Contacts of the helix formed by residues 80 - 94 (chain A) in PDB entry 1MRA
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 PRO 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LEU* 3.7 7.2 - - + +
79A ALA* 1.3 86.0 - - - +
81A VAL* 1.3 64.1 + - + +
83A LEU* 3.3 12.7 - - + +
84A GLU* 2.9 27.7 + - - +
108A ASP* 3.7 8.6 - - - +
111A ALA* 4.1 19.7 - - + -
112A TRP* 3.4 51.6 - - + +
115A LEU* 4.1 18.6 - - + -
278A THR* 4.2 3.4 - - - -
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ALA* 3.1 1.8 + - + -
80A PRO* 1.3 76.3 - - + +
82A SER* 1.3 63.2 + - - +
84A GLU* 3.7 8.2 - - - +
85A ALA* 3.4 18.9 + - - +
112A TRP* 4.4 20.4 - - + -
278A THR* 4.5 13.9 - - + -
282A ARG* 4.0 18.6 + - - +
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Residues in contact with SER 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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77A PRO* 6.5 0.4 - - - -
79A ALA* 2.7 26.9 + - - +
81A VAL* 1.3 73.0 - - - +
83A LEU* 1.3 64.6 + - - -
85A ALA* 3.1 9.0 + - - +
86A MET* 3.0 22.8 + - - +
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Residues in contact with LEU 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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6A ILE* 3.3 31.0 - - + -
73A ILE* 4.7 7.4 - - + -
76A GLU* 4.0 21.8 - - + +
77A PRO 4.1 11.2 + - - +
78A LEU* 5.1 0.2 - - - -
79A ALA 2.8 15.3 + - - +
80A PRO* 3.3 14.8 - - + +
82A SER* 1.3 75.4 - - - +
84A GLU* 1.3 56.6 + - - +
86A MET* 3.1 33.7 + - + +
87A LEU* 2.9 41.2 + - + +
107A ILE* 4.9 10.8 - - + -
108A ASP* 6.5 0.7 - - - -
111A ALA* 4.7 10.8 - - + -
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Residues in contact with GLU 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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80A PRO 2.9 14.7 + - - +
81A VAL 3.7 5.4 - - - +
83A LEU* 1.3 80.8 - - - +
85A ALA* 1.3 70.1 + - - +
87A LEU* 3.2 10.1 + - - -
88A ALA* 3.0 19.9 + - - +
96A TYR* 2.9 31.8 + - - +
101A ARG* 5.3 2.1 + - - -
108A ASP* 4.6 8.3 - - + +
275A GLY 5.5 3.6 - - - +
278A THR* 4.0 20.2 - - + -
279A GLY 5.9 0.2 - - - +
282A ARG* 3.0 30.6 + - - -
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL 3.4 10.7 + - - +
82A SER* 3.1 12.0 + - - +
84A GLU* 1.3 86.8 - - - +
86A MET* 1.3 64.1 + - - +
88A ALA* 3.1 14.9 + - - +
89A LYS* 3.2 13.3 + - - +
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Residues in contact with MET 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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72A MET* 3.7 21.3 - - - +
73A ILE* 4.5 7.4 - - + -
76A GLU* 3.9 16.6 - - + +
82A SER 3.0 11.3 + - - +
83A LEU* 3.4 36.1 - - + +
85A ALA* 1.3 79.0 - - - +
87A LEU* 1.3 69.7 + - + +
89A LYS* 3.4 5.9 + - - +
90A ARG* 2.8 66.2 + - + +
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Residues in contact with LEU 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 MET* 3.7 27.4 - - + -
72A MET* 4.3 12.3 - - - -
73A ILE* 4.3 18.6 - - + -
83A LEU* 2.9 30.6 + - + +
84A GLU* 3.2 9.2 + - - +
85A ALA 3.2 0.4 - - - -
86A MET* 1.3 87.3 - - + +
88A ALA* 1.3 63.8 + - - +
90A ARG* 3.3 3.0 + - - -
91A PHE* 3.2 40.2 + - + -
96A TYR* 3.8 13.7 - - + +
104A ALA* 4.2 25.6 - - + +
107A ILE* 5.1 7.4 - - + -
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Residues in contact with ALA 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 GLU* 3.0 19.3 + - - +
85A ALA* 3.1 7.6 + - - +
87A LEU* 1.3 78.9 - - - +
89A LYS* 1.3 59.1 + - - +
91A PHE 3.6 0.9 + - - -
92A CYS* 3.4 22.7 + - - +
96A TYR* 3.5 38.5 - - + +
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Residues in contact with LYS 89 (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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85A ALA 3.2 10.8 + - - +
86A MET* 4.0 7.6 - - - +
88A ALA* 1.3 73.9 - - - +
90A ARG* 1.3 71.1 - - + +
91A PHE 3.2 1.3 + - - -
92A CYS* 3.2 28.0 - - - -
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Residues in contact with ARG 90 (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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72A MET* 2.8 68.7 + - + +
76A GLU* 5.9 1.0 + - - -
86A MET* 2.8 47.4 + - - +
87A LEU* 3.3 4.5 + - - +
89A LYS* 1.3 85.9 - - - +
91A PHE* 1.3 64.0 + - + +
92A CYS* 3.6 0.7 - - - -
93A LEU* 5.4 0.6 - - - +
94A ALA* 5.9 0.2 - - - +
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Residues in contact with PHE 91 (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 LEU* 5.2 5.2 - - + -
69A MET* 4.1 25.6 - - + -
72A MET* 4.0 22.0 - - + -
87A LEU* 3.2 50.4 + - + +
88A ALA 4.1 1.3 - - - -
89A LYS 3.2 0.2 - - - -
90A ARG* 1.3 82.9 - - - +
92A CYS* 1.3 64.3 + - - +
93A LEU 2.8 6.9 + - - -
94A ALA* 3.0 10.3 + - + +
95A GLY 2.8 25.3 + - - +
96A TYR* 3.6 17.2 + + + +
100A ILE* 3.5 50.3 - - + -
104A ALA* 6.0 0.9 - - + -
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Residues in contact with CYS 92 (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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88A ALA 3.4 16.2 + - - +
89A LYS* 3.2 21.5 - - - +
90A ARG 3.6 0.4 - - - -
91A PHE* 1.3 77.3 - - - +
93A LEU* 1.4 78.5 - - - +
95A GLY* 4.2 4.8 + - - -
96A TYR* 5.0 5.8 + - - +
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Residues in contact with LEU 93 (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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90A ARG 5.3 0.8 + - - +
91A PHE 3.0 1.2 - - - -
92A CYS* 1.4 93.4 - - - +
94A ALA* 1.3 67.4 + - - +
95A GLY 3.2 1.9 + - - -
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Residues in contact with ALA 94 (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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90A ARG 5.9 0.2 - - - +
91A PHE* 3.0 16.7 + - + +
93A LEU* 1.3 82.0 - - - +
95A GLY* 1.3 58.8 + - - +
100A ILE* 4.2 21.8 - - + +
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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