Contacts of the helix formed by residues 945 - 965 (chain B) in PDB entry 6VSB
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 945 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726B ILE* 3.5 34.1 - - + -
822B LEU* 3.6 46.9 - - + +
825B LYS* 4.2 20.0 - - + +
826B VAL* 4.5 9.2 - - + -
938B LEU* 4.9 9.2 - - + -
943B SER* 3.2 2.5 - - - +
944B ALA* 1.3 83.2 - - + +
946B GLY* 1.3 64.3 + - - +
947B LYS 3.2 3.6 - - - +
948B LEU* 3.0 37.9 + - + +
949B GLN* 3.1 13.8 + - - +
1057B PRO* 6.2 0.2 - - + -
1061B VAL* 4.4 2.7 - - + -
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Residues in contact with GLY 946 (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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943B SER* 3.9 12.7 + - - -
944B ALA 3.5 3.4 + - - -
945B LEU* 1.3 76.4 - - - +
947B LYS* 1.3 59.9 + - - +
949B GLN* 4.0 6.7 - - - +
950B ASP* 2.8 30.1 + - - +
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Residues in contact with LYS 947 (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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725B GLU* 5.7 1.2 - - - +
726B ILE* 2.8 47.1 + - + +
727B LEU* 3.6 16.6 - - - +
728B PRO* 4.4 19.1 - - + +
945B LEU 3.2 1.2 - - - -
946B GLY* 1.3 77.2 - - - +
948B LEU* 1.3 60.9 + - - +
950B ASP* 2.6 28.3 - - - +
951B VAL* 3.8 8.8 - - - +
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Residues in contact with LEU 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B ILE* 3.5 29.6 - - + -
728B PRO* 4.1 15.0 - - + -
826B VAL* 4.6 10.1 - - + -
945B LEU* 3.0 32.9 + - + +
947B LYS* 1.3 76.5 - - - +
949B GLN* 1.3 63.8 + - - +
951B VAL* 3.4 8.2 + - + +
952B VAL* 3.4 23.4 + - - +
1056B ALA* 3.6 26.5 - - + -
1057B PRO* 4.4 9.6 - - + -
1058B HIS* 4.2 8.9 - - + +
1059B GLY* 3.8 27.4 - - - +
1061B VAL* 4.6 1.6 - - + -
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Residues in contact with GLN 949 (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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825B LYS 4.1 4.3 - - - +
826B VAL* 3.6 14.1 - - + +
827B THR* 3.4 44.0 + - - +
945B LEU* 3.1 14.8 + - + +
946B GLY* 4.0 7.2 - - - +
948B LEU* 1.3 74.7 - - - +
950B ASP* 1.3 60.6 + - - +
952B VAL* 3.2 12.4 + - - +
953B ASN* 2.7 71.5 + - - +
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Residues in contact with ASP 950 (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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946B GLY 2.8 18.1 + - - +
947B LYS* 2.6 25.4 - - - +
949B GLN* 1.3 76.8 - - - +
951B VAL* 1.3 79.6 + - - +
953B ASN* 3.1 7.4 + - - +
954B GLN* 2.6 58.7 + - + +
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Residues in contact with VAL 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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728B PRO* 4.0 22.2 - - + -
730B SER 3.7 22.9 - - - +
731B MET* 4.2 19.4 - - + +
947B LYS 3.8 10.1 - - - +
948B LEU* 3.4 8.6 + - - +
949B GLN 3.3 0.4 - - - -
950B ASP* 1.3 94.4 + - - +
952B VAL* 1.3 64.9 + - - +
954B GLN* 4.1 8.6 - - - +
955B ASN* 3.0 24.8 + - + +
1014B ARG* 5.9 3.0 - - - +
1018B ILE* 4.0 12.1 - - + -
1058B HIS* 4.7 11.4 - - + -
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Residues in contact with VAL 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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732B THR* 6.4 1.3 - - - -
826B VAL* 5.5 8.5 - - + -
827B THR 4.1 20.0 - - - +
828B LEU* 4.2 20.4 - - + +
948B LEU* 3.4 12.3 + - + +
949B GLN* 3.2 18.2 + - - +
951B VAL* 1.3 77.5 - - - +
953B ASN* 1.3 66.2 + - - +
955B ASN* 3.4 5.7 + - - +
956B ALA* 3.1 23.3 + - + +
1057B PRO* 5.9 0.4 - - + -
1058B HIS* 3.3 35.4 - - + +
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Residues in contact with ASN 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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827B THR 5.6 0.2 - - - +
949B GLN* 2.7 61.0 + - - +
950B ASP* 3.6 7.4 - - - +
952B VAL* 1.3 75.1 - - - +
954B GLN* 1.3 57.5 + - + +
956B ALA* 3.3 6.9 + - - +
957B GLN* 2.8 30.2 + - - +
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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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950B ASP* 2.6 43.6 + - + +
951B VAL* 4.1 6.6 - - - +
953B ASN* 1.3 70.3 - - + +
955B ASN* 1.3 67.2 + - - +
957B GLN* 3.2 7.9 + - - +
958B ALA* 2.9 17.5 + - - +
1014B ARG* 2.9 49.2 + - - +
1017B GLU* 5.4 3.8 + - - -
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Residues in contact with ASN 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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731B MET* 4.2 9.8 - - + +
732B THR* 2.6 46.9 + - + +
734B THR* 4.0 8.4 + - - -
951B VAL* 3.0 20.9 + - + +
952B VAL* 3.7 5.8 + - - +
954B GLN* 1.3 76.6 - - - +
956B ALA* 1.3 65.4 + - - +
958B ALA* 3.2 4.4 + - - +
959B LEU* 3.0 29.4 + - - +
1007B TYR* 4.6 3.8 + - - -
1011B GLN* 4.2 14.6 + - - +
1014B ARG* 3.5 9.7 - - - +
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Residues in contact with ALA 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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853B GLN 6.3 1.8 - - - +
952B VAL* 3.1 19.5 + - + +
953B ASN* 3.6 5.8 - - - +
955B ASN* 1.3 80.1 - - - +
957B GLN* 1.3 57.7 + - - +
959B LEU* 3.3 5.0 + - - +
960B ASN* 2.7 34.3 + - + +
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Residues in contact with GLN 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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953B ASN 2.8 17.6 + - - +
954B GLN* 3.6 8.7 - - - +
955B ASN 3.2 0.2 - - - -
956B ALA* 1.3 75.7 - - - +
958B ALA* 1.3 59.1 + - - +
960B ASN* 4.4 14.2 + - - +
961B THR* 2.9 36.0 + - + +
765C ARG* 3.2 46.7 - - - +
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Residues in contact with ALA 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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954B GLN 2.9 14.2 + - - +
955B ASN* 3.5 8.1 - - - +
957B GLN* 1.3 77.7 - - - +
959B LEU* 1.3 59.7 + - - +
961B THR* 3.0 26.2 - - - +
962B LEU* 3.2 10.9 + - - +
1007B TYR* 3.5 27.2 - - + +
1010B GLN* 5.4 7.6 - - + +
1011B GLN* 3.9 6.3 - - - +
1014B ARG* 3.9 18.8 - - - +
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Residues in contact with LEU 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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734B THR* 3.8 21.1 - - + +
853B GLN* 3.2 40.2 - - - +
854B LYS* 4.7 4.0 - - + +
858B LEU* 4.1 24.9 - - + -
860B VAL* 5.1 10.5 - - + -
955B ASN* 3.0 22.8 + - - +
956B ALA* 3.9 6.1 - - - +
958B ALA* 1.3 75.4 - - - +
960B ASN* 1.3 64.9 + - - +
962B LEU* 3.3 5.4 + - + +
963B VAL* 3.1 27.4 + - - +
1007B TYR* 3.5 27.6 - - + +
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Residues in contact with ASN 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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569A ILE* 3.2 35.0 - - - +
956B ALA 2.7 23.4 + - - +
957B GLN* 3.9 17.1 + - - +
959B LEU* 1.3 72.4 - - - +
961B THR* 1.3 63.3 + - - +
963B VAL* 3.3 8.7 + - - +
964B LYS* 3.1 36.2 + - - +
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Residues in contact with THR 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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957B GLN* 2.9 25.0 + - + +
958B ALA* 3.0 29.4 - - - +
960B ASN* 1.3 78.3 - - - +
962B LEU* 1.3 63.9 + - + +
964B LYS* 3.1 18.9 + - - +
965B GLN* 3.1 17.8 + - - +
1007B TYR* 5.5 2.0 - - + -
758C SER* 3.3 20.8 + - - -
762C GLN* 3.8 29.6 + - - +
765C ARG* 5.3 6.8 + - - +
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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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736B VAL* 4.5 3.8 - - + -
741B TYR* 2.7 55.0 + - + +
858B LEU* 3.8 29.2 - - + -
958B ALA 3.2 12.7 + - - +
959B LEU* 3.6 5.8 - - + +
960B ASN 3.3 0.2 - - - -
961B THR* 1.3 83.5 - - + +
963B VAL* 1.3 61.6 + - - +
965B GLN* 3.3 11.4 + - + +
966B LEU* 3.3 2.8 - - - +
1003B SER* 3.7 25.4 - - - +
1004B LEU* 4.1 10.3 - - + -
1007B TYR* 3.8 39.5 - - + -
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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
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569A ILE* 4.6 7.6 - - + +
570A ALA* 3.6 23.0 - - + +
572A THR* 4.3 19.5 - - + -
741B TYR* 5.0 0.4 - - - -
853B GLN 4.8 7.9 - - - +
855B PHE* 5.8 5.2 - - + +
856B ASN* 5.6 5.2 - - - +
858B LEU* 3.4 27.4 - - + -
959B LEU 3.1 16.1 + - - +
960B ASN* 3.7 10.1 - - - +
961B THR 3.3 0.2 - - - -
962B LEU* 1.3 75.9 - - - +
964B LYS* 1.3 64.1 + - - +
966B LEU* 3.0 34.1 + - + +
967B SER 4.5 0.3 + - - -
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Residues in contact with LYS 964 (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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569A ILE* 5.2 7.7 - - + +
570A ALA* 3.5 26.4 - - + +
49B HIS* 5.5 9.7 + - - -
304B LYS* 5.6 11.9 - - - +
960B ASN* 3.1 29.8 + - - +
961B THR* 3.5 13.2 - - - +
963B VAL* 1.3 77.1 - - - +
965B GLN* 1.3 65.5 + - - +
966B LEU 3.0 1.0 + - - -
967B SER* 2.9 25.3 + - - +
968B SER* 4.1 0.9 + - - -
758C SER* 5.5 11.4 - - - +
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Residues in contact with GLN 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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741B TYR* 3.9 8.3 - - - +
961B THR* 3.1 16.6 + - - +
962B LEU* 3.4 13.2 - - - +
963B VAL 3.1 0.8 - - - -
964B LYS* 1.3 77.7 - - - +
966B LEU* 1.3 62.1 + - - +
967B SER 3.1 0.4 - - - -
968B SER* 3.0 21.0 + - - -
970B PHE* 3.7 19.1 - - + -
1000B ARG* 4.9 1.8 - - + +
1003B SER* 4.0 17.5 - - - +
756C TYR 3.5 7.3 - - - +
757C GLY* 3.6 5.4 - - - -
758C SER* 2.9 45.5 + - - +
759C PHE* 3.2 29.7 - - - +
762C GLN* 6.0 1.1 + - - -
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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