Contacts of the helix formed by residues 950 - 964 (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 LEU 950 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920A TYR* 4.0 8.6 + - - +
948A ILE 3.8 0.2 - - - -
949A THR* 1.3 81.9 + - - +
951A PRO* 1.4 70.9 - - + +
952A GLY 3.4 2.0 - - - +
953A HIS* 3.0 44.5 + - + +
954A GLN* 2.9 25.5 + - - +
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Residues in contact with PRO 951 (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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949A THR 3.1 9.3 - - - +
950A LEU* 1.4 89.9 - - + +
952A GLY* 1.3 59.3 + - - +
954A GLN* 3.3 11.7 + - + +
955A LYS* 2.9 29.5 + - - +
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Residues in contact with GLY 952 (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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950A LEU* 3.4 1.0 - - - +
951A PRO* 1.3 80.1 - - - +
953A HIS* 1.3 64.4 + - - +
955A LYS* 3.7 8.1 - - - +
956A ARG* 2.9 27.9 + - - +
963B GLY 4.6 2.4 - - - +
964B PHE* 5.5 1.9 - - - +
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Residues in contact with HIS 953 (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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917A MET* 3.9 29.5 - - + +
919A ARG* 3.9 23.7 + - - -
920A TYR* 2.6 36.9 + + + +
948A ILE* 4.6 3.4 - - + -
950A LEU* 3.0 34.5 + - + +
952A GLY* 1.3 81.5 - - - +
954A GLN* 1.3 65.6 + - - +
956A ARG* 3.2 7.6 + - + +
957A ILE* 2.9 30.9 + - - +
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Residues in contact with GLN 954 (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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940A ALA* 3.3 29.6 + - - +
943A LEU* 3.8 19.7 - - + -
944A THR* 3.0 26.5 + - - +
948A ILE* 2.8 30.6 + - + +
949A THR* 3.8 12.4 + - - +
950A LEU 2.9 14.2 + - - +
951A PRO* 3.6 11.0 - - - +
953A HIS* 1.3 77.9 - - - +
955A LYS* 1.3 56.0 + - - +
957A ILE* 3.7 1.7 - - - +
958A LEU* 2.8 40.2 + - + +
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Residues in contact with LYS 955 (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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951A PRO 2.9 17.7 + - - +
952A GLY* 3.7 9.0 - - - +
954A GLN* 1.3 74.4 - - - +
956A ARG* 1.3 59.9 + - - +
958A LEU* 4.6 5.2 - - - +
959A CYS* 2.8 53.7 + - - +
962B GLN* 3.5 40.0 + - - +
963B GLY* 4.3 2.0 - - - +
964B PHE 5.9 0.9 - - - +
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Residues in contact with ARG 956 (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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915A ILE* 2.9 40.1 + - + +
916A ARG* 3.9 5.7 + - - +
917A MET* 3.8 27.3 - - + +
919A ARG* 5.4 1.2 - - - +
952A GLY 2.9 20.3 + - - +
953A HIS* 3.2 12.2 + - - +
955A LYS* 1.3 72.5 - - - +
957A ILE* 1.3 61.7 + - - +
959A CYS* 4.1 1.2 - - - +
960A SER* 3.2 24.1 + - - -
903B ILE 5.9 0.2 - - - +
904B PRO* 3.5 35.7 - - - +
905B TYR* 5.4 2.2 - - - -
960B SER 5.8 0.4 - - - -
963B GLY* 2.8 38.2 + - - +
964B PHE* 2.9 22.9 + - - +
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Residues in contact with ILE 957 (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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911A TRP* 3.9 22.0 - - + -
912A LEU* 4.7 2.7 - - + -
915A ILE* 3.9 19.7 - - + -
917A MET* 4.1 21.3 - - + -
920A TYR* 4.4 7.0 - - + -
924A PHE* 4.3 13.2 - - + -
938A LEU* 4.7 0.7 - - + -
943A LEU* 4.0 17.9 - - + -
948A ILE* 4.0 33.2 - - + -
953A HIS 2.9 20.8 + - - +
954A GLN 3.7 3.1 - - - +
956A ARG* 1.3 76.4 - - - +
958A LEU* 1.3 62.6 + - + +
960A SER* 3.3 4.7 + - - -
961A ILE* 3.1 32.6 + - + +
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Residues in contact with LEU 958 (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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938A LEU* 3.4 36.3 - - + +
939A THR* 4.1 1.6 - - - -
940A ALA* 3.7 32.8 - - + +
943A LEU* 4.0 15.5 - - + -
954A GLN* 2.8 28.4 + - + +
955A LYS* 4.3 4.0 - - - +
957A ILE* 1.3 71.6 - - - +
959A CYS* 1.3 63.3 + - - +
961A ILE* 3.4 10.3 + - + +
962A GLN* 3.1 30.7 + - + +
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Residues in contact with CYS 959 (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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955A LYS* 2.8 49.1 + - - +
956A ARG 4.2 0.2 - - - +
958A LEU* 1.3 73.9 - - - +
960A SER* 1.3 56.1 + - - +
962A GLN* 3.4 6.8 + - - +
963A GLY 2.9 23.2 + - - -
959B CYS* 3.3 32.8 - - - +
960B SER* 5.6 0.2 - - - -
962B GLN* 4.0 14.1 - - - -
963B GLY* 3.8 18.2 - - - -
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Residues in contact with SER 960 (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* 4.6 2.4 + - - -
911A TRP* 2.8 32.2 + - - -
915A ILE* 3.6 21.5 - - - +
956A ARG 3.2 20.2 + - - -
957A ILE 3.3 5.4 + - - -
959A CYS* 1.3 75.4 - - - +
961A ILE* 1.3 57.4 + - - +
963A GLY* 3.0 18.5 + - - -
964A PHE* 3.3 18.9 + - - -
959B CYS* 5.6 1.3 - - - -
960B SER* 5.9 3.3 - - - +
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Residues in contact with ILE 961 (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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911A TRP* 3.8 20.6 - - + -
935A VAL* 3.5 20.0 - - + +
936A LEU* 3.5 33.9 - - + +
938A LEU* 4.2 14.6 - - + +
957A ILE* 3.1 33.8 + - + +
958A LEU* 3.8 11.2 - - + +
960A SER* 1.3 76.6 - - - +
962A GLN* 1.3 69.0 + - - +
964A PHE* 3.1 39.1 + - + +
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Residues in contact with GLN 962 (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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936A LEU 5.2 3.4 + - - -
938A LEU 6.0 0.4 + - - -
958A LEU* 3.1 21.0 + - + +
959A CYS* 3.6 7.9 - - - +
961A ILE* 1.3 85.1 - - - +
963A GLY* 1.3 57.3 + - - +
964A PHE 3.5 0.2 + - - -
955B LYS* 3.2 29.3 + - - +
959B CYS* 4.0 13.0 - - - -
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Residues in contact with GLY 963 (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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959A CYS 2.9 10.1 + - - -
960A SER* 3.0 7.9 + - - -
962A GLN* 1.3 76.5 - - - +
964A PHE* 1.4 62.8 + - - +
952B GLY 4.9 0.3 - - - +
955B LYS* 3.7 7.3 - - - -
956B ARG* 2.8 37.3 + - - +
959B CYS* 3.7 23.1 - - - -
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Residues in contact with PHE 964 (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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902A GLY* 3.7 11.6 + - - -
903A ILE* 4.3 13.5 - - + +
904A PRO* 3.7 21.7 - - + +
905A TYR* 3.6 19.3 - + - -
911A TRP* 3.7 12.1 - - - -
932A MET* 3.5 33.2 - - + -
935A VAL* 4.4 0.9 - - + -
936A LEU* 3.9 27.1 - - + -
960A SER* 3.3 24.5 - - - -
961A ILE* 3.1 36.6 + - + +
962A GLN 3.3 0.4 - - - +
963A GLY* 1.4 77.9 - - - +
952B GLY 5.8 0.2 - - - +
955B LYS* 3.1 25.8 + - - -
956B ARG* 2.6 30.0 + - - +
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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