Contacts of the helix formed by residues 945 - 956 (chain F) in PDB entry 5LHY
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 PRO 945 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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938F TYR* 3.8 28.9 - - + +
943F LYS 3.9 2.9 - - - +
944F LEU* 1.3 88.3 - - + +
946F ASP* 1.3 62.1 + - - +
947F TYR* 3.4 29.2 - - + -
948F ILE* 3.1 15.2 + - + +
949F LYS* 2.9 24.1 + - - +
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Residues in contact with ASP 946 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944F LEU 4.7 2.4 - - - +
945F PRO* 1.3 75.8 - - - +
947F TYR* 1.3 59.5 + - - +
949F LYS* 3.0 16.7 + - - +
950F GLN* 2.9 32.8 + - - +
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Residues in contact with TYR 947 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928F TYR* 3.4 38.8 - + - -
930F SER* 6.0 0.7 - - - -
936F THR* 5.6 2.4 + - - -
938F TYR* 4.5 6.6 + - - -
945F PRO* 3.5 27.8 - - + -
946F ASP* 1.3 77.0 - - - +
948F ILE* 1.3 77.7 + - + +
950F GLN* 3.8 20.5 - - - +
951F LYS* 3.4 32.1 - - - +
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Residues in contact with ILE 948 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917E LEU* 4.9 9.0 - - + +
926F ILE* 4.7 13.5 - - + -
928F TYR* 3.4 44.2 - - + -
938F TYR* 4.5 11.0 - - + +
944F LEU* 3.7 25.6 - - + -
945F PRO* 3.1 24.4 + - + +
946F ASP 3.1 0.6 - - - -
947F TYR* 1.3 104.7 - - + +
949F LYS* 1.3 59.1 + - - +
951F LYS* 3.3 4.6 + - - +
952F LEU* 2.9 30.2 + - + +
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Residues in contact with LYS 949 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902F LEU* 3.4 32.1 - - + +
944F LEU* 4.8 10.7 - - + +
945F PRO 2.9 15.7 + - - +
946F ASP* 3.0 16.7 + - - +
948F ILE* 1.3 78.5 - - - +
950F GLN* 1.3 57.3 + - - +
952F LEU* 3.4 5.6 + - - -
953F GLN* 2.8 45.8 + - + +
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Residues in contact with GLN 950 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890E SER* 5.2 9.5 + - - -
891E VAL* 5.1 16.1 - - - +
946F ASP 2.9 17.5 + - - +
947F TYR* 3.8 24.3 - - - +
949F LYS* 1.3 78.9 - - - +
951F LYS* 1.3 65.3 + - + +
953F GLN* 3.1 12.7 + - + +
954F CYS* 3.0 30.6 + - - -
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Residues in contact with LYS 951 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891E VAL* 4.0 22.7 - - + -
911E PHE* 3.7 22.8 - - + -
913E ASP* 3.5 18.4 + - - -
915E SER* 2.9 25.6 + - - +
917E LEU* 3.9 17.0 - - + +
928F TYR* 2.7 40.2 + - + +
931F PRO* 5.0 1.4 - - - +
947F TYR* 3.4 21.9 + - - +
948F ILE* 3.3 8.6 + - - +
949F LYS 3.3 0.4 - - - -
950F GLN* 1.3 80.8 - - + +
952F LEU* 1.3 65.2 + - - +
954F CYS* 3.3 19.9 + - - +
955F LEU* 3.7 4.9 + - - +
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Residues in contact with LEU 952 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917E LEU* 4.1 11.8 - - + +
919E VAL* 4.6 21.3 - - + -
901F GLN 5.2 1.7 - - - +
902F LEU* 3.3 49.5 - - + +
903F THR* 4.8 4.3 - - + -
923F VAL* 5.7 1.6 - - + -
926F ILE* 3.5 29.2 - - + -
944F LEU* 4.4 11.2 - - + -
948F ILE* 2.9 16.6 + - + +
949F LYS* 3.7 1.8 - - - +
951F LYS* 1.3 75.9 - - - +
953F GLN* 1.3 63.0 + - - +
955F LEU* 3.1 27.6 + - + +
956F SER* 3.3 10.4 + - - -
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Residues in contact with GLN 953 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902F LEU* 3.5 27.8 - - + +
949F LYS* 2.8 38.4 + - + +
950F GLN* 3.1 16.5 + - - +
952F LEU* 1.3 74.7 - - - +
954F CYS* 1.3 61.5 + - - +
956F SER* 2.5 41.9 + - - +
964G ASN 3.7 1.0 - - - +
965G PRO* 3.3 11.7 - - + +
966G THR* 3.0 37.4 + - - +
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Residues in contact with CYS 954 (chain F).
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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891E VAL* 3.3 31.6 - - - -
892E PHE* 4.8 1.8 - - - -
893E VAL* 4.4 21.2 - - + +
911E PHE* 4.4 5.6 - - + -
950F GLN* 3.0 21.2 + - - -
951F LYS* 3.6 13.7 - - - +
952F LEU 3.2 0.8 - - - -
953F GLN* 1.3 77.1 - - - +
955F LEU* 1.3 63.7 + - - +
956F SER 3.7 3.5 + - - +
957F SER* 5.7 0.7 - - - -
892G PHE* 6.0 2.7 - - - -
963G SER* 5.3 5.5 + - - -
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Residues in contact with LEU 955 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893E VAL* 4.3 12.6 - - + -
896E VAL* 5.2 2.7 - - + -
907E VAL* 4.6 11.4 - - + -
909E VAL* 3.7 42.8 - - + -
911E PHE* 5.2 1.1 - - + -
917E LEU* 5.3 4.5 - - + -
919E VAL* 4.8 12.3 - - + -
900F THR* 3.7 5.2 + - - -
951F LYS 4.3 10.1 - - - +
952F LEU* 3.1 27.0 + - + +
953F GLN 3.1 0.4 - - - -
954F CYS* 1.3 81.4 - - - +
956F SER* 1.3 63.1 + - - +
957F SER* 3.1 13.9 + - - -
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Residues in contact with SER 956 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900F THR* 3.6 19.7 - - - -
901F GLN* 4.2 15.9 + - - -
902F LEU* 5.0 0.7 - - - -
952F LEU 3.3 6.8 + - - -
953F GLN* 2.5 37.6 + - - +
954F CYS 4.3 2.8 - - - +
955F LEU* 1.3 76.3 - - - +
957F SER* 1.3 59.5 + - - +
963G SER* 4.0 3.6 - - - -
964G ASN* 3.0 39.0 + - - -
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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