Contacts of the helix formed by residues 53 - 77 (chain M) in PDB entry 7PRC
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 ALA 53 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M GLY* 1.3 69.6 - - - -
54M SER* 1.3 63.4 + - - +
55M GLY 3.0 1.6 - - - -
56M ILE* 3.3 7.9 + - - +
57M ALA* 2.8 29.2 + - - +
704M LDA 4.1 19.1 - - + +
804M SO4 3.0 15.9 + - - +
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Residues in contact with SER 54 (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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53M ALA* 1.3 77.8 - - - +
55M GLY* 1.3 56.9 + - - +
57M ALA* 4.0 6.5 - - - -
58M ALA* 2.9 25.5 + - - +
126M SER* 3.2 31.2 - - - +
129M ILE* 3.6 18.1 - - - +
130M ARG* 3.3 14.9 + - - +
704M LDA 3.9 11.6 - - - +
804M SO4 2.8 32.1 + - - -
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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 4.3 1.1 - - - -
52M GLY 3.8 6.3 + - - -
53M ALA 3.0 0.6 - - - -
54M SER* 1.3 79.6 + - - +
56M ILE* 1.3 65.2 + - - +
58M ALA* 3.0 6.2 + - - +
59M PHE* 2.9 23.6 + - - +
127M TRP* 4.8 5.1 - - - -
130M ARG* 4.0 32.1 - - - +
804M SO4 4.5 0.8 + - - -
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Residues in contact with ILE 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M ASP* 5.6 1.1 - - - +
51M LEU* 4.3 30.0 + - + -
52M GLY 3.1 24.7 + - - +
53M ALA* 3.3 7.2 + - - +
55M GLY* 1.3 71.7 - - - +
57M ALA* 1.3 66.0 + - - +
59M PHE* 3.0 11.1 + - + +
60M ALA* 3.0 25.6 + - + +
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Residues in contact with ALA 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M ALA 2.8 17.9 + - - +
54M SER 3.5 5.8 - - - +
56M ILE* 1.3 77.0 - - - +
58M ALA* 1.3 62.6 + - - +
60M ALA* 3.0 7.3 + - - +
61M PHE* 2.9 40.1 + - + -
126M SER* 3.8 11.2 - - - -
704M LDA 3.9 19.3 - - + -
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Residues in contact with ALA 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401L BPB 3.6 6.4 - - + +
54M SER 2.9 20.6 + - - +
55M GLY 3.0 4.7 + - - +
57M ALA* 1.3 73.9 - - - +
59M PHE* 1.3 57.7 + - - +
62M GLY* 2.9 26.2 + - - -
123M SER* 3.5 29.0 + - - +
126M SER* 3.5 7.8 - - - -
127M TRP* 3.7 31.6 - - + +
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Residues in contact with PHE 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401L BPB 3.6 93.0 - - + +
55M GLY 2.9 13.1 + - - +
56M ILE* 3.4 12.6 - - + +
58M ALA* 1.3 75.8 - - - +
60M ALA* 1.3 62.3 + - + +
62M GLY* 3.9 0.2 - - - -
63M SER* 2.8 41.6 + - - -
127M TRP* 5.6 1.7 - - + -
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Residues in contact with ALA 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M ILE* 3.0 15.9 + - + +
57M ALA* 3.5 9.6 - - - +
59M PHE* 1.3 81.6 - - + +
61M PHE* 1.3 65.0 + - + +
63M SER* 3.5 4.6 + - - -
64M THR* 2.9 27.2 + - - -
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Residues in contact with PHE 61 (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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57M ALA* 2.9 37.1 + - + +
60M ALA* 1.3 75.0 - - + +
62M GLY* 1.3 67.1 + - - +
64M THR* 3.0 9.9 + - - -
65M ALA* 3.0 19.4 + - - +
119M PHE* 3.6 37.8 - + - +
122M LEU* 3.7 35.4 - - + -
123M SER* 3.7 7.9 - - - +
126M SER* 3.6 21.5 - - - -
704M LDA 4.1 16.4 - - + -
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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
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401L BPB 3.7 16.4 - - - -
58M ALA 2.9 19.6 + - - -
61M PHE* 1.3 76.8 - - - +
63M SER* 1.3 57.4 + - - +
65M ALA* 3.1 5.2 + - - +
66M ILE* 2.9 24.2 + - - +
123M SER* 3.5 17.1 - - - -
806M BCB 3.4 14.0 - - - +
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Residues in contact with SER 63 (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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401L BPB 3.7 37.4 - - - +
59M PHE* 2.8 33.8 + - - -
60M ALA* 3.8 5.8 - - - -
62M GLY* 1.3 72.4 - - - +
64M THR* 1.3 65.7 + - - +
66M ILE* 3.0 11.6 + - - +
67M LEU* 2.9 32.4 + - - +
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Residues in contact with THR 64 (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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60M ALA 2.9 17.3 + - - -
61M PHE* 3.0 8.8 + - - -
63M SER* 1.3 72.4 - - - +
65M ALA* 1.3 65.3 + - - +
67M LEU* 2.9 22.0 + - - +
68M ILE* 3.1 32.0 + - + +
119M PHE* 3.8 29.3 - - + -
706M LDA 4.5 19.1 - - + +
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Residues in contact with ALA 65 (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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61M PHE 3.0 7.6 + - - +
62M GLY 3.2 9.6 - - - +
64M THR* 1.3 78.2 - - - +
66M ILE* 1.3 65.6 + - - +
68M ILE* 3.2 13.2 + - - +
69M ILE* 3.1 30.7 + - + +
116M ALA* 4.0 11.3 - - + +
119M PHE* 4.0 4.9 - - + +
120M MET* 3.9 20.9 - - + +
806M BCB 3.6 17.9 - - + -
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Residues in contact with ILE 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401L BPB 3.7 47.8 - - + -
62M GLY 2.9 19.1 + - - +
63M SER* 3.0 7.8 + - - +
65M ALA* 1.3 77.0 - - - +
67M LEU* 1.3 58.9 + - + +
69M ILE* 3.2 7.3 + - + +
70M LEU* 2.8 51.6 + - + +
600M NS5 4.0 32.3 - - + -
806M BCB 3.8 22.4 - - + -
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Residues in contact with LEU 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401L BPB 4.3 22.7 - - + -
63M SER* 3.3 18.6 - - - +
64M THR* 2.9 12.0 + - - +
66M ILE* 1.3 77.7 - - + +
68M ILE* 1.3 57.7 + - - +
70M LEU* 4.4 13.0 - - + +
71M PHE* 2.8 43.0 + - + +
706M LDA 3.8 30.3 - - + -
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Residues in contact with ILE 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 THR* 3.1 42.8 + - + +
65M ALA* 3.2 9.2 + - - +
67M LEU* 1.3 72.4 - - - +
69M ILE* 1.3 67.7 + - - +
71M PHE* 4.0 0.2 - - - +
72M ASN* 2.8 34.6 + - - +
93M LEU* 4.1 4.5 - - + -
112M TRP* 3.5 52.9 - - + +
115M MET* 4.7 4.3 - - + -
116M ALA* 4.2 9.9 - - + +
119M PHE* 4.2 15.9 - - + -
706M LDA 4.1 21.1 - - + -
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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 ALA* 3.1 21.5 + - + +
66M ILE* 3.7 9.4 - - + +
68M ILE* 1.3 78.5 - - - +
70M LEU* 1.3 53.0 + - - +
72M ASN* 3.0 2.4 + - - +
73M MET* 2.8 56.5 + - + +
93M LEU* 3.5 25.5 - - + +
116M ALA* 4.0 6.3 - - + -
175M PHE* 3.3 52.0 - - + +
600M NS5 4.4 19.3 - - + -
806M BCB 4.8 9.6 - - + -
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Residues in contact with LEU 70 (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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401L BPB 6.3 1.3 - - + -
66M ILE* 2.8 41.4 + - + +
67M LEU* 4.1 11.7 - - + +
69M ILE* 1.3 71.3 - - - +
71M PHE* 1.3 60.1 + - + +
73M MET* 3.2 8.0 + - - +
74M ALA* 2.7 30.2 + - - +
84M PHE* 3.9 16.2 - - + -
88M PHE* 3.7 31.0 - - + -
600M NS5 3.8 36.6 - - + -
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Residues in contact with PHE 71 (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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67M LEU* 2.8 29.8 + - + +
68M ILE 4.0 1.1 - - - +
70M LEU* 1.3 81.2 - - + +
72M ASN* 1.3 57.3 + - - +
74M ALA* 3.2 7.7 + - + +
75M ALA* 2.9 27.0 + - - +
79M PHE* 4.0 22.3 - + - -
706M LDA 3.6 50.5 - - + +
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Residues in contact with ASN 72 (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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68M ILE* 2.8 27.8 + - - +
69M ILE 3.0 4.5 + - - +
71M PHE* 1.3 77.4 - - - +
73M MET* 1.3 64.7 + - - +
75M ALA* 3.1 13.3 + - - +
76M GLU* 3.2 13.2 + - - +
92M GLY 5.0 4.3 - - - +
93M LEU* 4.1 22.3 - - + +
112M TRP* 3.5 32.9 - - - +
706M LDA 3.0 57.6 + - - +
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Residues in contact with MET 73 (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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69M ILE* 2.8 37.1 + - + +
70M LEU* 3.4 16.6 - - + +
72M ASN* 1.3 76.7 - - - +
74M ALA* 1.3 62.2 + - - +
76M GLU* 3.0 24.6 + - - +
77M VAL* 3.7 3.1 + - - +
84M PHE* 3.7 7.9 - - + -
88M PHE* 3.1 51.4 - - + +
91M LEU* 3.7 39.3 - - + +
92M GLY* 4.0 16.2 - - - +
176M GLY* 5.1 4.0 - - - -
177M ILE* 6.4 0.4 - - + -
600M NS5 4.8 5.8 - - + -
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Residues in contact with ALA 74 (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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70M LEU 2.7 19.2 + - - +
71M PHE* 3.2 8.9 + - + +
73M MET* 1.3 72.0 - - - +
75M ALA* 1.3 60.1 + - - +
76M GLU 3.3 0.3 + - - -
77M VAL* 3.4 3.7 + - - +
78M HIS 3.3 2.4 + - - -
79M PHE* 2.7 49.9 + - + -
84M PHE* 3.5 21.9 - - + -
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Residues in contact with ALA 75 (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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71M PHE 2.9 10.1 + - - +
72M ASN 3.1 10.3 + - - +
74M ALA* 1.3 76.2 - - - +
76M GLU* 1.3 58.1 + - - +
78M HIS* 2.8 20.8 + - - +
79M PHE* 3.6 22.9 - - + -
706M LDA 3.5 38.8 - - - +
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Residues in contact with GLU 76 (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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169C ARG 4.2 10.6 - - - +
170C SER 4.9 0.7 - - - +
172C TYR* 5.0 5.7 - - - +
173C VAL* 3.4 26.5 + - + +
186C ASN* 3.6 20.1 + - - +
72M ASN 3.2 8.5 + - - +
73M MET* 3.0 15.0 + - - +
75M ALA* 1.3 80.6 - - - +
77M VAL* 1.3 58.6 + - - +
78M HIS* 3.1 2.1 + - - +
90M TRP 4.8 1.6 - - - +
91M LEU* 3.2 21.8 - - + +
92M GLY 2.8 39.9 + - - +
94M TYR* 4.6 4.8 - - - -
706M LDA 5.9 1.6 - - - +
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Residues in contact with VAL 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C SER* 3.6 13.7 - - - +
73M MET 4.2 2.2 - - - +
74M ALA* 3.6 9.9 - - - +
76M GLU* 1.3 73.8 - - - +
78M HIS* 1.3 69.3 + - - +
79M PHE* 4.3 1.1 - - - +
80M ASP* 2.8 25.2 + - - +
83M GLN* 3.6 17.0 - - + +
84M PHE* 3.6 40.8 - - + +
87M GLN* 3.2 35.7 - - + +
91M LEU* 3.9 13.7 - - + -
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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) + - + + + + + -
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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