Contacts of the helix formed by residues 58 - 73 (chain G) in PDB entry 1RFU
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 ASN 58 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G LEU* 1.3 74.9 - - - +
59G SER* 1.3 58.7 + - - +
60G ASP* 2.7 28.1 + - - +
61G GLU* 2.7 49.5 + - - +
62G LEU* 3.0 9.7 + - - +
87G ASP* 3.3 16.8 - - - +
90G PHE* 4.2 5.4 - - - -
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Residues in contact with SER 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G ASN* 1.3 72.6 - - - +
60G ASP* 1.3 62.9 + - - +
62G LEU* 3.3 2.5 + - - -
63G GLN* 2.8 24.2 + - - +
87G ASP* 4.2 2.6 + - - -
89G SER* 2.9 36.8 - - - -
90G PHE* 4.3 11.2 - - - +
93G MET* 3.1 27.1 - - - +
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Residues in contact with ASP 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G ASN* 2.7 23.5 + - - +
59G SER* 1.3 76.9 + - - +
61G GLU* 1.3 64.0 + - + +
63G GLN* 3.2 7.6 + - - +
64G GLU* 2.9 25.9 + - - +
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Residues in contact with GLU 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D GLN* 4.0 23.4 + - - +
56G VAL 3.0 25.2 - - - +
57G LEU* 3.1 27.2 - - + -
58G ASN* 2.7 37.7 + - - +
60G ASP* 1.3 74.2 - - + +
62G LEU* 1.3 60.2 + - - +
64G GLU* 3.5 17.0 - - - +
65G LEU* 3.4 21.0 - - - +
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Residues in contact with LEU 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ILE* 4.9 5.8 - - + -
38G VAL* 3.8 32.5 - - + -
57G LEU* 4.5 0.8 - - - +
58G ASN 3.0 5.5 + - - -
59G SER 3.6 7.6 - - - +
61G GLU* 1.3 76.2 - - - +
63G GLN* 1.3 66.1 + - - +
65G LEU* 3.3 8.4 + - + +
66G TYR* 3.0 21.6 + - + +
90G PHE* 3.4 35.4 - - + +
93G MET* 3.8 23.6 - - + -
94G VAL* 3.8 21.1 - - + -
97G ILE* 3.8 20.9 - - + -
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Residues in contact with GLN 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G SER 2.8 17.4 + - - +
60G ASP* 3.2 9.6 + - - +
62G LEU* 1.3 74.6 - - - +
64G GLU* 1.3 58.0 + - - +
66G TYR* 3.0 17.1 + - - +
67G ASP* 2.6 73.6 + - - +
93G MET* 2.7 33.5 - - + +
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Residues in contact with GLU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY* 5.7 0.2 - - - -
197A ASP* 3.3 31.3 - - - +
198A TYR* 5.0 6.1 + - - -
224A HIS* 5.4 3.1 - - - -
53D LYS* 3.9 20.0 - - + +
54D GLY 3.5 17.6 - - - +
55D GLN* 2.7 29.2 - - - +
60G ASP 2.9 12.3 + - - +
61G GLU* 3.5 13.7 - - - +
63G GLN* 1.3 76.0 - - - +
65G LEU* 1.3 53.5 + - + +
67G ASP* 3.3 7.3 + - - +
68G GLY* 2.7 32.2 + - - -
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Residues in contact with LEU 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 4.2 14.4 - - + -
42D GLN* 3.8 32.3 - - + +
43D PHE 4.1 14.6 - - - -
44D SER* 4.0 7.5 - - - +
53D LYS 5.4 0.4 - - - -
54D GLY* 4.1 13.7 - - - -
55D GLN* 3.9 15.0 - - - +
38G VAL* 3.9 29.6 - - + -
57G LEU* 3.9 8.3 - - + -
61G GLU 3.4 17.0 - - - +
62G LEU* 3.6 9.4 - - + +
63G GLN 3.2 0.4 - - - -
64G GLU* 1.3 76.8 - - - +
66G TYR* 1.3 68.2 + - - +
68G GLY* 2.9 3.3 + - - -
69G LEU* 2.9 28.0 + - + +
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Residues in contact with TYR 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LEU* 5.3 3.6 - - + -
62G LEU* 3.0 16.6 + - + +
63G GLN* 3.5 20.6 - - - +
65G LEU* 1.3 75.0 - - - +
67G ASP* 1.3 55.6 + - - +
69G LEU* 3.0 19.1 + - + +
70G LYS* 2.5 43.3 + - + +
75G ASN* 3.3 32.3 + - + -
77G TYR* 5.2 3.8 - + - -
97G ILE* 3.7 49.8 - - + +
100G GLU* 3.3 36.5 + - - +
101G LEU* 3.4 22.8 - - + +
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Residues in contact with ASP 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LYS* 4.9 6.6 - - - -
63G GLN* 2.6 55.7 + - - +
64G GLU* 3.4 7.9 + - - +
66G TYR* 1.3 73.6 - - - +
68G GLY* 1.3 55.2 + - - +
70G LYS* 2.9 11.4 + - - +
71G LEU* 2.5 50.3 + - + +
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Residues in contact with GLY 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D SER* 4.0 18.4 - - - -
51D HIS* 6.1 0.2 - - - -
52D TRP* 5.7 0.9 - - - -
53D LYS* 4.3 11.0 - - - +
64G GLU 2.7 19.1 + - - -
65G LEU 2.9 5.1 + - - -
67G ASP* 1.3 75.0 - - - +
69G LEU* 1.3 61.0 + - - +
71G LEU* 3.5 11.1 + - - +
72G ASN* 3.1 29.0 + - - -
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Residues in contact with LEU 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 4.2 20.0 - - + -
16D ARG* 4.1 18.4 - - + -
44D SER* 4.1 24.9 - - - +
45D ASN* 5.0 2.0 - - - +
8G LEU* 5.0 6.3 - - + -
36G ASP* 4.8 0.4 - - - +
38G VAL* 5.4 3.4 - - + -
65G LEU 2.9 18.1 + - - +
66G TYR* 3.4 21.3 - - + +
68G GLY* 1.3 71.3 - - - +
70G LYS* 1.3 70.3 + - - +
72G ASN* 3.1 2.6 + - - +
73G HIS 3.0 14.7 + - - -
74G VAL* 3.1 29.0 + - + +
75G ASN* 4.4 11.0 - - + +
77G TYR* 3.4 25.1 - - + +
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Residues in contact with LYS 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G TYR* 2.5 25.0 + - + +
67G ASP* 3.1 17.5 - - - +
69G LEU* 1.3 70.6 - - - +
71G LEU* 1.3 57.2 + - + +
73G HIS* 2.6 38.5 + - - -
75G ASN* 3.1 38.8 + - - +
100G GLU* 3.9 14.7 + - - +
104G GLN* 3.8 12.3 + - - +
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Residues in contact with LEU 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D HIS* 4.3 37.7 + - + +
53D LYS* 3.4 38.8 - - + +
67G ASP* 2.5 28.6 + - + +
68G GLY* 3.6 8.7 - - - +
70G LYS* 1.3 74.7 - - + +
72G ASN* 1.3 59.6 + - - +
73G HIS* 3.7 16.5 + - - -
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Residues in contact with ASN 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ASN* 3.5 12.5 - - - +
49D TYR* 4.3 19.8 - - + +
50D SER* 4.3 3.6 + - - -
51D HIS* 3.2 51.8 + - - +
68G GLY 3.1 19.6 + - - -
69G LEU 3.1 2.0 + - - +
70G LYS 3.0 1.0 - - - -
71G LEU* 1.3 75.3 - - - +
73G HIS* 1.3 78.8 + - - +
74G VAL* 3.3 24.5 - - + +
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Residues in contact with HIS 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G LEU 3.0 0.2 + - - -
70G LYS* 2.6 27.3 + - - -
71G LEU* 3.9 14.1 + - - -
72G ASN* 1.3 81.1 - - - +
74G VAL* 1.3 62.3 + - - +
75G ASN* 3.4 10.5 + - - -
76G GLN* 3.6 18.4 + - - +
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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