Contacts of the helix formed by residues 78 - 92 (chain Z) in PDB entry 1MVW
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 ASN 78 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68Z LYS* 5.4 0.8 - - - +
70Z PRO* 3.2 16.4 + - + +
76Z ILE* 4.1 2.5 - - - -
77Z THR* 1.3 80.1 - - + +
79Z TRP* 1.3 63.1 + - - +
80Z ASP* 3.3 17.3 + - - +
81Z ASP* 3.0 45.8 + - + +
82Z MET* 3.1 25.6 + - - +
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Residues in contact with TRP 79 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Z ILE* 3.8 48.9 + - + -
77Z THR 4.6 6.9 + - - -
78Z ASN* 1.3 73.5 + - - +
80Z ASP* 1.3 61.6 + - - +
82Z MET* 3.8 3.9 - - + +
83Z GLU* 3.3 26.0 + - - +
86Z TRP* 4.6 5.6 - + - -
115Z ASN* 3.6 52.8 + - + -
118Z LYS* 3.8 32.9 - - + +
119Z MET* 3.8 23.6 - - + -
122Z ILE* 3.6 23.7 - - + +
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Residues in contact with ASP 80 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Z ARG* 3.3 14.2 + - - -
78Z ASN* 3.3 14.7 + - - +
79Z TRP* 1.3 77.4 - - - +
81Z ASP* 1.3 86.8 + - - +
83Z GLU* 3.6 7.9 + - - +
84Z LYS* 3.3 37.2 + - - +
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Residues in contact with ASP 81 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Z VAL* 3.4 20.0 - - + +
37Z ARG* 2.9 27.4 + - - -
68Z LYS* 3.1 32.4 - - - +
70Z PRO* 3.4 19.7 - - + +
78Z ASN* 3.0 29.1 + - - +
80Z ASP* 1.3 89.2 + - - +
82Z MET* 1.3 61.4 + - - +
84Z LYS* 3.5 10.1 - - - +
85Z ILE* 3.3 16.5 + - - +
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Residues in contact with MET 82 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Z ASN* 3.5 26.5 - - + +
17Z VAL* 5.8 0.9 - - + -
33Z SER* 5.3 1.3 - - - +
70Z PRO* 3.9 11.4 - - - +
71Z ILE* 3.7 37.2 - - + -
76Z ILE* 3.8 20.0 - - + -
78Z ASN 3.1 16.6 + - - +
79Z TRP* 4.0 5.8 - - + +
80Z ASP 3.3 0.4 - - - -
81Z ASP* 1.3 70.7 - - - +
83Z GLU* 1.3 59.6 + - - +
84Z LYS 3.0 1.3 - - - -
85Z ILE* 2.7 45.3 + - + +
86Z TRP* 2.9 45.1 + - + +
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Residues in contact with GLU 83 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Z TRP 3.3 16.6 + - - +
80Z ASP* 3.8 7.7 - - - +
82Z MET* 1.3 76.6 - - - +
84Z LYS* 1.3 57.6 + - - +
86Z TRP* 3.5 13.5 + - + -
87Z HIS* 2.9 31.7 + - + +
122Z ILE* 4.1 20.1 - - + +
126Z THR* 4.2 28.5 + - - +
127Z PHE* 3.7 16.3 - - + -
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Residues in contact with LYS 84 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Z VAL* 4.0 10.1 - - + -
37Z ARG* 3.4 33.6 - - - +
51Z ASP* 5.2 5.3 + - - +
52Z SER* 3.5 26.2 - - - +
54Z VAL* 4.4 10.4 - - + +
80Z ASP* 3.3 27.0 + - - +
81Z ASP* 3.5 25.6 - - - +
82Z MET 3.0 0.4 - - - -
83Z GLU* 1.3 79.3 - - - +
85Z ILE* 1.4 61.8 + - - +
87Z HIS* 3.2 8.2 + - + +
88Z HIS* 3.1 22.5 + - - +
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Residues in contact with ILE 85 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Z VAL* 3.7 28.7 - - + -
31Z PHE* 4.2 11.3 - - + -
33Z SER* 3.9 27.4 - - - +
34Z ILE 4.1 0.7 - - - +
35Z VAL* 3.8 12.6 - - + -
54Z VAL* 4.0 13.0 - - + -
70Z PRO* 3.6 37.0 - - + -
81Z ASP 3.3 7.6 + - - +
82Z MET* 2.7 26.6 + - + +
84Z LYS* 1.4 70.2 - - - +
86Z TRP* 1.3 55.0 + - + +
88Z HIS* 3.3 3.6 + - - +
89Z THR* 2.7 32.3 + - - +
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Residues in contact with TRP 86 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Z CYS* 4.0 16.0 - - - -
12Z ASN* 2.9 37.0 + - - +
76Z ILE* 4.2 11.0 - - + -
79Z TRP* 4.6 1.8 - + - -
82Z MET* 2.9 38.4 + - + +
83Z GLU* 3.8 18.4 - - - +
85Z ILE* 1.3 75.5 - - + +
87Z HIS* 1.3 60.6 + - - +
89Z THR* 2.8 23.5 + - - -
90Z PHE* 3.0 27.2 + + + -
105Z LEU* 4.4 4.2 - - + +
119Z MET* 3.9 29.8 - - + -
122Z ILE* 4.1 24.9 - - + -
123Z MET* 3.3 30.0 - - + +
127Z PHE* 3.6 19.5 - + + -
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Residues in contact with HIS 87 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Z GLU* 2.9 19.7 + - + +
84Z LYS* 3.2 8.9 + - - +
86Z TRP* 1.3 76.6 - - - +
88Z HIS* 1.3 59.5 + - - +
90Z PHE* 4.5 0.7 - - - -
91Z TYR* 2.9 65.4 + + + +
92Z ASN* 4.6 6.6 + - - -
127Z PHE* 3.9 17.4 - - + -
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Residues in contact with HIS 88 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z PHE* 3.6 21.4 - + - -
54Z VAL* 3.9 38.5 + - + +
55Z GLY* 5.2 0.4 - - - -
56Z ASP 5.9 0.4 + - - -
84Z LYS 3.1 9.8 + - - +
85Z ILE 3.4 9.0 - - - +
87Z HIS* 1.3 79.3 - - - +
89Z THR* 1.3 62.9 + - - +
92Z ASN* 2.8 54.7 + - + -
93Z GLU* 2.9 41.5 + - + -
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Residues in contact with THR 89 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Z CYS* 4.7 9.4 - - + -
17Z VAL* 4.5 7.5 - - + +
19Z ALA* 3.6 31.0 - - + -
31Z PHE* 3.7 20.2 - - + -
85Z ILE* 2.7 26.5 + - - +
86Z TRP* 2.8 15.1 + - - -
88Z HIS* 1.3 75.9 - - - +
90Z PHE* 1.3 62.0 + - + -
93Z GLU* 3.4 8.5 - - + +
94Z LEU* 2.9 36.9 + - + +
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Residues in contact with PHE 90 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Z LEU* 4.0 28.9 - - + -
10Z CYS* 5.8 6.5 - - + -
86Z TRP* 3.0 27.4 + + + -
87Z HIS* 4.1 2.2 - - - +
89Z THR* 1.3 83.1 - - + +
91Z TYR* 1.3 62.0 + + + +
94Z LEU* 3.5 4.9 - - + -
95Z ARG 2.8 26.2 + - - -
96Z VAL* 3.1 25.2 + - + +
98Z PRO* 3.9 27.1 - - + -
103Z THR* 4.4 16.4 - - + -
105Z LEU* 6.1 0.4 - - + -
123Z MET* 4.1 24.5 - - + -
127Z PHE* 3.6 45.3 - + - -
129Z VAL* 4.8 0.9 - - + -
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Residues in contact with TYR 91 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Z HIS* 2.9 61.2 + + - +
90Z PHE* 1.3 82.7 - - + +
92Z ASN* 1.3 72.9 + - - +
95Z ARG* 3.4 16.7 - - - +
96Z VAL 3.8 12.1 - - - -
97Z ALA* 4.6 5.2 - - + -
98Z PRO* 3.7 34.7 - - + +
99Z GLU* 4.2 10.2 + - - -
127Z PHE* 4.9 9.3 + + - -
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Residues in contact with ASN 92 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Z HIS* 4.2 7.4 + - - +
88Z HIS* 2.8 49.9 + - + +
91Z TYR* 1.3 94.2 + - - +
93Z GLU* 1.3 67.9 + - - +
94Z LEU 3.6 0.2 - - - -
95Z ARG* 3.3 17.4 + - - +
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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
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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