75.5 - - - +
912A LEU* 1.3 74.4 + - + +
914A SER* 3.1 13.0 + - - -
915A ILE* 3.2 25.8 + - + +
924A PHE* 3.6 39.0 - + - -
932A MET* 3.7 18.6 - - + -
935A VAL* 3.8 14.8 - - + -
957A ILE* 3.9 18.2 - - + -
960A SER* 2.8 27.2 + - - -
961A ILE* 3.8 25.6 - - + -
964A PHE* 3.7 8.7 - + - -
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Residues in contact with LEU 912 (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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908A VAL* 2.9 23.3 + - + +
909A SER 4.1 2.5 - - - +
911A TRP* 1.3 103.1 - - + +
913A GLU* 1.3 58.5 + - - +
915A ILE* 3.2 7.3 + - + +
916A ARG 2.9 8.3 + - - -
917A MET* 2.8 50.9 + - + +
918A LYS* 3.8 15.5 - - + +
921A ILE* 3.6 36.6 - - + +
924A PHE* 3.8 32.5 - - + -
957A ILE* 4.7 1.8 - - + -
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Residues in contact with GLU 913 (chain A).
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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2A NO3 4.5 3.3 + - - +
909A SER* 3.0 20.7 + - - +
910A GLU* 3.7 7.1 - - - +
912A LEU* 1.3 75.9 - - - +
914A SER* 1.3 61.3 + - - +
916A ARG* 2.9 35.8 + - - +
918A LYS* 4.1 38.4 + - + +
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Residues in contact with SER 914 (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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905A TYR* 3.3 29.7 - - - -
910A GLU* 2.8 19.1 + - - +
911A TRP 3.1 8.7 + - - -
913A GLU* 1.3 75.2 - - - +
915A ILE* 1.3 52.2 + - - +
916A ARG* 3.4 7.4 + - - +
905B TYR* 2.6 36.8 + - - -
914B SER* 3.4 18.3 - - - +
916B ARG* 3.7 13.9 + - - -
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Residues in contact with ILE 915 (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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905A TYR* 4.7 9.0 - - - +
911A TRP* 3.2 43.7 + - + +
912A LEU* 3.5 10.8 - - + +
914A SER* 1.3 78.4 - - - +
916A ARG* 1.3 66.4 + - - +
917A MET* 3.4 9.4 + - + -
956A ARG* 2.9 39.4 + - + +
957A ILE* 3.9 27.1 - - + -
960A SER* 3.6 31.4 - - - +
904B PRO* 4.8 0.2 - - - +
905B TYR* 3.5 11.4 - - - +
915B ILE* 5.7 4.0 - - + -
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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