Contacts of the helix formed by residues 65 - 79 (chain A) in PDB entry 1N54
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 LYS 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASP 4.6 0.2 - - - -
61A LEU* 3.1 46.6 + - + +
64A TYR* 1.3 68.0 - - - +
66A SER* 1.3 56.2 + - - +
67A LYS 2.6 18.5 + - - -
68A ILE* 2.6 21.5 + - - +
69A LEU* 3.4 13.7 + - + -
97A ASN* 4.7 4.3 + - - +
99A ASN* 4.1 12.9 + - - +
100A PHE* 4.1 25.4 - - + +
103A GLU* 2.8 38.4 + - + +
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Residues in contact with SER 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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64A TYR* 5.4 3.6 - - - -
65A LYS* 1.3 77.0 - - - +
67A LYS* 1.3 64.1 + - - +
69A LEU* 3.4 15.0 - - - +
70A ARG* 3.1 45.1 + - - +
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Residues in contact with LYS 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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28A GLU* 3.6 61.1 + - + +
31A LEU* 4.3 16.6 - - + -
32A GLU* 5.3 5.2 + - - -
64A TYR* 4.4 7.5 + - + +
65A LYS 2.6 6.4 + - - +
66A SER* 1.3 71.1 - - - +
68A ILE* 1.3 53.2 + - - +
69A LEU 2.8 14.4 + - - -
70A ARG* 3.1 29.7 + - + +
71A LEU* 2.9 48.8 + - + +
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Residues in contact with ILE 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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31A LEU* 4.1 20.0 - - + -
35A ILE* 5.1 3.4 - - + -
57A LEU* 3.5 62.4 - - + +
60A ASP* 3.7 26.9 - - + +
61A LEU* 4.3 8.1 - - + -
64A TYR 4.2 5.8 - - - +
65A LYS 2.6 14.3 + - - +
67A LYS* 1.3 69.4 - - - +
69A LEU* 1.3 56.2 + - - -
71A LEU* 3.9 10.8 - - + -
72A LEU* 3.4 33.6 + - + +
93A LEU* 5.2 0.4 - - + -
100A PHE* 4.0 14.5 - - + -
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Residues in contact with LEU 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 LYS* 3.4 9.9 + - + +
66A SER* 3.4 21.5 - - - +
67A LYS 2.8 0.8 + - - -
68A ILE* 1.3 75.7 - - - +
70A ARG* 1.3 60.9 + - + +
71A LEU 2.9 9.5 + - - -
72A LEU* 3.2 4.0 + - - +
73A CYS* 3.1 27.2 + - - -
100A PHE* 4.1 22.4 - - + -
103A GLU* 3.8 39.7 - - + +
104A PHE* 3.8 21.9 - - + +
107A ALA* 4.8 9.6 - - + -
110A ARG* 5.7 3.6 - - - +
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Residues in contact with ARG 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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28A GLU* 5.3 2.0 + - - -
66A SER* 3.1 46.0 + - - +
67A LYS* 3.1 35.8 + - + +
69A LEU* 1.3 79.8 - - + +
71A LEU* 1.3 52.4 + - - +
73A CYS* 4.2 7.9 - - - +
74A THR* 2.5 28.0 + - - -
6B LEU* 5.6 1.0 - - - +
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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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31A LEU* 4.0 23.3 - - + -
32A GLU* 3.9 42.4 - - + +
35A ILE* 4.3 18.2 - - + -
67A LYS* 2.9 46.8 + - + +
68A ILE* 4.0 10.5 - - + +
69A LEU 2.9 0.4 - - - -
70A ARG* 1.3 79.1 - - - +
72A LEU* 1.3 65.1 + - - +
73A CYS 3.1 0.9 - - - -
74A THR* 3.1 12.7 + - - +
75A VAL* 2.9 24.2 + - - +
6B LEU* 6.2 2.5 - - + -
7B LYS* 4.9 8.3 - - - +
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Residues in contact with LEU 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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35A ILE* 4.3 14.1 - - + -
57A LEU* 4.9 0.7 - - + -
68A ILE* 3.4 22.8 + - + +
69A LEU 3.2 2.1 + - - +
71A LEU* 1.3 80.7 - - - +
73A CYS* 1.3 62.8 + - - +
75A VAL* 3.5 4.8 + - + +
76A ALA* 3.2 20.6 + - - +
86A TYR* 4.4 15.8 - - + +
89A LEU* 3.7 27.6 - - + -
90A VAL* 4.1 21.3 - - + -
93A LEU* 4.0 27.1 - - + -
100A PHE* 4.0 12.3 - - + -
104A PHE* 4.0 20.0 - - + -
130A PHE* 5.1 2.8 - - - -
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Residues in contact with CYS 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 LEU 3.1 18.7 + - - +
70A ARG* 4.5 7.6 - - - +
71A LEU 3.1 0.6 - - - -
72A LEU* 1.3 75.5 - - - +
74A THR* 1.3 67.3 + - - +
76A ALA* 3.0 18.7 + - - +
77A ARG* 3.4 11.3 + - - +
104A PHE* 3.5 27.4 - - - -
107A ALA* 3.8 25.1 - - - -
108A MET* 4.2 15.4 - - - +
111A GLN* 4.3 19.1 - - - +
127A LEU* 5.1 1.4 - - - +
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Residues in contact with THR 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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70A ARG 2.5 27.9 + - - -
71A LEU* 3.1 9.5 + - - +
73A CYS* 1.3 78.8 - - - +
75A VAL* 1.3 64.1 + - - +
76A ALA 2.9 1.4 + - - -
77A ARG* 2.9 29.5 + - - +
78A LEU* 2.9 44.7 + - + -
111A GLN* 5.9 0.2 - - - -
6B LEU* 4.0 26.9 - - + +
7B LYS* 4.4 13.9 - - + -
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Residues in contact with VAL 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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35A ILE* 3.6 24.0 - - + -
71A LEU 2.9 21.3 - - - +
72A LEU* 3.9 7.4 - - - +
73A CYS 3.3 0.2 - - - -
74A THR* 1.3 74.4 - - - +
76A ALA* 1.3 61.7 + - - +
78A LEU 5.2 0.2 - - - -
79A LEU* 3.4 54.8 + - + +
83A LEU* 6.1 0.2 - - - -
86A TYR* 3.3 42.8 - - + +
130A PHE* 5.1 3.1 - - - -
7B LYS* 3.7 10.8 - - - +
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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 LEU 3.2 12.4 + - - +
73A CYS 3.0 14.1 + - - +
74A THR 2.9 0.6 + - - -
75A VAL* 1.3 80.4 - - - +
77A ARG* 1.3 58.5 + - - +
79A LEU 5.3 0.2 - - - -
80A PRO* 5.2 4.0 - - - +
83A LEU* 5.2 2.4 - - - +
104A PHE* 4.9 0.2 - - + -
108A MET* 3.8 31.2 - - + -
126A TYR* 4.0 20.1 - - - +
127A LEU* 4.5 2.2 - - + +
130A PHE* 3.9 31.2 - - + +
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Residues in contact with ARG 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 CYS 3.5 7.9 - - - +
74A THR* 2.9 33.3 + - - +
76A ALA* 1.3 77.6 - - - +
78A LEU* 1.3 84.0 + - + +
79A LEU 3.3 7.7 + - - -
80A PRO* 3.4 19.2 - - - +
111A GLN* 3.5 33.9 + - - +
123A GLU* 2.9 42.7 + - + -
126A TYR* 3.7 16.7 - - - +
127A LEU* 4.0 17.5 - - + -
323A LYS* 5.0 0.7 + - - -
6B LEU* 4.5 14.3 - - - +
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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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74A THR* 2.9 39.5 + - + +
77A ARG* 1.3 109.8 - - + +
79A LEU* 1.3 64.6 + - - +
80A PRO* 3.4 7.5 - - - +
123A GLU* 3.6 9.9 - - + +
323A LYS* 4.2 16.4 + - - +
324A SER* 3.9 9.2 + - - -
6B LEU* 4.2 20.4 - - + +
7B LYS* 4.7 7.0 - - + -
9B LEU* 3.6 22.9 - - + +
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Residues in contact with LEU 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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36A CYS* 4.7 8.7 - - + -
75A VAL* 3.4 47.6 + - + +
77A ARG 3.3 1.6 - - - -
78A LEU* 1.3 82.2 - - - +
80A PRO* 1.3 66.2 - - - +
81A GLU* 3.4 26.9 - - + +
82A LYS* 3.2 38.0 + - + +
83A LEU* 3.5 8.0 + - - -
86A TYR* 4.9 4.4 - - - +
325A HIS* 5.8 1.3 - - - +
7B LYS* 4.3 23.8 - - + +
9B LEU* 4.5 19.7 - - + -
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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
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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