Contacts of the helix formed by residues 60 - 74 (chain C) in PDB entry 5M64
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 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C ILE* 1.3 80.0 - - - +
61C THR* 1.3 70.0 + - - +
62C SER* 2.8 35.2 + - - +
63C ILE* 3.4 4.4 + - + +
64C ALA* 2.9 29.3 + - - +
295C ARG 5.2 3.2 - - - +
298C PHE* 4.1 2.5 - - - -
78K TYR* 3.2 53.4 + - + +
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Residues in contact with THR 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018B THR* 3.9 10.8 + - - +
1019B GLY* 4.1 18.8 - - - +
1020B GLU* 4.4 9.4 + - + +
60C ASP* 1.3 81.5 + - - +
62C SER* 1.3 59.3 + - - +
64C ALA* 4.2 1.1 - - - -
65C ASN* 2.8 45.5 + - - +
229C LEU* 5.0 10.5 - - + -
295C ARG* 4.9 9.2 + - + +
298C PHE* 3.5 25.8 - - + -
74K ASN* 5.5 0.2 + - - -
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Residues in contact with SER 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ASP* 2.8 22.4 + - - -
61C THR* 1.3 79.8 + - - +
63C ILE* 1.3 66.8 + - - +
65C ASN* 4.0 0.9 - - - +
66C ALA* 3.0 28.9 + - - +
70K HIS 5.6 0.3 - - - +
74K ASN* 3.5 42.9 + - - +
75K ALA* 4.4 3.9 + - - +
78K TYR* 3.3 31.2 - - - +
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ILE* 4.0 24.5 - - + -
60C ASP* 3.4 5.4 + - + +
62C SER* 1.3 82.9 + - - +
64C ALA* 1.3 64.7 + - - +
66C ALA* 3.4 5.1 + - + +
67C PHE* 3.0 55.1 + - + -
75K ALA* 3.8 31.6 - - + +
78K TYR* 4.7 11.2 - - + -
79K VAL* 5.9 1.3 - - + -
124K LEU* 5.3 4.0 - - + -
127K LEU* 3.7 34.3 - - + -
131K VAL* 5.6 0.7 - - + -
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 6.2 0.2 - - - -
59C ILE* 3.9 17.6 - - + +
60C ASP 2.9 18.4 + - - +
61C THR* 4.0 2.0 - - - +
63C ILE* 1.3 76.7 - - - +
65C ASN* 1.3 59.8 + - - +
67C PHE* 3.0 10.9 + - - +
68C ARG 2.9 22.7 + - - -
227C TYR* 3.1 21.1 - - + -
298C PHE* 3.9 24.5 - - + -
300C PHE* 4.9 4.9 - - + -
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Residues in contact with ASN 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938B PHE* 3.2 39.8 - - - -
1016B GLY 5.0 4.3 - - - +
1017B ALA 5.7 0.2 - - - +
1018B THR 5.0 2.2 - - - +
1019B GLY* 3.2 29.6 + - - +
61C THR* 2.8 34.9 + - - +
62C SER* 4.4 1.3 - - - +
64C ALA* 1.3 75.8 - - - +
66C ALA* 1.3 56.7 + - - +
68C ARG* 3.2 21.1 + - - +
69C ARG* 2.9 37.4 + - - +
227C TYR* 4.7 4.1 - - - -
298C PHE* 5.2 2.9 - - - -
74K ASN* 5.8 1.3 - - - +
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C SER 3.0 21.6 + - - +
63C ILE* 3.5 8.7 - - + +
64C ALA 3.1 0.2 - - - -
65C ASN* 1.3 73.7 - - - +
67C PHE* 1.3 66.0 + - + +
69C ARG* 3.5 1.7 + - - +
70C ILE* 2.9 38.8 + - + +
321C LEU* 6.2 2.0 - - + -
70K HIS 5.3 0.4 - - - +
71K THR* 3.9 36.1 - - - +
75K ALA* 4.7 4.9 - - + -
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Residues in contact with PHE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 4.9 15.7 - - + -
59C ILE* 5.7 2.9 - - + -
63C ILE* 3.0 42.6 + - + -
64C ALA* 3.0 9.4 + - - +
66C ALA* 1.3 80.5 - - + +
68C ARG* 1.3 58.5 + - - +
70C ILE* 3.5 7.9 + - + +
71C MET* 3.0 35.8 + - + +
227C TYR* 3.9 8.7 - - - +
300C PHE* 4.9 5.8 - + + -
317C SER* 4.6 16.2 - - - +
318C VAL* 4.5 24.2 - - + -
321C LEU* 4.7 20.4 - - + -
127K LEU* 6.1 1.1 - - + -
128K CYS* 5.3 5.8 - - + -
131K VAL* 3.8 33.7 - - + -
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Residues in contact with ARG 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933B THR 4.0 18.4 + - - -
934B ILE 4.7 2.2 + - - -
936B MET 5.2 0.8 + - - -
938B PHE* 3.3 28.8 - - + +
944B GLN* 5.6 2.8 + - - +
1016B GLY* 3.3 24.4 + - - -
64C ALA 2.9 6.2 + - - +
65C ASN* 3.2 38.0 + - - +
66C ALA 3.3 0.2 - - - -
67C PHE* 1.3 75.9 - - - +
69C ARG* 1.3 79.4 + - - +
71C MET* 3.0 17.6 + - - +
72C ILE* 3.2 19.2 + - - +
225C ALA* 3.2 39.8 + - + +
226C SER* 4.3 2.9 - - - +
227C TYR* 3.4 35.8 + - + +
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934B ILE* 3.2 41.5 + - + +
935B ASP* 2.4 27.4 + - - -
1016B GLY 2.3 28.7 + - - -
1017B ALA* 3.2 18.0 + - - +
65C ASN* 2.9 26.7 + - - +
66C ALA* 6.2 0.2 - - - -
68C ARG* 1.3 87.7 - - - +
70C ILE* 1.3 54.5 + - - +
72C ILE* 3.2 9.5 + - + +
73C SER* 2.4 40.0 + - - +
69K ASP* 3.6 7.4 + - - -
70K HIS* 3.2 28.2 - - - +
71K THR* 3.6 24.9 - - + +
74K ASN* 6.1 0.2 - - - +
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Residues in contact with ILE 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ALA* 2.9 25.7 + - + +
67C PHE* 3.8 7.6 - - + +
69C ARG* 1.3 73.2 - - - +
71C MET* 1.3 65.4 + - - +
73C SER* 3.6 4.9 - - - -
74C GLU* 3.1 38.5 + - + +
75C VAL* 3.7 1.9 + - - +
316C LYS 4.5 0.2 - - - +
317C SER* 3.3 40.2 - - - +
320C ILE* 3.6 26.2 - - + -
321C LEU* 3.9 30.5 - - + -
71K THR* 4.3 14.6 - - + -
72K LEU* 5.8 0.7 - - + -
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Residues in contact with MET 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PHE* 3.0 20.9 + - + +
68C ARG* 3.0 13.6 + - - +
70C ILE* 1.3 77.4 - - - +
72C ILE* 1.3 56.5 + - - +
75C VAL* 3.3 20.4 - - - +
221C PRO* 5.3 0.2 - - - +
222C VAL* 4.1 22.7 - - + +
225C ALA* 4.5 11.0 - - + -
227C TYR* 4.9 5.2 - - - +
300C PHE* 6.3 3.4 - - + -
302C VAL* 5.3 17.3 - - + -
310C PRO 5.5 1.1 - - - +
313C ILE* 3.7 34.1 - - + +
314C PHE* 3.7 21.1 - - + -
317C SER* 3.3 32.3 - - - +
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Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933B THR* 3.8 30.5 - - + +
934B ILE* 5.5 2.2 - - + -
944B GLN* 5.2 11.2 - - + +
68C ARG* 3.2 20.9 + - - +
69C ARG* 3.3 22.0 - - + +
70C ILE 3.1 0.4 - - - -
71C MET* 1.3 79.2 - - - +
73C SER* 1.3 60.6 + - - +
75C VAL* 4.9 3.6 - - - -
213C GLY* 4.3 12.8 - - - +
220C SER* 4.7 14.1 - - - +
222C VAL* 5.0 13.2 - - + +
223C SER 5.0 7.6 - - - +
224C THR* 5.6 0.4 - - - -
225C ALA* 4.5 23.8 - - + +
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934B ILE* 3.6 28.9 - - - +
69C ARG* 2.4 27.2 + - - +
70C ILE 3.4 0.4 + - - -
72C ILE* 1.3 82.7 - - - +
74C GLU* 1.3 90.8 + - - +
75C VAL* 3.6 1.8 - - - -
212C ILE* 3.9 2.1 - - - +
213C GLY* 3.0 11.1 + - - -
214C GLY* 2.9 33.7 + - - +
71K THR* 5.0 0.2 - - - +
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Residues in contact with GLU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934B ILE* 5.1 3.7 - - - +
70C ILE* 3.1 21.4 + - + +
73C SER* 1.3 114.5 + - - +
75C VAL* 1.3 57.2 + - - +
76C PRO* 4.0 5.6 - - - +
212C ILE* 4.5 23.5 - - + +
214C GLY* 5.4 3.8 - - - -
316C LYS 4.1 1.0 - - - +
320C ILE* 3.8 36.6 - - + +
324C LYS* 6.3 3.4 - - - +
69K ASP* 6.0 1.9 - - - +
71K THR* 4.7 8.9 + - - +
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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