Contacts of the helix formed by residues 81 - 88 (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 GLY 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A SER* 1.3 78.9 - - - +
82A VAL* 1.3 64.8 + - - -
83A CYS* 3.3 3.1 - - - -
84A ASN* 3.1 5.7 + - - +
85A THR* 3.0 30.3 + - - +
302A LYS* 5.0 4.3 - - - -
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Residues in contact with VAL 82 (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* 5.4 1.6 - - + -
62A ALA* 4.5 15.7 - - + +
65A ALA* 4.0 17.9 - - + -
81A GLY* 1.3 69.7 - - - -
83A CYS* 1.3 69.1 + - - +
85A THR* 3.7 6.1 - - - -
86A CYS* 3.0 40.7 + - - +
97A ASN 4.5 1.6 - - - +
98A ALA* 4.2 5.4 - - - -
99A GLY* 3.8 26.5 - - - +
294A LEU* 4.7 19.3 - - + -
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Residues in contact with CYS 83 (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* 4.2 5.2 - - - -
69A MSE 3.7 33.1 - - + +
76A SER* 4.2 1.8 - - - -
81A GLY 3.3 0.6 - - - -
82A VAL* 1.3 84.9 - - - +
84A ASN* 1.3 57.4 + - - +
87A TYR* 2.9 31.4 + - - +
291A TRP* 3.6 31.2 - - - -
294A LEU* 5.0 4.7 - - - -
295A LEU* 4.8 2.0 - - - -
302A LYS* 3.7 42.5 - - + +
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Residues in contact with ASN 84 (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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76A SER* 3.1 25.3 + - - +
77A SER 3.5 7.5 + - - -
78A GLU* 4.5 4.9 + - - +
79A GLU 3.4 25.8 + - - +
80A SER* 4.7 3.6 - - - -
81A GLY 3.1 14.7 + - - +
83A CYS* 1.3 76.7 - - - +
85A THR* 1.3 65.8 + - + +
87A TYR* 3.3 1.6 + - - +
88A MSE 2.8 46.0 + - - +
90A ASN* 5.7 1.6 + - - -
442A LEU* 4.1 10.3 - - - +
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Residues in contact with THR 85 (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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81A GLY 3.0 19.0 + - - +
82A VAL* 3.5 8.0 + - - -
84A ASN* 1.3 81.5 - - + +
86A CYS* 1.3 63.2 + - - +
88A MSE 3.4 0.2 + - - -
89A PHE* 3.0 3.6 + - - -
90A ASN* 2.9 52.4 + - - +
91A HIS* 3.7 4.2 - - - -
97A ASN* 2.8 47.0 + - + +
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Residues in contact with CYS 86 (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 5.0 0.2 - - - -
65A ALA 3.9 17.3 - - - +
66A TYR* 3.9 35.4 - - - -
69A MSE 4.1 1.1 - - + -
70A LYS* 3.1 29.4 + - + +
82A VAL* 3.0 41.6 + - - +
83A CYS 3.9 1.8 - - - +
85A THR* 1.3 77.5 + - - +
87A TYR* 1.3 63.8 + - - +
89A PHE* 3.1 10.9 + - - -
91A HIS* 4.0 14.4 - - - -
97A ASN 4.4 1.8 - - - -
98A ALA* 4.8 2.7 - - - -
101A LEU* 5.8 0.2 - - - -
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Residues in contact with TYR 87 (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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69A MSE 3.5 26.6 - - + +
71A GLY 5.8 0.2 - - - -
74A MSE 4.4 1.1 - - - -
75A GLN* 3.3 23.5 - - + +
76A SER* 3.6 29.6 - - - +
83A CYS 2.9 19.3 + - - +
84A ASN 3.5 2.0 - - - +
86A CYS* 1.3 77.0 - - - +
88A MSE 1.3 83.8 + - + +
89A PHE* 3.4 4.5 + - - -
436A ARG* 2.8 31.4 + - - -
441A HIS* 2.7 31.7 + + - +
442A LEU* 3.0 42.0 + - + -
445A VAL* 3.6 18.7 - - + +
446A ASP* 5.1 0.3 - - - +
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Residues in contact with MSE 88 (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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84A ASN* 2.8 34.8 + - - +
85A THR 4.2 2.2 - - - +
87A TYR* 1.3 103.3 - - + +
89A PHE* 1.3 69.9 + - - +
90A ASN* 3.0 13.7 + - + +
442A LEU* 4.7 6.5 - - - -
443A PRO 3.5 23.3 - - - +
444A SER* 3.6 23.3 - - - +
445A VAL* 4.2 11.2 - - - +
446A ASP* 3.7 10.8 - - - +
455A LYS* 4.7 2.6 + - - -
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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