Contacts of the helix formed by residues 57 - 80 (chain A) in PDB entry 3PIK
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ALA 2.8 17.9 + - - +
54A LEU 5.8 0.2 - - - +
55A VAL 3.6 1.6 - - - +
56A ASN* 1.3 77.5 - - - +
58A ARG* 1.3 60.0 + - - +
59A ASP* 3.0 16.0 + - - +
60A LEU* 3.0 31.3 + - + +
61A ARG* 3.1 26.3 + - - +
144A VAL* 5.7 0.2 - - - +
148A LEU* 3.5 30.2 - - + +
227A LEU 4.3 2.8 + - - -
228A LEU* 2.6 41.0 + - - +
229A LEU 3.6 3.7 + - - -
230A GLY 4.7 0.9 - - - +
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL 4.6 3.6 + - - -
56A ASN* 3.1 27.5 + - - +
57A ASN* 1.3 72.8 - - - +
59A ASP* 1.3 65.3 + - - +
61A ARG* 3.3 39.3 + - - +
62A MET* 2.8 30.4 + - - +
227A LEU 5.7 0.8 + - - -
230A GLY* 5.3 8.0 - - - -
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Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASN* 3.0 13.9 + - - +
58A ARG* 1.3 78.1 - - - +
60A LEU* 1.3 58.4 + - - +
62A MET* 3.3 8.7 + - - +
63A ALA* 3.0 26.2 + - - +
144A VAL* 4.2 12.6 - - + +
148A LEU* 6.0 0.9 - - + -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.7 46.0 - - + +
57A ASN* 3.0 19.1 + - - +
59A ASP* 1.3 74.0 - - - +
61A ARG* 1.3 67.3 + - - +
63A ALA* 3.1 3.8 + - + +
64A THR* 2.9 28.7 + - - +
141A GLN* 3.7 24.0 - - - +
144A VAL* 4.0 12.8 - - + -
145A HIS* 4.0 35.7 - - + +
148A LEU* 4.1 14.4 - - + -
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL 5.7 2.9 - - - +
57A ASN 3.1 15.4 + - - +
58A ARG* 3.5 38.6 - - - +
60A LEU* 1.3 76.9 - - - +
62A MET* 1.3 57.8 + - - +
64A THR* 3.2 26.8 + - - +
65A LEU* 3.0 58.3 + - + +
68A GLN* 4.6 5.1 + - - +
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Residues in contact with MET 62 (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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58A ARG 2.8 17.6 + - - +
59A ASP* 3.5 9.0 - - - +
61A ARG* 1.3 76.5 - - - +
63A ALA* 1.3 58.5 + - - +
65A LEU* 3.2 19.5 + - + +
66A LYS* 3.0 49.4 + - - +
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Residues in contact with ALA 63 (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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59A ASP 3.0 14.4 + - - +
60A LEU* 3.1 8.7 + - + +
62A MET* 1.3 76.3 - - - +
64A THR* 1.3 62.4 + - - +
66A LYS* 3.3 13.6 + - - +
67A VAL* 3.2 24.9 + - - +
137A THR* 5.0 0.3 - - - +
140A ALA 5.5 0.4 - - - -
141A GLN* 3.7 17.5 - - + +
144A VAL* 4.0 29.6 - - + -
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Residues in contact with THR 64 (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 LEU* 2.9 18.5 + - - +
61A ARG* 3.4 26.5 - - - +
63A ALA* 1.3 74.9 - - - +
65A LEU* 1.3 64.6 + - - +
67A VAL* 3.2 15.2 + - + +
68A GLN* 3.2 28.2 + - + +
141A GLN* 3.2 24.5 + - - +
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Residues in contact with LEU 65 (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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61A ARG* 3.0 56.9 + - + +
62A MET* 3.2 19.9 + - - +
64A THR* 1.3 75.6 - - - +
66A LYS* 1.3 58.0 + - - +
68A GLN* 3.1 28.1 + - - +
69A GLU* 2.9 27.9 + - - +
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Residues in contact with LYS 66 (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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62A MET* 3.0 37.5 + - + +
63A ALA* 3.6 13.7 - - - +
64A THR 3.2 0.4 - - - -
65A LEU* 1.3 75.8 - - - +
67A VAL* 1.3 61.6 + - - +
69A GLU* 3.4 10.9 + - + +
70A ALA* 3.0 19.8 + - - +
137A THR* 3.5 18.7 - - + +
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Residues in contact with VAL 67 (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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63A ALA 3.2 16.0 + - - +
64A THR* 3.2 9.5 + - + +
66A LYS* 1.3 77.0 - - - +
68A GLN* 1.3 62.2 + - + +
70A ALA* 3.3 2.3 + - - +
71A ARG* 2.9 33.9 + - - +
134A TYR* 3.7 13.0 - - + -
137A THR* 3.6 30.5 - - + +
138A GLU* 3.5 29.8 - - + +
141A GLN* 3.6 18.8 - - + -
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Residues in contact with GLN 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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61A ARG* 4.6 5.6 + - - +
64A THR* 3.2 26.4 + - + +
65A LEU* 3.1 30.8 + - - +
67A VAL* 1.3 76.2 - - + +
69A GLU* 1.3 57.6 + - - +
71A ARG* 3.1 32.3 + - - +
72A ALA* 2.9 29.5 + - - +
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Residues in contact with GLU 69 (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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65A LEU 2.9 12.5 + - - +
66A LYS* 3.5 16.0 - - + +
68A GLN* 1.3 76.7 - - - +
70A ALA* 1.3 57.7 + - - +
72A ALA* 3.2 8.0 + - - +
73A GLN* 2.9 33.6 + - - +
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Residues in contact with ALA 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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66A LYS 3.0 18.3 + - - +
67A VAL 3.8 3.6 - - - +
69A GLU* 1.3 74.3 + - - +
71A ARG* 1.3 60.7 + - - +
73A GLN* 3.4 8.2 + - - +
74A TYR* 2.9 27.4 + - - +
130A GLU* 4.6 2.4 - - - +
133A ASN* 4.0 11.6 - - - +
134A TYR* 3.9 20.0 - - - +
137A THR* 3.8 22.9 - - + +
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Residues in contact with ARG 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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67A VAL* 2.9 28.8 + - - +
68A GLN* 3.1 40.7 + - - +
70A ALA* 1.3 77.0 - - - +
72A ALA* 1.3 56.6 + - - +
74A TYR* 3.1 10.5 + - + +
75A ARG* 3.0 60.7 + - + +
134A TYR* 3.3 42.3 + - + -
138A GLU* 4.8 2.6 + - - -
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Residues in contact with ALA 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 GLN 2.9 12.5 + - - +
69A GLU* 3.5 11.0 - - - +
71A ARG* 1.3 74.7 - - - +
73A GLN* 1.3 58.7 + - - +
75A ARG* 3.1 14.1 + - - +
76A LEU* 2.8 29.4 + - - +
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Residues in contact with GLN 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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69A GLU* 2.9 24.4 + - - +
70A ALA* 3.7 9.0 - - - +
72A ALA* 1.3 72.9 - - - +
74A TYR* 1.3 67.1 + - - +
76A LEU* 3.9 26.8 - - - +
77A THR* 3.0 53.1 + - - -
130A GLU* 3.4 28.1 + - - +
133A ASN* 5.7 0.9 - - - +
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Residues in contact with TYR 74 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ALA 2.9 14.6 + - - +
71A ARG* 3.1 16.8 + - + +
73A GLN* 1.3 78.2 - - - +
75A ARG* 1.3 66.3 + - + +
77A THR* 3.8 1.2 - - - -
78A ASP* 2.9 41.0 + - + +
127A SER* 3.5 25.1 - - - -
128A GLU* 5.5 0.2 - - - -
130A GLU* 3.8 19.0 - - + +
131A ARG* 3.6 51.0 - - + -
134A TYR* 4.5 13.2 - + + -
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Residues in contact with ARG 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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71A ARG* 3.0 44.8 + - - +
72A ALA* 3.1 13.1 + - - +
74A TYR* 1.3 85.6 - - + +
76A LEU* 1.3 61.6 + - - +
78A ASP* 3.3 7.0 + - - +
79A ALA* 2.9 25.0 + - - +
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Residues in contact with LEU 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 ALA 2.8 19.6 + - - +
73A GLN* 3.7 28.3 - - - +
75A ARG* 1.3 73.5 - - - +
77A THR* 1.3 62.4 + - - +
79A ALA* 3.4 11.2 + - + +
80A ASP* 3.2 29.6 - - - +
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Residues in contact with THR 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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73A GLN* 3.0 33.5 + - - -
74A TYR 3.8 3.1 - - - -
76A LEU* 1.3 73.9 - - - +
78A ASP* 1.3 66.0 + - - +
80A ASP* 3.2 27.1 + - - +
81A ARG* 4.1 5.2 + - - +
123A LEU* 5.0 1.3 - - - +
126A MET* 3.7 45.8 - - + +
127A SER* 3.8 5.2 - - - +
130A GLU* 3.4 14.4 + - + +
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Residues in contact with ASP 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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74A TYR* 2.9 34.4 + - + +
75A ARG* 3.7 7.6 - - - +
77A THR* 1.3 76.2 - - - +
79A ALA* 1.3 58.7 + - - +
81A ARG* 2.9 53.3 + - - +
82A TYR* 3.3 28.3 + - - -
127A SER* 2.9 23.8 + - - +
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Residues in contact with ALA 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 ARG 2.9 12.8 + - - +
76A LEU* 3.5 15.3 - - + +
77A THR 3.2 0.4 - - - -
78A ASP* 1.3 76.3 - - - +
80A ASP* 1.3 59.7 + - - +
82A TYR* 2.9 37.2 + - - +
84A GLN* 6.1 0.3 - - - +
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Residues in contact with ASP 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 LEU* 3.2 26.9 - - - +
77A THR* 3.4 21.0 - - - +
78A ASP 3.1 0.8 - - - -
79A ALA* 1.3 77.8 - - - +
81A ARG* 1.3 60.8 + - + +
82A TYR 3.3 4.6 + - - +
116A ASP* 5.0 2.4 - - - +
123A LEU* 3.6 28.1 - - + +
126A MET* 5.7 4.0 - - + +
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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