Contacts of the helix formed by residues 955 - 971 (chain B) in PDB entry 6CNB
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 VAL 955 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714A ILE* 5.4 2.2 - - + -
717A VAL* 4.0 10.8 - - + -
809A MET* 4.0 31.9 - - + -
852A PHE* 3.8 19.7 - - + +
853A PHE* 4.3 6.5 - - + +
693B HIS* 3.3 33.6 + - + +
953B MET* 4.1 0.8 - - + -
954B THR* 1.3 74.4 - - - +
956B GLY* 1.3 68.1 + - - +
957B LYS 3.4 0.9 - - - -
958B MET* 3.1 32.8 + - + +
959B ILE* 3.0 25.1 + - + +
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Residues in contact with GLY 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B PRO 4.9 0.7 - - - -
690B TYR* 4.0 15.2 - - - +
693B HIS* 3.6 20.1 - - - +
694B ASN* 3.4 9.0 + - - -
916B HIS* 3.5 15.5 - - - -
955B VAL* 1.3 77.9 - - - +
957B LYS* 1.3 64.4 + - - +
959B ILE* 2.9 9.3 + - - +
960B GLU* 2.9 19.2 + - - +
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Residues in contact with LYS 957 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759B VAL* 6.0 0.4 - - - -
914B SER* 2.4 39.0 + - - +
916B HIS* 2.8 37.0 + - + -
918B GLN* 4.5 2.9 - - + -
944B MET* 3.6 18.4 - - + -
949B PHE* 3.4 36.8 - - + -
954B THR 4.9 3.8 - - - +
955B VAL 3.4 0.4 - - - -
956B GLY* 1.3 70.2 - - - +
958B MET* 1.3 57.8 + - - +
960B GLU* 2.5 38.1 + - - +
961B LEU* 2.9 11.3 + - - +
1022B ILE* 3.2 39.0 - - + +
1024B TYR* 3.5 6.3 + - - -
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Residues in contact with MET 958 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ILE* 3.8 17.0 - - - -
713A GLY 3.4 20.4 - - - +
714A ILE* 3.1 28.8 - - + +
717A VAL* 3.6 28.5 - - + -
809A MET* 5.6 1.8 - - + -
949B PHE* 4.5 23.3 - - + -
954B THR 4.6 4.2 + - - +
955B VAL* 3.1 32.0 + - + +
957B LYS* 1.3 80.5 - - - +
959B ILE* 1.3 58.2 + - - +
961B LEU* 4.2 1.2 + - - -
962B ILE 4.2 1.2 + - - -
1018B PHE* 3.1 47.6 - - + -
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Residues in contact with ILE 959 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ILE* 3.8 15.0 - - + -
853A PHE* 4.6 10.5 - - + +
690B TYR* 4.2 21.8 - - + -
693B HIS* 3.4 42.8 - - + +
955B VAL* 3.0 13.6 + - + +
956B GLY* 2.9 8.7 + - - +
958B MET* 1.3 75.3 - - - +
960B GLU* 1.3 65.8 + - - +
961B LEU 3.0 2.0 - - - -
962B ILE* 2.9 18.1 + - + +
963B SER* 3.0 22.8 + - - +
984B LEU* 3.7 35.4 - - + -
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Residues in contact with GLU 960 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B PRO* 3.1 28.6 - - + +
690B TYR* 4.7 4.9 - - + -
735B MET 5.9 0.2 + - - -
736B VAL* 3.5 21.3 + - + +
914B SER 4.7 8.0 - - - +
915B ARG* 2.9 27.8 + - - -
916B HIS* 4.6 2.6 + - - -
956B GLY 2.9 8.1 + - - +
957B LYS* 2.5 33.3 + - + +
959B ILE* 1.3 73.5 - - - +
961B LEU* 1.3 54.9 + - - +
963B SER* 3.8 7.1 - - - -
964B GLY* 2.9 26.2 + - - -
1021B PRO 4.1 5.8 - - - +
1022B ILE* 4.8 12.6 - - + +
1023B TYR* 4.4 11.0 + - - +
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Residues in contact with LEU 961 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B VAL 4.1 4.7 - - - +
759B VAL* 4.7 5.4 - - + -
957B LYS 2.9 10.0 + - - +
958B MET* 4.8 0.4 - - - -
959B ILE 3.0 0.2 + - - -
960B GLU* 1.3 73.9 - - - +
962B ILE* 1.3 68.7 + - - +
964B GLY* 3.0 3.1 + - - -
965B LYS* 3.0 21.2 + - + +
1000B GLY* 4.9 3.6 - - - -
1018B PHE* 3.5 47.8 - - + +
1019B PHE* 3.3 20.2 - - - +
1020B GLY* 3.3 35.3 - - - +
1021B PRO 4.0 8.8 - - - +
1022B ILE* 3.6 27.1 - - + +
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Residues in contact with ILE 962 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ILE* 3.5 36.8 - - + -
958B MET 4.2 0.4 + - - +
959B ILE* 2.9 10.9 + - + +
961B LEU* 1.3 78.3 - - - +
963B SER* 1.3 66.4 + - - +
964B GLY 2.9 1.4 + - - -
965B LYS* 3.0 6.7 + - - +
966B ALA* 2.9 21.7 + - + +
984B LEU* 4.6 20.0 - - + -
987B MET* 3.8 29.6 - - + -
988B SER 5.5 0.7 - - - +
991B LEU* 5.1 9.0 - - + +
998B TYR 5.4 2.5 - - - +
999B SER* 4.7 6.1 - - - +
1000B GLY* 4.0 20.0 - - - +
1018B PHE* 4.0 16.8 - - + -
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Residues in contact with SER 963 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B TYR* 3.0 27.6 + - - -
736B VAL* 3.6 22.9 - - - +
959B ILE* 3.0 15.6 + - - +
960B GLU* 3.8 7.4 - - - -
962B ILE* 1.3 74.8 - - - +
964B GLY* 1.3 56.7 + - - +
966B ALA* 3.5 1.7 + - - +
967B GLY* 2.9 25.1 + - - -
974B GLU* 4.2 8.6 - - - +
975B TYR 5.2 0.2 - - - -
987B MET* 3.2 27.7 - - - +
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Residues in contact with GLY 964 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B MET* 4.0 20.3 - - - +
736B VAL* 4.1 2.9 - - - +
960B GLU 2.9 16.1 + - - -
961B LEU 3.4 3.8 - - - -
962B ILE 2.9 1.2 + - - -
963B SER* 1.3 73.2 - - - +
965B LYS* 1.3 65.9 + - - +
967B GLY* 2.8 12.3 + - - -
968B VAL* 3.1 15.9 + - - +
1021B PRO* 3.8 16.2 - - - -
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Residues in contact with LYS 965 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961B LEU* 3.0 13.4 + - + +
962B ILE* 3.9 6.7 - - - +
964B GLY* 1.3 73.7 - - - +
966B ALA* 1.3 61.6 + - - +
968B VAL* 3.3 20.6 - - + +
969B LEU* 3.4 15.2 - - + +
991B LEU* 3.9 20.2 - - + +
996B PHE* 3.6 38.2 - - + +
997B ASN 5.9 0.2 - - - +
1000B GLY* 3.6 18.8 + - - -
1001B LYS 5.2 0.2 + - - -
1002B ASP* 4.7 12.5 + - - +
1019B PHE* 3.1 33.2 + - - -
1020B GLY* 4.3 3.6 - - - -
1021B PRO* 3.5 17.3 - - + +
44J TYR* 4.5 16.4 - - + -
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Residues in contact with ALA 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 ILE 2.9 10.8 + - - +
963B SER 3.8 0.7 - - - +
965B LYS* 1.3 79.1 - - - +
967B GLY* 1.3 64.3 + - - +
969B LEU* 3.6 0.8 + - - -
970B ASN* 3.5 23.9 + - - +
974B GLU* 5.5 1.3 - - + -
987B MET* 3.5 37.2 - - + +
990B ILE* 4.0 11.3 - - + +
991B LEU* 3.5 27.0 - - + +
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Residues in contact with GLY 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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735B MET* 5.2 5.8 - - - -
963B SER 2.9 12.1 + - - -
964B GLY* 2.8 15.9 + - - -
966B ALA* 1.3 74.3 - - - +
968B VAL* 1.3 62.3 + - - -
969B LEU 2.9 1.9 + - - -
970B ASN* 3.2 1.2 + - - +
971B GLY 3.0 17.3 + - - -
972B THR* 3.2 28.9 + - - -
974B GLU* 4.3 9.8 - - - +
51J LEU* 5.4 0.4 - - - -
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Residues in contact with VAL 968 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B MET* 3.5 32.5 - - + -
964B GLY 3.1 9.6 + - - +
965B LYS* 3.3 20.2 - - + +
967B GLY* 1.3 73.9 - - - +
969B LEU* 1.3 60.3 + - + +
971B GLY* 3.7 6.7 + - - +
1021B PRO* 4.0 12.1 - - + -
44J TYR* 3.8 39.0 - - + +
47J ARG* 2.9 31.6 + - - -
48J ARG* 4.4 13.2 - - + -
51J LEU* 4.9 8.3 - - + -
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Residues in contact with LEU 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 LYS* 3.4 22.1 + - + +
966B ALA 4.0 3.6 - - - +
967B GLY 2.9 2.0 + - - -
968B VAL* 1.3 77.5 - - + +
970B ASN* 1.3 58.3 + - - +
971B GLY* 2.8 9.5 + - - -
990B ILE* 4.9 4.3 - - + -
991B LEU* 4.6 15.3 - - + -
994B GLN* 3.2 49.1 + - + +
996B PHE* 4.0 31.0 - - + -
33J GLY* 4.2 5.4 - - - -
42J LYS 5.4 4.0 - - - +
44J TYR* 4.3 18.6 - - + -
47J ARG* 2.8 27.5 + - - +
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Residues in contact with ASN 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 ALA 3.5 5.8 + - - +
967B GLY 3.2 3.4 + - - +
969B LEU* 1.3 75.2 - - - +
971B GLY* 1.3 58.7 + - - +
972B THR* 3.6 26.3 + - + +
974B GLU* 5.4 1.6 - - - +
990B ILE* 3.0 51.3 - - - +
994B GLN* 5.1 4.0 + - - -
33J GLY* 3.2 21.9 + - - -
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Residues in contact with GLY 971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967B GLY 3.0 3.5 + - - -
968B VAL 4.1 4.3 - - - -
969B LEU 2.8 8.1 + - - -
970B ASN* 1.3 78.7 - - - +
972B THR* 1.3 58.2 + - - +
973B LEU* 4.3 0.5 + - - +
32J GLU* 2.9 28.4 - - - +
33J GLY* 4.0 10.5 - - - -
36J LEU* 5.5 2.2 - - - -
47J ARG* 5.4 3.4 - - - -
51J LEU* 3.2 28.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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