Contacts of the helix formed by residues 61 - 70 (chain A) in PDB entry 3MYV
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 ALA 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A SER* 3.4 11.6 + - - +
58A TYR 3.8 0.2 - - - -
59A TYR 3.3 2.8 - - - -
60A GLY* 1.3 81.1 - - - +
62A ALA* 1.3 68.1 + - - +
63A MSE 3.3 2.0 - - - -
64A PHE* 3.0 19.0 + - - +
65A ALA* 3.1 12.2 + - - +
82A VAL* 5.4 3.1 - - + -
289A ASP 3.5 20.0 - - - +
291A TRP* 3.8 16.0 - - + +
294A LEU* 3.8 20.2 - - + -
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A SER 2.9 14.9 + - - +
57A GLY 3.3 27.1 - - - +
58A TYR 3.2 1.6 + - - -
61A ALA* 1.3 73.6 - - - +
63A MSE 1.3 62.3 + - - +
65A ALA* 3.3 8.8 + - - +
66A TYR* 3.0 23.9 + - - +
82A VAL* 4.5 11.7 - - + +
86A CYS* 5.0 0.2 - - - -
98A ALA 4.2 1.3 - - - +
99A GLY* 4.0 19.3 - - - +
101A LEU* 4.0 11.3 - - + +
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Residues in contact with MSE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR* 3.0 38.9 + - + +
59A TYR* 3.7 29.4 - - + -
61A ALA 3.2 0.2 + - - -
62A ALA* 1.3 76.4 - - - +
64A PHE* 1.3 60.5 + - + +
66A TYR* 3.4 9.3 + - + -
67A GLY* 3.0 23.4 + - - -
101A LEU* 3.7 17.7 - - + +
149A ASP* 4.1 19.5 - - - +
152A ARG* 4.8 7.6 - - - +
153A CYS* 4.1 13.7 - - - -
421A GLY* 4.4 3.8 - - - +
425A PHE* 3.7 33.7 - - + -
516A EDO 5.2 3.8 - - - +
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Residues in contact with PHE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.3 49.6 - + - -
61A ALA 3.0 12.9 + - - +
63A MSE 1.3 73.4 - - + +
65A ALA* 1.3 68.2 + - - +
66A TYR 3.1 1.3 - - - -
68A ASP* 2.9 31.5 + - - +
291A TRP* 3.3 35.9 - + + -
355A ASN* 3.5 20.4 - - + -
356A VAL 3.6 17.0 - - - -
357A VAL* 4.6 0.9 - - + -
420A GLU 3.5 28.7 - - - -
421A GLY* 4.1 4.9 - - - -
505A EDO 3.2 20.0 - - - -
516A EDO 3.9 11.7 - - - -
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA 3.1 9.9 + - - +
62A ALA 3.6 7.9 - - - +
64A PHE* 1.3 75.6 - - - +
66A TYR* 1.3 57.5 + - - +
69A MSE 2.9 37.6 + - - +
82A VAL* 4.0 31.6 - - + +
83A CYS* 4.2 12.6 - - - -
86A CYS* 3.9 2.8 - - - +
291A TRP* 3.6 23.8 - - + -
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Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA 3.0 16.9 + - - +
63A MSE 3.5 6.5 - - + +
65A ALA* 1.3 79.3 - - - +
67A GLY* 1.3 61.3 + - - +
70A LYS* 3.2 54.9 + - + +
86A CYS* 3.9 15.9 - - - -
98A ALA* 4.7 1.6 - - + -
101A LEU* 3.6 22.7 - - + -
152A ARG 4.8 0.4 + - - -
153A CYS* 3.5 29.6 + - - -
424A PHE* 3.8 17.5 - + - +
425A PHE* 3.6 31.4 - + - -
455A LYS 5.1 1.0 + - - -
456A CYS 4.0 12.0 + - - -
457A VAL* 4.2 1.0 - - - -
458A LEU* 3.6 36.2 + - + +
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A MSE 3.0 12.2 + - - -
66A TYR* 1.3 79.1 - - - +
68A ASP* 1.3 57.2 + - - +
421A GLY* 3.5 28.5 - - - -
423A ARG* 3.6 5.0 + - - -
424A PHE* 2.9 34.0 + - - +
425A PHE* 4.1 11.9 - - - -
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE 2.9 18.7 + - - +
67A GLY* 1.3 74.9 - - - +
69A MSE 1.3 67.0 + - + +
70A LYS 3.2 2.2 - - - -
71A GLY* 3.1 14.0 + - - -
73A ASP* 4.9 0.9 + - - +
74A MSE 3.6 38.2 + - + +
291A TRP* 3.9 7.3 - - + -
417A LEU 4.3 1.0 - - - +
418A VAL* 3.9 4.9 - - - +
419A GLY* 2.8 39.7 + - - +
421A GLY* 2.8 28.7 + - - -
422A HIS 4.6 1.9 + - - -
423A ARG* 4.9 10.0 + - - +
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Residues in contact with MSE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 2.9 29.6 + - - +
68A ASP* 1.3 72.4 - - - +
70A LYS* 1.3 57.3 + - - +
71A GLY 3.4 0.9 + - - +
74A MSE 3.8 23.0 - - + +
75A GLN* 3.3 39.7 - - - +
76A SER* 3.5 3.6 - - - -
83A CYS* 3.7 52.0 - - + +
86A CYS* 4.1 1.8 - - + -
87A TYR* 3.5 20.7 - - - +
291A TRP* 4.0 6.3 - - + -
295A LEU* 3.9 22.7 - - + -
303A GLY* 4.0 6.1 - - - -
436A ARG* 3.1 18.5 + - - -
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Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A TYR* 3.2 65.2 + - + +
68A ASP 3.2 0.6 - - - -
69A MSE 1.3 77.1 - - - +
71A GLY* 1.3 62.4 + - - +
86A CYS* 3.1 29.2 + - + +
89A PHE* 3.2 36.9 - - + -
91A HIS* 2.9 29.9 + - - -
424A PHE* 3.4 32.2 - - + -
434A ILE* 3.6 7.8 - - - +
436A ARG* 3.5 16.4 + - - +
449A VAL* 5.3 0.2 - - - +
455A LYS 4.6 1.0 + - - -
458A LEU* 5.3 0.2 - - - -
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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