Contacts of the helix formed by residues 85 - 98 (chain M) in PDB entry 5A0Q
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 THR 85 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83M MET 3.8 1.7 + - - -
84M THR* 1.3 75.3 - - - +
86M GLY* 1.3 57.3 + - - +
88M ILE* 3.2 12.4 + - + +
89M ALA* 3.1 24.1 + - - +
110M ILE* 3.7 17.8 - - + +
112M GLY* 3.3 46.6 + - - +
113M LEU 3.9 9.2 + - - -
114M ASP* 4.5 9.0 + - - -
120M ALA* 3.7 20.2 - - + -
122M TYR* 4.0 8.7 - - + -
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Residues in contact with GLY 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E TYR 4.2 2.4 - - - +
104E ASN* 4.6 8.5 + - - +
84M THR* 3.3 10.6 - - - +
85M THR* 1.3 75.4 - - - +
87M ALA* 1.3 63.6 + - - +
89M ALA* 3.4 10.1 + - - +
90M ALA* 3.3 21.5 + - - +
122M TYR* 4.6 9.8 + - - -
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Residues in contact with ALA 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E TYR* 3.5 27.3 - - + +
105E GLU* 3.7 23.1 - - + +
75M TYR* 5.6 0.4 - - + -
83M MET* 3.5 17.5 - - - -
84M THR* 3.2 20.5 + - - +
86M GLY* 1.3 76.7 - - - +
88M ILE* 1.4 56.1 + - - +
90M ALA* 3.5 2.1 + - - -
91M MET* 3.0 30.4 + - - +
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Residues in contact with ILE 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M THR* 4.1 30.5 - - + +
68M ILE* 5.2 7.4 - - + -
72M LEU* 5.2 7.0 - - + -
83M MET* 3.5 29.8 - - + +
84M THR 3.4 13.0 - - - +
85M THR* 3.2 15.6 + - + +
87M ALA* 1.4 74.0 - - - +
89M ALA* 1.3 58.9 + - - +
91M MET* 4.0 14.8 - - + -
92M LEU* 2.9 39.8 + - + +
110M ILE* 3.8 33.7 - - + -
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Residues in contact with ALA 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M THR 3.1 11.3 + - - +
86M GLY* 3.6 9.9 - - - +
87M ALA 3.3 0.2 - - - -
88M ILE* 1.3 77.1 - - - +
90M ALA* 1.4 58.5 + - - +
93M SER* 3.8 3.1 + - - -
110M ILE* 5.7 0.2 - - - -
122M TYR* 3.5 41.9 - - + -
124M PHE* 3.7 14.2 - - - -
130M TYR* 3.0 37.3 - - + +
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Residues in contact with ALA 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E PHE 4.2 1.6 - - - +
102E THR 3.2 7.5 - - - +
103E TYR 3.8 9.6 - - - -
104E ASN* 3.4 35.0 - - + +
57L ARG* 3.8 17.8 + - - +
86M GLY 3.3 6.6 + - - +
87M ALA 4.0 0.2 - - - +
89M ALA* 1.4 77.5 - - - +
91M MET* 1.3 59.7 + - - +
92M LEU 3.7 0.2 - - - -
93M SER* 3.4 15.6 + - - -
94M THR* 3.5 12.5 - - - +
130M TYR* 4.8 8.7 - - + -
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Residues in contact with MET 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E THR* 3.1 12.3 - - + +
103E TYR* 3.7 12.3 - - + -
68M ILE* 4.8 15.9 - - + +
71M ARG* 3.3 43.1 - - + +
72M LEU 5.5 0.2 - - - -
83M MET* 3.9 24.9 - - + -
87M ALA 3.0 19.0 + - - +
88M ILE* 3.3 15.5 + - + +
90M ALA* 1.3 75.7 - - - +
92M LEU* 1.3 81.6 + - + +
93M SER 3.2 1.3 - - - -
94M THR* 2.7 22.4 + - - -
95M ILE* 3.1 30.1 + - + +
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Residues in contact with LEU 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M ILE* 4.2 3.4 - - + -
64M LEU* 4.9 3.8 - - + -
68M ILE* 3.4 35.2 - - + -
88M ILE* 2.9 23.9 + - + +
91M MET* 1.3 85.8 - - + +
93M SER* 1.4 58.7 + - - +
95M ILE* 3.1 9.5 + - + +
96M LEU* 3.0 47.9 + - + +
108M ASN* 4.5 10.1 - - + +
110M ILE* 4.1 22.7 - - + -
124M PHE* 3.5 26.5 - - + -
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Residues in contact with SER 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L SER* 6.0 1.1 - - - -
54L PHE* 6.1 0.4 - - - -
57L ARG* 5.3 3.6 - - - -
89M ALA 3.8 3.6 + - - -
90M ALA 3.4 14.6 + - - -
92M LEU* 1.4 78.6 - - - +
94M THR* 1.3 59.6 + - - +
96M LEU* 3.3 3.4 + - - +
97M TYR* 2.8 40.2 + - - -
124M PHE* 3.9 10.0 - - - -
128M GLY* 4.0 21.5 - - - -
130M TYR* 3.8 33.7 - - - -
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Residues in contact with THR 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E PHE* 3.9 36.1 - - + +
102E THR* 4.1 12.6 - - - +
54L PHE* 4.1 14.8 - - + -
57L ARG* 4.7 4.9 - - - +
71M ARG* 5.0 1.0 + - - -
90M ALA 3.5 17.7 - - - +
91M MET* 2.7 20.8 + - - -
93M SER* 1.3 76.3 - - - +
95M ILE* 1.4 61.5 + - - +
97M TYR* 3.3 8.9 + - - +
98M SER* 3.0 27.2 + - - -
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Residues in contact with ILE 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M LEU* 3.6 29.6 - - + -
67M ILE* 4.2 22.0 - - + -
68M ILE* 4.7 7.6 - - + -
71M ARG* 3.5 34.1 - - + +
91M MET* 3.1 40.9 + - + +
92M LEU* 3.1 12.6 + - + +
94M THR* 1.4 76.6 - - - +
96M LEU* 1.3 60.2 + - - +
98M SER* 2.8 26.8 + - - +
99M ARG 4.0 1.7 + - - -
104M TYR* 4.6 8.8 - - + -
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Residues in contact with LEU 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M LEU* 4.2 27.8 - - + -
92M LEU* 3.0 36.3 + - + +
93M SER 3.6 5.6 - - - +
94M THR 3.3 0.2 - - - -
95M ILE* 1.3 75.6 - - - +
97M TYR* 1.3 57.4 + - - +
99M ARG 2.7 27.6 - - - +
100M ARG* 3.8 3.8 - - - +
104M TYR* 4.6 19.0 - - + +
106M VAL* 4.9 1.8 - - + +
108M ASN* 4.4 4.9 - - - +
124M PHE* 3.7 7.0 - - + -
125M ASP 3.3 24.2 - - - +
126M PRO* 3.8 22.8 - - + +
127M VAL 3.8 7.0 - - - -
128M GLY* 3.6 17.3 - - - -
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Residues in contact with TYR 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L ALA* 1.8 65.7 + - + +
51L ASP* 4.4 3.4 - - - -
53L SER* 4.5 3.6 - - - -
54L PHE* 3.7 52.7 - + + -
55L TRP* 6.1 2.9 - + - -
93M SER* 2.8 31.8 + - - +
94M THR 3.3 7.8 + - - +
96M LEU* 1.3 75.5 - - - +
98M SER* 1.4 61.3 + - - +
99M ARG 3.1 2.2 + - - -
100M ARG* 3.0 51.0 + - - +
101M PHE* 6.1 0.2 - - - -
127M VAL 2.6 17.7 - - - -
128M GLY* 3.8 7.9 - - - -
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Residues in contact with SER 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94M THR 3.0 12.8 + - - -
95M ILE* 2.8 24.6 + - - +
96M LEU 3.3 0.8 - - - -
97M TYR* 1.4 76.0 - - - +
99M ARG* 1.3 61.2 + - - +
100M ARG 3.7 0.4 - - - -
104M TYR* 5.1 1.4 - - - -
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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