Contacts of the helix formed by residues 77 - 89 (chain H) in PDB entry 3MQT
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 GLU 77 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122F TYR* 3.7 5.0 - - - -
123F LYS* 3.2 41.3 + - + +
126F GLY 3.2 18.2 - - - +
127F GLY* 3.5 21.9 - - - -
128F ALA* 3.5 11.2 + - - +
73H ARG* 5.6 2.8 - - - +
74H ASP* 3.2 23.4 + - + +
75H PRO 3.1 3.4 - - - -
76H LEU* 1.3 74.7 - - - +
78H PHE* 1.3 58.3 + - - +
80H ALA* 3.4 9.8 + - + +
81H ASN* 2.9 35.9 + - - +
84H ARG* 4.5 7.8 + - - -
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Residues in contact with PHE 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F GLY* 3.6 4.5 + - - -
75H PRO 3.1 24.9 - - - -
76H LEU* 3.1 30.6 + - + -
77H GLU* 1.3 71.4 - - - +
79H ARG* 1.3 58.6 + - + +
81H ASN* 4.0 3.3 - - - +
82H TYR* 2.9 33.1 + - - +
106H ASP* 4.6 3.5 - - - +
109H LEU* 3.8 25.8 - - + -
110H TYR* 3.5 57.9 - + - +
113H ALA* 3.9 16.4 - - + -
124H LEU* 4.0 23.3 - - + -
290H THR* 3.6 11.3 + - + +
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Residues in contact with ARG 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F ARG* 5.3 8.1 - - - +
125F MET 4.2 18.9 + - - -
126F GLY* 3.4 14.6 + - - +
129F GLN* 3.9 12.6 - - - +
293F LEU* 4.1 19.8 + - - +
294F ARG* 6.3 0.2 - - - +
296F MET* 3.8 22.9 - - - +
297F ASP* 2.7 43.9 + - - -
326F VAL* 5.3 0.7 - - - -
328F HIS* 6.1 1.0 - - - -
78H PHE* 1.3 79.4 - - + +
80H ALA* 1.3 57.1 + - - +
82H TYR* 3.7 1.0 - - - +
83H ASN* 2.9 43.4 + - - +
290H THR* 4.4 16.2 - - + -
294H ARG* 3.8 24.0 - - - +
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Residues in contact with ALA 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F GLY 3.1 14.0 + - - +
127F GLY* 4.0 6.5 - - - -
128F ALA 3.7 13.2 - - - +
129F GLN* 3.6 30.5 - - + -
77H GLU* 4.0 7.6 - - + +
79H ARG* 1.3 79.1 - - - +
81H ASN* 1.3 57.6 + - - +
83H ASN* 3.8 1.0 - - - +
84H ARG* 2.8 47.2 + - - +
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Residues in contact with ASN 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H ILE* 5.1 1.0 - - - +
69H ALA 4.3 1.0 + - - -
70H VAL* 4.3 10.9 - - + +
73H ARG* 3.6 19.0 - - - +
74H ASP 2.9 26.2 + - - +
75H PRO* 3.9 7.3 - - - +
77H GLU* 2.9 26.7 + - - +
78H PHE* 4.0 2.9 - - - +
80H ALA* 1.3 73.7 - - - +
82H TYR* 1.3 64.9 + - - +
84H ARG* 2.8 29.8 + - - +
85H MET* 2.9 31.6 + - - +
109H LEU* 4.2 20.7 - - + +
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Residues in contact with TYR 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H PHE 2.9 23.1 + - - +
79H ARG 3.7 2.7 - - - +
81H ASN* 1.3 73.8 - - - +
83H ASN* 1.3 74.4 + - - +
85H MET* 3.4 10.9 + - - +
86H TYR* 2.9 47.3 + + + +
99H LEU* 3.6 21.3 - - - +
102H ILE* 3.8 18.0 - - + +
106H ASP* 4.3 6.9 + - + +
264H ARG* 4.7 7.0 - - - -
287H GLY* 3.1 30.5 - - - -
290H THR* 4.1 24.7 - - + -
291H GLU* 3.4 38.5 + - + +
294H ARG* 6.1 1.8 - - - -
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Residues in contact with ASN 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F GLN* 2.5 35.2 + - - +
328F HIS* 3.7 20.1 + - + -
79H ARG* 2.9 24.2 + - - +
80H ALA 3.8 1.8 - - - +
82H TYR* 1.3 88.5 - - - +
84H ARG* 1.3 60.5 + - - +
86H TYR* 3.3 4.2 + - - +
87H ASP* 2.8 44.7 + - - +
264H ARG* 5.3 5.0 + - - -
294H ARG* 5.5 3.6 + - - -
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Residues in contact with ARG 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F ALA 4.6 5.9 + - - -
69H ALA* 2.9 35.3 + - + +
73H ARG* 3.5 45.9 - - - +
77H GLU* 4.5 5.9 + - - -
80H ALA* 2.8 40.6 + - - +
81H ASN* 2.8 32.3 - - - +
83H ASN* 1.3 73.6 - - - +
85H MET* 1.3 67.1 + - - +
87H ASP* 4.8 3.1 - - - -
88H THR* 3.0 40.1 + - + +
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Residues in contact with MET 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H ILE* 4.2 15.3 - - + +
69H ALA* 3.6 13.9 - - + +
70H VAL* 3.7 20.0 - - + -
81H ASN 2.9 23.6 + - - +
82H TYR* 3.6 12.1 - - - +
84H ARG* 1.3 76.4 - - - +
86H TYR* 1.3 61.7 + - - +
88H THR* 4.1 0.7 - - - -
89H THR* 2.8 31.0 + - - +
102H ILE* 4.1 34.1 - - + +
105H ILE* 3.7 47.1 - - + -
106H ASP* 4.1 11.4 - - + +
109H LEU* 4.4 7.2 - - + -
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Residues in contact with TYR 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E ASP* 2.5 29.5 + - - -
82H TYR* 2.9 43.5 + + + +
83H ASN* 3.6 5.8 - - - +
84H ARG 3.2 0.2 - - - -
85H MET* 1.3 79.5 - - - +
87H ASP* 1.3 73.9 + - - +
89H THR* 3.5 2.1 + - - -
90H LYS* 3.3 39.8 + - + +
94H MET* 3.1 42.1 + - + +
95H ARG* 3.1 10.6 + - - -
99H LEU* 4.1 10.8 - - + -
102H ILE* 3.8 17.7 - - + +
263H THR* 4.5 4.5 - - + -
265H PHE* 3.8 9.0 - + - -
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Residues in contact with ASP 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E GLN* 6.1 0.4 - - - -
62H TRP* 3.6 23.3 - - + -
83H ASN* 2.8 31.1 + - - +
84H ARG* 4.1 3.3 - - - +
86H TYR* 1.3 81.8 - - - +
88H THR* 1.3 65.6 + - + +
89H THR 3.1 1.7 + - - -
90H LYS* 3.3 35.9 + - - +
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Residues in contact with THR 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H LYS 4.1 8.3 - - - +
62H TRP 3.3 6.2 - - - -
64H ASN* 2.9 50.0 + - - +
65H ASN 5.1 1.4 + - - -
69H ALA* 3.7 15.4 + - + +
84H ARG* 3.0 32.9 + - + +
85H MET 3.7 4.7 + - - -
87H ASP* 1.3 79.6 - - + +
89H THR* 1.3 64.0 + - - +
90H LYS 3.7 0.2 - - - -
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Residues in contact with THR 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H PHE* 5.3 6.2 - - + -
62H TRP 3.2 4.0 - - - -
64H ASN 3.4 24.9 - - - +
66H ILE* 4.0 25.5 - - + +
85H MET 2.8 22.6 + - - +
86H TYR* 3.6 5.2 + - - -
87H ASP 3.1 0.4 - - - -
88H THR* 1.3 86.7 - - - +
90H LYS* 1.3 53.0 + - - +
91H TRP 3.2 3.1 - - - -
92H ILE* 3.0 16.7 + - + +
93H GLY* 2.6 39.1 + - - -
94H MET 5.4 0.2 + - - -
98H GLY 5.6 0.7 + - - -
102H ILE* 4.3 10.2 - - - +
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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