Contacts of the helix formed by residues 67 - 82 (chain A) in PDB entry 3PJF
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 GLU 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASP* 2.6 37.3 + - - +
66A ALA* 1.3 85.5 - - + +
68A ASP* 1.3 66.3 + - - +
69A ALA* 4.3 4.7 - - + +
70A SER* 3.1 24.8 + - - +
71A ILE* 3.3 12.6 + - - +
110B ARG* 3.7 3.6 - - - -
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Residues in contact with ASP 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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66A ALA 4.2 0.2 + - - -
67A GLU* 1.3 70.7 - - - +
69A ALA* 1.3 62.6 + - - +
71A ILE* 3.2 10.6 + - - +
72A ASP* 3.0 33.9 + - - +
122A TYR* 4.5 7.6 + - - -
126A ALA* 5.0 1.7 - - - +
110B ARG* 2.8 44.7 + - - +
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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
----------------------------------------------------------
67A GLU* 3.1 5.1 - - + +
68A ASP* 1.3 77.3 - - - +
70A SER* 1.3 60.6 + - - +
72A ASP* 3.9 7.6 - - - +
73A THR* 2.9 37.2 + - - +
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Residues in contact with SER 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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62A GLN* 3.2 21.6 + - - +
63A CYS* 3.4 2.1 - - - -
64A ASP* 2.9 45.0 + - - -
67A GLU* 3.1 17.6 + - - +
69A ALA* 1.3 79.7 - - - +
71A ILE* 1.3 62.4 + - - +
73A THR* 3.8 5.3 - - - -
74A MET* 3.1 24.1 + - - +
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Residues in contact with ILE 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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63A CYS* 4.0 14.4 - - - -
65A VAL* 3.8 41.3 - - + +
67A GLU 3.5 11.7 - - - +
68A ASP* 3.2 9.1 + - - +
69A ALA 3.2 0.6 - - - -
70A SER* 1.3 75.4 - - - +
72A ASP* 1.3 66.3 + - - +
74A MET* 3.3 2.6 + - - +
75A PHE* 3.1 38.6 + - + -
126A ALA* 3.9 27.1 - - + +
127A MET* 4.2 11.4 - - + -
130A ALA* 3.7 24.0 - - + -
110B ARG* 4.0 5.2 - - - +
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Residues in contact with ASP 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 ASP* 3.0 28.8 + - - +
69A ALA* 3.9 7.4 - - - +
71A ILE* 1.3 75.3 - - - +
73A THR* 1.3 58.1 + - - +
75A PHE* 3.3 3.3 + - - +
76A ALA* 2.8 30.1 + - - +
130A ALA* 3.6 23.1 - - - +
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Residues in contact with THR 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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62A GLN 6.1 0.2 - - - +
69A ALA* 2.9 23.1 + - - +
70A SER* 3.8 5.8 - - - -
72A ASP* 1.3 77.3 - - - +
74A MET* 1.3 62.5 - - - +
76A ALA* 3.1 8.8 + - + +
77A GLU* 3.0 35.2 + - + +
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Residues in contact with MET 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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10A LEU* 3.8 20.0 - - + -
38A THR* 4.0 13.0 - - + -
61A LEU* 3.5 25.7 - - + +
62A GLN 3.5 21.1 - - - +
63A CYS* 4.0 21.3 - - + -
70A SER 3.1 18.7 + - - +
71A ILE* 3.6 2.2 - - + +
72A ASP 3.2 0.4 - - - -
73A THR* 1.3 77.8 - - - +
75A PHE* 1.3 101.8 + - + +
77A GLU* 3.1 9.8 + - - +
78A LEU* 2.9 25.6 + - - -
127A MET* 4.2 7.2 - - + -
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Residues in contact with PHE 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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10A LEU* 3.7 15.7 - - + -
71A ILE* 3.1 34.4 + - + +
72A ASP* 3.9 3.4 - - - +
74A MET* 1.3 97.6 - - + +
76A ALA* 1.3 56.9 + - - +
78A LEU* 3.9 12.1 - - + -
79A GLY* 3.0 23.0 + - - -
85A PHE* 3.6 16.6 - + - -
88A PHE* 4.6 1.8 - + - -
127A MET* 3.4 39.5 - - + -
130A ALA* 3.6 26.7 - - + +
131A CYS* 3.5 29.2 - - + -
134A MET* 3.6 18.5 - - - +
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Residues in contact with ALA 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 ASP 2.8 14.8 + - - +
73A THR* 3.3 14.6 - - + +
75A PHE* 1.3 77.8 - - - +
77A GLU* 1.3 64.4 + - + +
79A GLY* 3.5 8.9 + - - -
80A LYS* 3.8 15.1 + - - +
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Residues in contact with GLU 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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61A LEU* 3.9 23.7 - - + +
73A THR* 3.0 28.1 + - + +
74A MET* 3.5 8.3 - - - +
76A ALA* 1.3 76.7 - - - +
78A LEU* 1.3 65.5 + - - +
80A LYS* 3.0 52.7 + - - +
81A VAL* 4.0 4.2 + - - +
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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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10A LEU* 4.1 19.5 - - + -
36A ALA* 4.0 6.5 - - + -
59A ILE* 3.8 26.2 - - + -
61A LEU* 3.6 11.1 - - + +
74A MET* 2.9 16.6 + - - +
75A PHE* 3.8 27.4 - - + +
76A ALA 3.4 0.2 - - - -
77A GLU* 1.3 76.8 - - - +
79A GLY* 1.3 51.8 + - - +
81A VAL* 3.0 11.2 + - + +
82A TRP* 2.7 64.6 + - + -
85A PHE* 4.0 22.0 - - + -
134A MET* 4.5 2.0 - - + -
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Residues in contact with GLY 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 PHE 3.0 13.6 + - - -
76A ALA 3.5 4.5 + - - -
77A GLU 3.1 1.0 - - - -
78A LEU* 1.3 76.8 - - - +
80A LYS* 1.3 60.7 + - - +
82A TRP 3.6 12.6 - - - -
83A PRO* 3.3 25.5 - - - +
134A MET* 3.7 11.9 - - - +
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Residues in contact with LYS 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 ALA 3.8 10.7 + - - +
77A GLU* 3.0 49.0 + - - +
79A GLY* 1.3 79.3 - - - +
81A VAL* 1.3 64.4 + - + +
83A PRO* 5.2 1.2 - - - +
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Residues in contact with VAL 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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8A ARG* 3.8 7.1 + - - -
59A ILE* 3.6 42.6 - - + -
77A GLU 4.6 2.5 - - - +
78A LEU* 3.3 16.2 - - + +
80A LYS* 1.3 85.6 - - + +
82A TRP* 1.3 72.2 + - + +
83A PRO* 3.7 8.5 - - - +
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Residues in contact with TRP 82 (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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8A ARG* 3.4 46.1 - - + +
9A ILE 3.4 38.4 - - - -
10A LEU* 4.1 2.7 - - + -
34A GLU* 3.5 25.6 + - + -
35A LEU 3.9 11.2 - - - -
36A ALA* 3.5 21.5 - - + -
59A ILE* 3.6 16.2 - - + +
78A LEU* 2.7 35.3 + - + +
79A GLY* 3.6 1.5 - - - -
81A VAL* 1.3 101.6 - - + +
83A PRO* 1.3 68.2 - - - +
84A LYS* 2.7 15.0 + - - +
85A PHE* 3.5 21.1 - + + -
134A MET* 3.5 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