Contacts of the helix formed by residues 1002 - 1010 (chain F) in PDB entry 3U5P
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 ASP1002 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982F PHE* 3.3 14.4 - - - +
984F GLU 3.8 11.7 - - - +
985F PRO* 3.0 39.6 - - + +
986F VAL* 5.5 1.6 - - + +
1000F PRO* 6.1 0.3 - - - +
1001F MET* 1.3 82.7 + - - +
1003F LEU* 1.3 62.4 + - - +
1004F SER* 3.0 18.5 + - - -
1005F THR* 3.1 13.9 + - - -
1006F VAL* 3.1 15.9 + - - +
1031F ILE* 3.3 14.8 - - + +
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Residues in contact with LEU1003 (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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970F LEU* 3.9 14.2 - - + +
973F LEU* 3.9 36.8 - - + -
974F TYR* 3.6 26.7 - - + +
979F SER* 4.4 13.7 - - - +
982F PHE* 2.9 24.6 + - + +
983F GLN* 3.7 27.1 - - + -
1002F ASP* 1.3 71.0 - - - +
1004F SER* 1.3 52.6 + - - +
1006F VAL* 2.8 9.6 + - + +
1007F LYS* 2.6 34.8 + - - +
1028F VAL* 5.6 1.6 - - + -
1031F ILE* 3.5 16.6 - - + +
1032F PHE* 5.3 4.0 - - + -
1069F VAL* 6.2 0.2 - - + -
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Residues in contact with SER1004 (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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974F TYR* 3.1 17.0 + - - -
983F GLN 2.8 22.2 + - - -
984F GLU* 3.9 16.6 + - - -
985F PRO* 3.9 11.8 - - - +
1002F ASP* 3.0 11.8 + - - -
1003F LEU* 1.3 71.8 - - - +
1005F THR* 1.3 61.9 + - - +
1007F LYS* 3.1 20.4 - - - +
1008F LYS* 3.4 19.1 + - - +
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Residues in contact with THR1005 (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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985F PRO* 5.2 3.6 - - - +
1001F MET* 3.5 29.8 - - + -
1002F ASP* 3.1 22.5 + - - -
1003F LEU 3.0 0.4 - - - -
1004F SER* 1.3 79.7 + - - +
1006F VAL* 1.3 60.4 + - - +
1007F LYS 3.0 1.3 - - - -
1008F LYS* 2.7 32.3 + - + +
1009F LYS* 3.0 24.2 + - + +
1014F HIS* 5.7 2.2 - - + +
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Residues in contact with VAL1006 (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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970F LEU* 3.7 22.9 - - + -
1001F MET* 3.8 19.7 - - - -
1002F ASP 3.1 9.8 + - - +
1003F LEU* 2.8 12.4 + - + +
1005F THR* 1.3 73.2 - - - +
1007F LYS* 1.3 62.1 - - - +
1009F LYS* 3.4 4.2 + - - +
1010F LEU* 3.1 21.3 + - - +
1018F TYR* 3.4 26.4 - - + +
1024F PHE* 3.8 23.6 - - + -
1027F ASP* 4.3 8.1 - - + +
1028F VAL* 4.7 9.2 - - + -
1031F ILE* 4.4 12.6 - - + -
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Residues in contact with LYS1007 (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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912F THR 2.8 25.7 + - - -
913F CYS* 4.4 1.6 + - - +
914F HIS 3.0 9.3 + - - -
915F VAL* 3.3 30.7 - - + +
916F PRO* 4.8 0.7 - - - -
917F THR* 2.8 30.4 + - - +
970F LEU* 3.4 23.3 - - + +
974F TYR* 4.3 13.6 - - + +
1003F LEU 2.6 14.9 + - - +
1004F SER* 3.1 16.6 - - - +
1006F VAL* 1.3 74.6 - - - +
1008F LYS* 1.3 59.0 + - + +
1010F LEU* 3.7 12.6 - - + +
1011F GLN* 3.8 13.9 + - - +
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Residues in contact with LYS1008 (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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1004F SER* 3.4 18.5 + - - +
1005F THR* 2.7 26.0 + - + +
1007F LYS* 1.3 70.5 - - + +
1009F LYS* 1.3 58.6 + - - +
1010F LEU 3.1 1.8 - - - -
1011F GLN* 3.0 39.7 + - - +
1014F HIS* 3.3 33.9 - - + +
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Residues in contact with LYS1009 (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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1001F MET* 4.6 6.3 - - - +
1005F THR* 3.0 29.3 + - + +
1006F VAL 3.7 4.0 - - - +
1008F LYS* 1.3 75.4 - - - +
1010F LEU* 1.3 55.8 + - - +
1011F GLN 3.1 2.2 + - - +
1014F HIS* 3.8 22.0 - - + -
1016F GLN* 3.6 43.9 + - - +
1017F HIS* 2.8 28.4 + - - -
1018F TYR* 3.3 42.6 + - + +
1027F ASP* 3.0 27.9 + - - +
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Residues in contact with LEU1010 (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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915F VAL* 6.1 0.7 - - + -
945F ASN* 3.3 4.3 + - - -
958F LEU* 5.0 5.4 - - + -
963F GLN* 3.2 39.1 + - - +
966F CYS* 4.2 23.3 - - + +
967F GLU* 4.5 16.6 - - + +
970F LEU* 3.8 22.0 - - + -
1006F VAL 3.1 11.9 + - - +
1007F LYS* 3.7 9.2 - - + +
1008F LYS 3.1 1.0 - - - -
1009F LYS* 1.3 74.6 - - - +
1011F GLN* 1.3 60.0 + - - +
1017F HIS* 4.5 2.8 - - + -
1018F TYR* 3.6 23.8 - - + -
1024F PHE* 3.4 32.3 - - + -
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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