Contacts of the helix formed by residues 67 - 81 (chain A) in PDB entry 1RPK
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ILE* 4.0 9.0 - - - -
61A ASP* 3.2 28.4 + - + +
66A GLY* 1.3 75.3 - - - -
68A ALA* 1.3 60.5 + - - +
69A ALA* 3.9 10.5 - - - +
70A GLU* 2.9 49.3 + - - +
71A LEU* 2.8 28.2 + - - +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ILE* 3.7 27.8 - - + +
61A ASP* 2.9 16.4 + - - +
67A ASN* 1.3 76.0 - - - +
69A ALA* 1.3 56.9 + - - +
71A LEU* 3.8 3.1 - - - +
72A LYS* 2.9 44.5 + - - +
167A TRP* 6.2 1.3 - - + -
171A ASP* 5.5 0.4 - - - +
172A LEU* 4.3 10.9 - - + +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 4.6 0.6 + - - -
67A ASN* 3.2 13.3 + - - +
68A ALA* 1.3 78.0 - - - +
70A GLU* 1.3 59.8 + - + +
72A LYS* 3.4 9.4 + - - +
73A SER* 3.0 33.4 + - - -
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLY 4.8 0.3 - - - +
18A GLY* 5.3 1.7 - - - -
20A TYR* 4.0 13.9 - - + +
21A ASN* 3.0 43.4 + - - +
24A MET* 5.2 1.0 - - - +
65A TYR 4.6 0.7 - - - +
66A GLY* 3.0 26.0 - - - -
67A ASN* 2.9 34.2 + - - +
69A ALA* 1.3 80.5 - - + +
71A LEU* 1.3 61.6 + - - +
73A SER* 3.4 7.3 + - - -
74A LEU* 3.1 21.8 + - - +
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 3.7 38.3 - - + +
40A LEU* 4.2 14.4 - - + -
43A PRO* 3.6 30.5 - - + -
60A ILE* 4.3 5.8 - - + -
67A ASN 2.8 16.7 + - - +
68A ALA* 3.8 6.1 - - - +
70A GLU* 1.3 75.4 - - - +
72A LYS* 1.3 64.8 + - - +
74A LEU* 3.1 4.3 + - + +
75A ILE* 2.9 41.3 + - + +
172A LEU* 3.9 15.7 - - + -
174A PHE* 3.8 15.3 - - + -
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA* 2.9 31.2 + - - +
69A ALA* 3.7 8.7 - - - +
71A LEU* 1.3 76.5 - - - +
73A SER* 1.3 58.7 + - - +
75A ILE* 3.4 1.0 + - - +
76A GLY* 2.9 28.1 + - - -
171A ASP* 2.9 48.5 + - - +
172A LEU* 3.8 29.7 - - + +
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MET* 3.7 22.9 - - - +
69A ALA* 3.0 21.3 + - - +
70A GLU* 3.6 8.2 - - - -
71A LEU 3.2 0.2 - - - -
72A LYS* 1.3 76.6 - - - +
74A LEU* 1.3 57.4 + - - +
76A GLY* 3.4 1.4 + - - -
77A ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 4.0 26.5 - - + +
23A MET* 3.8 39.5 - - + -
24A MET* 3.6 12.5 - - - +
27A VAL* 3.9 22.2 - - + -
40A LEU* 3.9 30.1 - - + -
70A GLU 3.1 10.7 + - - +
71A LEU* 3.1 9.5 + - + +
73A SER* 1.3 77.5 - - - +
75A ILE* 1.3 61.5 + - - +
77A ALA* 3.2 2.3 + - - +
78A LEU* 2.9 36.8 + - + +
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.1 11.7 - - + -
71A LEU* 2.9 39.4 + - + +
72A LYS 4.0 1.3 - - - +
74A LEU* 1.3 75.3 - - - +
76A GLY* 1.3 58.3 + - - +
78A LEU* 3.3 7.5 + - - +
79A HIS* 2.8 58.4 + - + +
85A ALA* 3.8 15.7 - - + -
172A LEU 3.6 23.3 - - - +
173A GLY* 3.6 9.0 - - - +
174A PHE* 3.8 31.6 - - + -
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS 2.9 17.9 + - - -
73A SER* 3.8 2.2 - - - -
75A ILE* 1.3 79.5 - - - +
77A ALA* 1.3 54.7 + - - +
79A HIS* 3.3 8.6 + - - +
80A GLY* 2.8 25.8 + - - -
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MET* 4.1 17.0 - - + +
27A VAL* 3.8 28.2 - - + +
73A SER 3.0 14.5 + - - +
74A LEU 3.5 7.6 - - - +
76A GLY* 1.3 74.5 - - - +
78A LEU* 1.3 66.5 + - - +
80A GLY* 3.0 12.3 + - - +
81A LYS* 3.3 9.4 + - - +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A MET* 6.3 2.0 - - + -
27A VAL* 4.2 29.2 - - + -
30A ILE* 4.9 6.7 - - + -
38A VAL* 3.8 29.2 - - + -
40A LEU* 4.3 12.8 - - + -
74A LEU* 2.9 33.4 + - + +
75A ILE* 3.3 12.3 + - - +
77A ALA* 1.3 75.7 - - - +
79A HIS* 1.3 58.5 + - + +
81A LYS* 2.8 19.2 + - - +
83A VAL* 3.0 53.0 + - + +
84A GLN 4.8 1.1 - - - +
85A ALA* 4.6 7.6 - - + -
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Residues in contact with HIS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 2.8 37.1 + - + +
76A GLY* 3.6 7.4 - - - +
78A LEU* 1.3 73.5 - - + +
80A GLY* 1.3 62.7 + - - +
82A GLY* 3.0 14.6 + - - +
83A VAL 3.2 20.6 - - - +
84A GLN* 4.2 3.4 - - + -
85A ALA 4.1 1.2 + - - -
173A GLY* 3.0 28.3 - - - -
175A ASP* 2.6 30.5 + - - -
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Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLY 2.8 16.0 + - - -
77A ALA* 3.0 7.5 + - - -
79A HIS* 1.3 75.4 - - - +
81A LYS* 1.3 65.1 + - - +
82A GLY 3.5 0.4 + - - -
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 4.1 7.9 - - + -
28A ASP* 3.4 34.2 + - - +
31A ALA* 3.7 26.9 - - + +
77A ALA 3.3 8.9 + - - +
78A LEU 2.8 9.3 + - - +
80A GLY* 1.3 85.2 - - - +
82A GLY* 1.3 59.4 + - - +
83A VAL* 3.2 7.4 + - + +
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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