Contacts of the helix formed by residues 959 - 971 (chain B) in PDB entry 4UN5
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 LYS 959 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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762B GLU* 4.3 3.6 - - - +
763B MET 6.0 0.7 - - - -
765B ARG* 6.0 1.8 - - - +
919B ARG* 3.2 22.9 + - - +
920B GLN* 3.6 27.2 - - - +
921B LEU* 4.0 13.1 + - - +
922B VAL 3.9 9.0 - - - -
923B GLU* 3.7 43.7 - - - +
924B THR* 4.9 4.5 + - - +
925B ARG* 4.9 4.8 - - - +
958B LEU* 1.3 78.9 - - - +
960B SER* 1.3 66.1 + - - +
961B LYS* 3.1 5.6 + - + +
962B LEU* 3.4 18.4 + - + +
963B VAL* 4.4 2.4 + - - +
990B ASN* 5.6 0.9 - - - +
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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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762B GLU* 2.7 36.1 + - - +
763B MET 4.1 7.2 + - - -
764B ALA* 4.6 3.8 - - - -
765B ARG* 5.3 1.8 + - - -
959B LYS* 1.3 72.6 - - - +
961B LYS* 1.3 58.1 + - - +
962B LEU 3.2 0.4 + - - -
963B VAL* 3.4 6.6 + - - +
964B SER* 2.9 31.3 + - - -
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Residues in contact with LYS 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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848B LYS* 5.0 22.2 - - + +
920B GLN* 3.3 58.1 - - + +
921B LEU* 4.2 11.7 - - + +
959B LYS* 3.1 2.6 - - + +
960B SER* 1.3 79.2 - - - +
962B LEU* 1.3 56.9 + - - +
964B SER* 4.1 6.1 - - - -
965B ASP* 2.6 70.0 + - - +
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Residues in contact with LEU 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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921B LEU* 4.3 42.8 - - + +
958B LEU* 4.1 30.3 - - + -
959B LYS 3.4 9.1 + - - +
960B SER 3.2 0.8 - - - -
961B LYS* 1.3 77.9 - - - +
963B VAL* 1.3 59.7 + - + +
965B ASP* 3.8 5.3 - - - +
966B PHE* 2.9 28.6 + - - +
993B VAL* 4.8 11.0 - - + -
997B LEU* 4.1 21.1 - - + -
1008B PHE* 4.5 3.8 - - + -
1042B ILE* 4.9 3.4 - - + -
1043B MET* 3.8 38.5 - - + +
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Residues in contact with VAL 963 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958B LEU* 5.2 3.6 - - + -
959B LYS 4.4 2.0 + - - +
960B SER* 3.4 8.0 + - - +
962B LEU* 1.3 77.5 - - + +
964B SER* 1.3 60.2 + - - +
966B PHE* 3.4 6.4 - - - +
967B ARG* 2.9 33.3 + - - +
986B ASP* 4.1 17.5 - - - +
989B LEU* 3.8 48.0 - - + +
990B ASN* 3.2 30.1 - - - +
993B VAL* 4.3 11.0 - - + -
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Residues in contact with SER 964 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960B SER* 2.9 20.2 + - - -
961B LYS* 3.7 8.1 - - - -
963B VAL* 1.3 78.0 - - - +
965B ASP* 1.3 60.2 + - - +
967B ARG* 3.2 11.4 + - - +
968B LYS* 2.9 48.7 + - - +
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Residues in contact with ASP 965 (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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921B LEU* 5.7 1.9 - - - +
961B LYS* 2.6 58.8 + - - +
962B LEU* 3.8 5.8 - - - +
964B SER* 1.3 77.5 + - - +
966B PHE* 1.3 56.7 + - - +
968B LYS* 3.3 14.6 + - - +
969B ASP* 2.9 42.3 + - - +
1043B MET* 6.4 1.6 - - + -
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Residues in contact with PHE 966 (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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962B LEU 2.9 19.3 + - - +
963B VAL* 3.4 10.1 - - - +
965B ASP* 1.3 76.4 - - - +
967B ARG* 1.3 64.5 + - + +
969B ASP* 3.3 1.0 + - - -
970B PHE* 3.1 61.0 + + - +
972B PHE* 4.0 27.8 - + - -
989B LEU* 4.4 20.9 - - + -
992B VAL* 5.4 9.0 - - + -
993B VAL* 3.8 26.0 - - + -
1043B MET* 4.7 14.1 - - + -
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Residues in contact with ARG 967 (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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963B VAL* 2.9 24.8 + - - +
964B SER* 3.2 10.3 + - - +
966B PHE* 1.3 77.9 - - + +
968B LYS* 1.3 58.2 + - + +
971B GLN* 3.1 10.2 + - - -
972B PHE* 2.9 59.0 + - + +
973B TYR* 3.6 16.9 + - + -
974B LYS* 3.4 39.2 - - - +
982B HIS* 4.2 6.1 + - - +
985B HIS* 4.3 17.1 + - - +
986B ASP* 2.4 41.9 + - - +
989B LEU* 3.6 32.4 - - + +
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Residues in contact with LYS 968 (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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964B SER* 2.9 34.5 + - - +
965B ASP* 3.7 14.3 + - - +
966B PHE 3.2 0.2 - - - -
967B ARG* 1.3 77.2 - - + +
969B ASP* 1.3 64.2 + - - +
970B PHE 3.5 0.2 - - - -
971B GLN* 4.3 4.4 + - - +
973B TYR* 4.4 23.4 + - + -
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Residues in contact with ASP 969 (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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965B ASP* 2.9 24.2 + - - +
966B PHE* 3.9 3.1 - - - +
967B ARG 3.3 0.6 - - - -
968B LYS* 1.3 83.6 - - - +
970B PHE* 1.3 83.6 + - + +
971B GLN* 3.6 3.9 + - - +
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Residues in contact with PHE 970 (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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966B PHE* 3.1 59.0 + + - -
967B ARG 4.0 0.2 - - - -
969B ASP* 1.3 95.9 - - + +
971B GLN* 1.3 73.0 + - - +
972B PHE* 3.4 30.8 + + + -
1043B MET 5.6 6.1 - - - -
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Residues in contact with GLN 971 (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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967B ARG 3.1 7.9 + - - -
968B LYS 4.3 3.5 - - - +
969B ASP 3.6 3.4 + - - +
970B PHE* 1.3 83.4 - - - +
972B PHE* 1.3 65.5 + - - +
973B TYR* 3.2 45.3 + - + +
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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