Contacts of the helix formed by residues 964 - 978 (chain B) in PDB entry 6MZL
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 ASP 964 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B GLY* 3.3 15.7 - - - +
188B PHE* 5.1 5.0 - - - -
313B TYR* 3.2 41.7 - - - +
920B PRO* 4.5 8.1 - - - +
923B ARG* 5.7 0.2 + - - -
961B THR 3.0 19.0 + - - +
962B SER* 4.7 1.5 - - - -
963B HIS* 1.3 90.8 - - - +
965B TRP* 1.3 68.0 + - - +
966B ARG 4.1 0.4 - - - +
967B LEU* 3.5 35.1 + - + +
968B ARG* 4.0 3.1 + - - +
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Residues in contact with TRP 965 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR* 3.6 26.2 - - + -
110B TYR* 3.2 28.3 - + - -
114B VAL* 3.6 29.6 - - + -
182B TYR* 4.9 14.1 - - + -
184B ASN 3.7 7.8 + - - -
185B SER* 6.1 0.2 - - - -
187B ARG* 4.2 17.3 - - - -
188B PHE* 3.2 38.4 - + - -
313B TYR* 4.1 3.2 + - - +
439B HIS* 3.1 65.9 + + + +
964B ASP* 1.3 75.9 - - - +
966B ARG* 1.3 63.1 + - + +
967B LEU 3.1 0.9 + - - -
968B ARG* 3.2 10.4 + - - +
969B CYS* 2.9 28.8 + - - -
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Residues in contact with ARG 966 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TYR* 5.8 2.7 - - + -
313B TYR* 2.5 76.0 + - + +
314B VAL* 3.8 5.1 - - - +
441B LEU 5.9 0.2 - - - +
443B TRP* 3.3 50.6 - - + +
920B PRO 4.1 2.8 + - - -
921B TYR* 4.0 10.9 - - - +
924B HIS* 3.2 48.5 + - + +
927B LEU* 5.6 0.5 - - - +
965B TRP* 1.3 77.2 - - + +
967B LEU* 1.3 72.4 + - + +
969B CYS* 3.5 13.6 - - + +
970B GLY* 2.8 24.4 + - - -
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Residues in contact with LEU 967 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B TYR* 5.6 0.2 - - + -
914B ILE* 6.2 2.0 - - + -
920B PRO* 4.7 3.6 - - + +
923B ARG* 3.7 54.7 - - + +
924B HIS* 4.3 9.2 - - - +
927B LEU* 4.1 15.9 - - + +
961B THR* 3.6 19.3 - - + -
963B HIS* 4.3 6.1 - - + -
964B ASP* 3.5 42.4 - - + +
965B TRP 3.2 0.4 - - - -
966B ARG* 1.3 89.4 - - + +
968B ARG* 1.3 58.3 + - - +
970B GLY* 3.1 4.0 + - - -
971B ALA* 2.9 23.4 + - - +
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Residues in contact with ARG 968 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR* 3.5 22.4 + - - -
91B LEU* 4.9 4.6 + - - +
106B PHE* 5.5 4.8 - - + -
110B TYR* 3.3 38.9 - - + +
957B MET* 3.1 24.5 + - + +
958B ASN* 2.4 29.3 + - - +
959B SER 4.1 0.2 - - - -
960B GLY 4.6 0.2 - - - +
961B THR* 2.8 54.9 + - + +
962B SER* 3.2 11.8 - - - +
964B ASP 4.0 2.5 - - - +
965B TRP* 3.3 17.5 - - - +
967B LEU* 1.3 76.2 - - - +
969B CYS* 1.3 61.5 + - - +
971B ALA* 3.6 9.1 - - + +
972B VAL* 2.9 33.1 + - + +
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Residues in contact with CYS 969 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 6.0 2.0 - - - -
439B HIS* 3.5 29.8 - - - -
440B THR* 4.0 7.1 - - - +
441B LEU 3.3 28.4 - - - +
442B SER* 5.1 0.9 - - - -
443B TRP* 5.9 1.6 - - + -
965B TRP* 2.9 26.8 + - - -
966B ARG* 3.5 13.9 - - + +
967B LEU 3.2 0.4 - - - -
968B ARG* 1.3 77.9 - - - +
970B GLY* 1.3 56.6 + - - +
972B VAL* 3.2 11.5 + - - +
973B ASP* 2.9 33.2 + - - +
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Residues in contact with GLY 970 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927B LEU* 4.5 18.6 - - - +
931B THR* 4.4 1.8 + - - -
966B ARG 2.8 15.6 + - - -
967B LEU 3.1 4.2 + - - -
969B CYS* 1.3 73.8 - - - +
971B ALA* 1.3 60.6 + - - +
973B ASP* 3.0 15.9 + - - +
974B LEU* 2.8 32.8 + - - +
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Residues in contact with ALA 971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927B LEU* 5.0 1.5 - - + +
953B LEU* 5.4 1.6 - - + +
956B LEU* 4.7 6.5 - - + +
957B MET* 3.7 36.5 - - + +
961B THR* 5.6 0.7 - - + -
967B LEU 2.9 13.3 + - - +
968B ARG* 3.2 13.6 + - - +
970B GLY* 1.3 73.0 - - - +
972B VAL* 1.3 61.9 + - - +
974B LEU* 3.1 20.0 + - + +
975B TYR* 3.0 24.1 + - - -
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Residues in contact with VAL 972 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.6 8.6 - - + +
106B PHE* 4.3 13.9 - - + -
107B SER* 6.1 2.5 - - - -
110B TYR* 5.9 6.3 - - + -
431B LEU* 3.7 31.2 - - + +
432B HIS* 4.6 11.2 - - + -
440B THR* 5.1 7.6 - - + +
957B MET* 3.7 20.6 - - + -
968B ARG 2.9 20.2 + - - +
969B CYS* 3.2 13.2 - - - +
971B ALA* 1.3 76.5 - - - +
973B ASP* 1.3 58.8 + - - +
975B TYR* 3.3 3.3 + - - +
976B PHE* 2.8 26.0 + - - +
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Residues in contact with ASP 973 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B LEU* 3.3 19.6 - - - +
441B LEU 5.7 0.2 - - - -
442B SER* 3.7 29.2 - - - -
443B TRP 5.2 0.5 + - - -
444B GLU* 6.4 1.6 - - - -
931B THR* 3.6 19.2 - - + +
969B CYS 2.9 16.4 + - - +
970B GLY* 3.0 16.9 + - - +
972B VAL* 1.3 73.2 - - - +
974B LEU* 1.3 60.5 + - - +
976B PHE* 3.2 9.6 + - + +
977B THR* 3.0 32.7 + - - -
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Residues in contact with LEU 974 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911B LEU* 6.2 2.0 - - + -
914B ILE* 5.8 1.3 - - + -
927B LEU* 3.8 23.1 - - + -
930B LEU* 3.8 26.9 - - + -
931B THR* 3.5 22.4 - - + +
953B LEU* 4.1 22.9 - - + -
970B GLY 2.8 15.1 + - - +
971B ALA* 3.1 21.3 + - + +
973B ASP* 1.3 76.7 - - - +
975B TYR* 1.3 64.6 + - + +
976B PHE 3.3 0.2 + - - -
977B THR* 3.3 1.2 + - - -
978B LEU* 2.7 50.1 + - + +
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Residues in contact with TYR 975 (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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101B ARG 4.2 9.4 - - - -
102B ASN* 5.0 7.2 - - - -
103B LEU* 5.1 13.7 - - + +
431B LEU* 5.5 0.2 - - - -
950B VAL* 2.5 34.1 + - + +
953B LEU* 3.2 24.9 - - + +
954B TRP* 2.7 45.7 + + - +
957B MET* 3.4 24.7 - - + -
971B ALA 3.0 13.2 + - - +
972B VAL 3.3 3.6 + - - +
974B LEU* 1.3 79.2 - - + +
976B PHE* 1.3 61.6 + - - +
978B LEU* 2.9 15.6 - - + +
979B PHE* 3.1 36.8 - + - +
980B GLY* 3.1 16.5 - - - +
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Residues in contact with PHE 976 (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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103B LEU* 5.3 4.0 - - + -
408B LYS 5.9 2.5 - - - -
409B THR* 4.9 20.0 - - + -
430B HIS* 3.4 24.0 - - + -
431B LEU* 3.5 40.4 - - + +
931B THR* 6.0 0.7 - - + -
938B LYS* 4.8 2.3 + - - +
972B VAL 2.8 14.4 + - - +
973B ASP* 3.3 8.7 - - - +
974B LEU 3.1 0.4 - - - -
975B TYR* 1.3 76.6 - - - +
977B THR* 1.3 77.0 + - - +
980B GLY* 3.3 20.9 + - - -
981B LEU* 5.9 6.1 - - + -
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Residues in contact with THR 977 (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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931B THR* 3.3 22.7 + - - +
934B PRO* 4.2 31.0 - - + -
937B THR* 5.6 6.3 - - + -
938B LYS* 3.3 19.9 - - - +
973B ASP 3.0 14.3 + - - -
974B LEU* 3.9 2.2 - - - -
976B PHE* 1.3 90.0 - - - +
978B LEU* 1.3 70.5 + - + +
979B PHE 3.1 4.2 + - - -
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Residues in contact with LEU 978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930B LEU* 6.4 0.4 - - + -
934B PRO* 4.6 4.3 - - + -
935B PRO* 3.4 21.3 - - + +
936B PHE* 3.2 34.5 - - + +
937B THR* 4.4 4.0 - - - +
938B LYS* 4.5 2.2 - - - +
945B CYS* 5.5 1.1 - - - -
949B LEU* 6.4 0.7 - - + -
953B LEU* 4.5 20.6 - - + -
974B LEU* 2.7 36.2 + - + +
975B TYR* 2.9 23.8 - - + +
977B THR* 1.3 79.7 - - + +
979B PHE* 1.3 86.5 + - + +
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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