Contacts of the helix formed by residues 52 - 77 (chain M) in PDB entry 2RCR
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 52 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M ALA* 4.2 5.6 - - - +
50M TYR* 3.9 4.5 - - - +
51M LEU* 1.3 79.6 - - - +
53M SER* 1.3 69.0 + - - +
55M GLY* 3.4 12.7 + - - -
56M VAL* 3.4 12.8 + - - +
130M ARG* 4.8 7.9 - - - +
134M ARG* 3.5 22.7 - - - -
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Residues in contact with SER 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M GLY* 1.3 65.5 - - - +
54M LEU* 1.3 71.5 + - - +
55M GLY 2.8 12.8 + - - -
56M VAL* 2.9 28.3 + - - +
57M LEU* 3.9 0.9 + - - +
134M ARG* 4.2 5.9 - - - +
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Residues in contact with LEU 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M SER* 1.3 92.5 + - - +
55M GLY* 1.3 60.9 + - - +
56M VAL 3.1 1.1 + - - -
57M LEU* 3.7 4.8 + - - +
58M SER* 3.6 7.6 + - - -
125M TRP 5.6 0.2 - - - +
126M SER* 3.3 47.0 + - - +
129M GLY* 3.3 36.6 - - - +
130M ARG* 4.6 6.1 - - + +
133M LEU* 4.8 16.2 - - + -
134M ARG* 5.4 6.7 - - - +
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Residues in contact with GLY 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M LEU 6.0 0.4 - - - -
52M GLY 3.4 10.9 + - - -
53M SER 2.8 2.6 + - - -
54M LEU* 1.3 80.7 - - - +
56M VAL* 1.3 57.2 + - - +
58M SER* 4.2 9.6 - - - -
59M LEU* 3.5 18.4 - - - +
126M SER 5.3 0.2 - - - -
127M TRP* 4.3 1.8 - - - -
130M ARG* 3.0 44.7 + - - +
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Residues in contact with VAL 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M GLY 3.4 7.2 + - - +
53M SER* 2.9 20.3 + - - +
55M GLY* 1.3 76.5 - - - +
57M LEU* 1.3 75.0 + - + +
58M SER 3.1 2.0 - - - -
59M LEU* 2.7 33.7 + - + +
60M PHE* 2.9 14.8 + - + +
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Residues in contact with LEU 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M SER 5.0 0.7 - - - +
54M LEU* 3.7 5.8 + - - +
56M VAL* 1.3 87.7 - - + +
58M SER* 1.3 54.0 + - - +
60M PHE* 3.8 32.5 - - + -
61M SER* 2.7 51.4 + - - +
122M VAL* 4.1 16.4 - - + -
126M SER* 3.6 21.1 - - - +
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Residues in contact with SER 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M LEU 3.6 7.5 + - - -
55M GLY 4.2 2.7 - - - -
56M VAL 3.1 0.4 - - - -
57M LEU* 1.3 79.0 - - - +
59M LEU* 1.3 56.7 - - - +
62M GLY* 2.9 25.3 + - - -
123M ALA* 2.9 33.2 + - - +
126M SER* 3.9 8.0 - - - -
127M TRP* 3.2 25.2 - - - -
500M BPH 2.8 35.2 - - - +
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Residues in contact with LEU 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800L UQ 3.2 58.8 - - + -
55M GLY 3.5 20.4 - - - +
56M VAL* 2.7 18.8 + - + +
58M SER* 1.3 78.4 - - - +
60M PHE* 1.4 51.1 + - - +
61M SER 3.1 1.1 - - - -
63M LEU* 2.6 57.6 + - + +
127M TRP* 5.2 2.2 - - + -
130M ARG* 5.4 0.2 - - - +
500M BPH 5.5 16.4 - - + -
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Residues in contact with PHE 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M VAL* 2.9 13.6 + - + +
57M LEU* 3.5 36.3 - - + +
59M LEU* 1.4 68.3 - - - +
61M SER* 1.3 63.6 + - - +
63M LEU* 4.3 3.9 - - - +
64M MET* 3.0 40.1 + - + +
119M PHE* 6.1 1.8 - + - -
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Residues in contact with SER 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M LEU* 2.7 28.0 + - - +
60M PHE* 1.3 79.4 - - - +
62M GLY* 1.3 71.7 - - - -
63M LEU 3.0 1.1 - - - -
64M MET* 2.9 19.4 + - - +
65M TRP* 2.9 14.6 + - - +
119M PHE* 3.8 17.0 - - - +
122M VAL* 3.5 22.7 - - - +
123M ALA* 3.7 22.2 - - - -
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Residues in contact with GLY 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M SER 2.9 21.2 + - - -
61M SER* 1.3 80.2 - - - +
63M LEU* 1.3 62.0 + - - +
65M TRP* 2.8 39.8 - - - +
66M PHE* 3.8 0.6 - - - +
123M ALA* 3.7 12.7 - - - +
500M BPH 4.5 13.9 - - - -
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Residues in contact with LEU 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M LEU* 2.6 37.6 + - + +
60M PHE* 4.3 4.0 - - - +
61M SER 2.9 0.4 + - - -
62M GLY* 1.3 66.8 - - - +
64M MET* 1.3 53.1 + - - +
65M TRP 2.6 16.9 + - - -
66M PHE* 2.9 24.6 + - + +
67M PHE* 3.3 20.8 + - + +
500M BPH 4.5 25.6 - - + +
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Residues in contact with MET 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M PHE* 3.0 31.7 + - + +
61M SER* 2.9 7.2 + - - +
63M LEU* 1.3 74.1 - - - +
65M TRP* 1.3 58.0 + - - +
67M PHE* 3.7 7.0 - - - +
68M THR* 3.0 32.9 + - - +
115M ILE* 5.1 3.1 - - + -
119M PHE* 3.1 59.9 - - + -
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Residues in contact with TRP 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M SER 2.9 10.0 + - - +
62M GLY* 2.8 37.0 - - - +
63M LEU 2.6 3.6 + - - -
64M MET* 1.3 70.7 - - - +
66M PHE* 1.3 94.5 + + + +
67M PHE 2.7 3.2 + - - -
68M THR* 2.9 14.9 + - - -
69M ILE* 3.4 32.0 + - + +
116M ALA* 3.3 43.7 - - + +
119M PHE* 4.5 7.0 - - + -
120M MET* 4.3 31.1 - - + +
175M TYR* 3.9 14.2 - + - -
400M BCL 4.3 35.2 - - + -
500M BPH 4.0 26.0 - - + -
601M BCL 6.4 0.7 - - + -
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Residues in contact with PHE 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M GLY 3.8 1.8 - - - +
63M LEU* 2.9 16.8 + - + +
65M TRP* 1.3 105.3 - + + +
67M PHE* 1.3 89.7 + + - +
69M ILE* 3.1 27.2 - - - +
70M GLY* 3.2 7.3 + - - -
400M BCL 6.1 0.2 - - + -
500M BPH 3.4 51.8 - - + -
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Residues in contact with PHE 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M LEU* 3.9 16.6 - - + +
64M MET* 3.7 13.0 - - - +
65M TRP 2.7 3.4 + - - -
66M PHE* 1.3 103.6 - + - +
68M THR* 1.3 52.2 + - - +
69M ILE 2.5 16.3 + - - -
70M GLY* 2.6 4.4 + - - +
71M ILE* 2.5 57.6 + - + -
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Residues in contact with THR 68 (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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64M MET* 3.0 21.3 + - - +
65M TRP 2.9 9.5 + - - -
67M PHE* 1.3 73.0 - - - +
69M ILE* 1.3 49.1 + - - +
71M ILE* 4.3 9.2 - - - +
72M TRP* 2.8 36.1 + - - +
93M LEU* 4.1 0.4 - - + -
112M LEU* 3.2 31.4 - - + +
115M ILE* 4.4 12.4 - - + +
116M ALA* 3.6 33.2 - - + +
119M PHE* 6.0 0.4 - - - -
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Residues in contact with ILE 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M TRP* 3.4 34.9 + - + +
66M PHE* 3.1 12.6 - - - +
67M PHE 2.5 4.9 + - - -
68M THR* 1.3 70.6 - - - +
70M GLY* 1.3 56.5 + - - +
71M ILE 3.1 1.6 - - - -
72M TRP 2.8 2.3 + - - -
73M PHE* 2.5 64.5 + - + -
93M LEU* 2.7 22.1 - - + +
116M ALA* 4.2 8.7 - - + -
175M TYR* 3.3 44.2 - - + +
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Residues in contact with GLY 70 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M PHE* 3.2 6.4 + - - -
67M PHE* 2.6 11.5 + - - -
69M ILE* 1.3 77.6 - - - +
71M ILE* 1.3 60.0 + - - -
73M PHE* 3.3 39.2 - - - +
74M TRP* 4.1 1.9 + - - +
84M PHE* 5.2 7.5 - - - -
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Residues in contact with ILE 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M PHE* 2.5 62.3 + - + +
68M THR* 4.3 8.3 - - - +
70M GLY* 1.3 73.7 - - - -
72M TRP* 1.3 56.5 + - - +
74M TRP* 2.7 48.5 - - + +
79M TRP* 6.3 7.4 - - + -
112M LEU* 5.8 3.6 - - + -
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Residues in contact with TRP 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M THR 2.8 21.7 + - - +
69M ILE 2.8 1.6 + - - -
71M ILE* 1.3 78.0 - - - +
73M PHE* 1.3 55.9 + - - +
74M TRP* 3.1 12.8 + + - -
75M TYR* 2.9 52.0 + + + +
76M GLN* 5.0 1.2 + - - +
93M LEU* 3.1 40.8 - - + +
94M GLU 5.6 3.0 + - - -
108M LYS* 4.6 27.8 + - + -
110M GLY* 5.5 4.4 - - - +
112M LEU* 3.0 46.6 - - + +
113M TRP 4.5 0.9 - - - +
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Residues in contact with PHE 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69M ILE* 2.5 62.2 + - + -
70M GLY* 3.3 18.4 + - - +
71M ILE 3.3 0.6 - - - -
72M TRP* 1.3 68.0 - - - +
74M TRP* 1.3 57.0 - - - +
76M GLN* 4.9 4.5 - - + +
77M ALA* 4.0 11.0 - - - +
84M PHE* 3.8 33.2 - + - -
88M LEU* 4.8 17.3 - - + -
91M PHE* 3.3 55.7 - + + -
92M SER* 4.1 9.0 - - - +
93M LEU* 3.7 13.9 - - + -
175M TYR 5.2 2.2 - - - -
176M GLY* 6.0 2.5 - - - -
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Residues in contact with TRP 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70M GLY 4.5 2.2 - - - +
71M ILE* 2.7 40.4 - - + +
72M TRP* 3.1 7.9 + + - -
73M PHE* 1.3 74.1 - - - +
75M TYR* 1.3 63.2 + + + +
76M GLN 3.0 3.6 - - - +
77M ALA* 2.5 38.4 + - - +
78M GLY* 3.2 5.0 + - - -
79M TRP* 2.8 56.5 - + + +
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Residues in contact with TYR 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72M TRP* 2.9 41.3 + + + +
74M TRP* 1.3 90.4 - - + +
76M GLN* 1.3 64.3 - - + +
77M ALA 3.3 2.1 + - - -
78M GLY 4.8 1.8 + - - -
108M LYS* 4.5 21.3 + - + -
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Residues in contact with GLN 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72M TRP 5.0 1.2 + - - +
73M PHE* 5.8 2.9 - - + -
74M TRP 3.0 3.0 - - - +
75M TYR* 1.3 85.2 - - + +
77M ALA* 1.3 57.2 - - - +
91M PHE* 3.0 25.7 - - + -
92M SER 5.6 1.4 - - - +
94M GLU* 4.5 15.0 + - - +
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Residues in contact with ALA 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73M PHE 4.0 3.4 - - - +
74M TRP* 2.5 33.6 + - - +
75M TYR 3.3 1.2 + - - -
76M GLN* 1.3 75.1 - - - +
78M GLY* 1.3 57.0 + - - +
79M TRP* 2.9 15.8 + - - +
83M VAL* 3.0 35.4 - - + +
84M PHE* 6.3 1.1 - - + -
91M PHE* 3.8 14.1 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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