Contacts of the helix formed by residues 950 - 963 (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 LEU 950 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920B TYR* 4.5 11.0 + - - +
948B ILE 3.8 0.4 - - - -
949B THR* 1.3 87.4 + - - +
951B PRO* 1.3 73.3 - - + +
952B GLY* 4.4 2.0 - - - +
953B HIS* 3.0 52.3 + - + +
954B GLN* 3.0 13.0 + - - +
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Residues in contact with PRO 951 (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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949B THR 3.3 9.9 - - - +
950B LEU* 1.3 84.8 - - + +
952B GLY* 1.3 57.9 + - - +
954B GLN* 3.4 11.0 + - + +
955B LYS* 2.9 30.3 + - - +
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Residues in contact with GLY 952 (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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963A GLY 4.9 0.2 - - - +
964A PHE* 5.8 0.2 - - - +
950B LEU* 3.1 3.3 - - - +
951B PRO* 1.3 79.2 - - - +
953B HIS* 1.3 65.0 + - - +
955B LYS* 3.5 15.3 + - - +
956B ARG* 3.1 27.7 + - - +
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Residues in contact with HIS 953 (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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917B MET* 3.2 38.1 - - + +
919B ARG* 3.6 34.9 + - - -
920B TYR* 2.7 30.9 + - + +
948B ILE* 4.4 4.0 - - + -
950B LEU* 3.0 38.7 + - + +
952B GLY* 1.3 79.3 - - - +
954B GLN* 1.3 65.6 + - - +
956B ARG* 3.4 5.6 + - + +
957B ILE* 3.1 20.9 + - - +
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Residues in contact with GLN 954 (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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940B ALA* 3.4 27.0 + - - +
943B LEU* 3.7 19.3 - - + -
944B THR* 3.0 31.9 + - - +
948B ILE* 2.8 32.5 + - + +
949B THR* 3.9 11.4 + - - +
950B LEU 3.0 11.6 + - - +
951B PRO* 3.7 11.8 - - + +
953B HIS* 1.3 77.0 - - - +
955B LYS* 1.3 56.8 + - - +
957B ILE* 3.3 2.4 + - - +
958B LEU* 2.8 40.9 + - + +
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Residues in contact with LYS 955 (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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962A GLN 3.2 20.9 + - - +
963A GLY 3.7 8.3 - - - -
964A PHE 3.1 25.8 + - - -
951B PRO 2.9 17.8 + - - +
952B GLY* 3.7 12.3 - - - +
954B GLN* 1.3 72.1 - - - +
956B ARG* 1.3 59.5 + - - +
958B LEU* 4.7 3.6 - - - -
959B CYS* 2.7 56.1 + - - +
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Residues in contact with ARG 956 (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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902A GLY 3.5 14.8 - - - +
904A PRO* 3.5 32.4 - - - +
905A TYR* 5.4 2.0 - - - -
963A GLY* 2.8 32.8 + - - +
964A PHE* 2.6 24.5 + - - -
915B ILE* 2.9 43.0 + - + +
916B ARG* 3.9 10.3 + - - +
917B MET* 3.7 17.1 - - + +
952B GLY 3.1 15.1 + - - +
953B HIS* 3.6 15.1 - - + +
955B LYS* 1.3 75.6 - - - +
957B ILE* 1.3 61.6 + - - +
959B CYS* 4.2 0.9 - - - +
960B SER* 3.2 25.2 + - - -
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Residues in contact with ILE 957 (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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911B TRP* 4.0 21.5 - - + -
912B LEU* 4.8 2.2 - - + -
915B ILE* 3.9 16.4 - - + -
917B MET* 3.2 36.8 - - + -
920B TYR* 4.5 1.3 - - + -
924B PHE* 4.3 11.2 - - + -
938B LEU* 4.6 0.2 - - + -
943B LEU* 4.0 23.8 - - + -
948B ILE* 4.0 31.2 - - + -
953B HIS 3.1 11.5 + - - +
954B GLN 3.7 2.9 - - - +
956B ARG* 1.3 76.4 - - - +
958B LEU* 1.3 65.1 + - + +
960B SER* 3.2 5.0 - - - -
961B ILE* 3.1 31.5 + - + +
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Residues in contact with LEU 958 (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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938B LEU* 3.6 31.4 - - + +
939B THR* 4.1 6.7 - - - -
940B ALA* 3.8 31.6 - - + +
943B LEU* 3.7 17.7 - - + -
954B GLN* 2.8 28.9 + - + +
955B LYS* 4.2 3.6 - - - +
957B ILE* 1.3 69.7 - - - +
959B CYS* 1.3 66.7 + - - +
961B ILE* 3.4 10.2 + - + +
962B GLN* 3.0 29.0 + - + +
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Residues in contact with CYS 959 (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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959A CYS* 3.3 35.3 - - + +
962A GLN* 4.0 11.2 - - - -
963A GLY* 3.7 17.9 - - - -
955B LYS* 2.7 45.3 + - - +
956B ARG 4.2 0.2 - - - +
958B LEU* 1.3 70.8 - - - +
960B SER* 1.3 63.6 + - - +
962B GLN* 3.3 6.3 + - - +
963B GLY 3.0 17.2 + - - -
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Residues in contact with SER 960 (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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956A ARG* 5.8 0.3 - - - -
959A CYS 5.9 0.9 - - - -
960A SER* 5.9 3.1 - - - +
905B TYR* 5.3 1.4 + - - -
911B TRP* 3.6 18.5 - - - -
915B ILE* 2.7 37.5 - - - +
956B ARG 3.2 10.7 + - - -
957B ILE 3.2 10.5 - - - -
959B CYS* 1.3 77.8 - - - +
961B ILE* 1.3 64.1 + - - +
963B GLY* 2.9 13.4 + - - -
964B PHE* 3.3 18.0 + - - -
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Residues in contact with ILE 961 (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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911B TRP* 3.7 24.0 - - + -
935B VAL* 3.4 20.4 - - + +
936B LEU* 3.6 26.5 - - + +
938B LEU* 3.7 28.9 - - + +
957B ILE* 3.1 21.4 + - + +
958B LEU* 3.9 10.5 - - + +
959B CYS 3.4 0.2 - - - -
960B SER* 1.3 79.5 - - - +
962B GLN* 1.3 71.0 + - - +
964B PHE* 3.1 42.1 + - + +
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Residues in contact with GLN 962 (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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955A LYS* 3.5 37.5 + - - +
959A CYS* 4.0 14.1 - - - -
936B LEU 5.3 3.2 + - - -
958B LEU* 3.0 21.1 + - + +
959B CYS* 3.7 7.2 - - - +
960B SER 3.3 0.4 - - - -
961B ILE* 1.3 85.9 + - - +
963B GLY* 1.3 59.4 + - - +
964B PHE 3.5 4.5 + - - +
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Residues in contact with GLY 963 (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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952A GLY 4.6 1.4 - - - +
955A LYS* 4.2 3.3 - - - +
956A ARG* 2.8 44.0 + - - +
959A CYS* 3.8 21.7 - - - -
959B CYS 3.0 5.5 + - - -
960B SER 2.9 11.5 + - - -
962B GLN* 1.3 76.2 - - - +
964B PHE* 1.3 61.8 + - - +
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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