Contacts of the helix formed by residues 55 - 73 (chain A) in PDB entry 1C03
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN* 3.3 14.8 - - - +
53A GLU* 2.7 34.0 + - + +
54A LYS* 1.3 73.8 - - - +
56A LEU* 1.3 65.0 + - - +
57A THR* 2.9 28.5 + - - -
58A GLU* 3.1 27.4 + - + +
59A LEU* 3.2 15.1 + - - +
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Residues in contact with LEU 56 (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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54A LYS 3.6 4.4 + - - +
55A ASN* 1.3 72.2 + - - +
57A THR* 1.3 58.3 + - - +
59A LEU* 3.7 7.1 + - + +
60A ASP* 3.1 24.4 + - - +
89A GLY* 3.4 32.4 - - - +
91A LYS* 4.2 15.0 - - + -
134A ASN* 4.1 31.2 - - + +
137A TYR* 4.5 13.0 - - + -
138A LEU* 3.4 35.7 - - + -
141A ILE* 3.9 20.2 - - + -
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Residues in contact with THR 57 (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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55A ASN* 2.9 14.3 + - - -
56A LEU* 1.3 73.4 - - - +
58A GLU* 1.3 62.5 - - - +
60A ASP* 3.0 11.6 + - + +
61A ASN* 2.9 46.5 + - - +
89A GLY 5.5 0.2 - - - -
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Residues in contact with GLU 58 (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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49A GLN* 3.5 35.8 + - - +
53A GLU* 4.4 4.0 - - - +
55A ASN* 3.1 25.1 + - - +
57A THR* 1.3 78.6 - - - +
59A LEU* 1.3 57.0 + - - +
61A ASN* 3.0 21.6 + - - +
62A LEU* 2.9 44.2 + - + +
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Residues in contact with LEU 59 (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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46A MET* 3.6 41.5 - - + +
49A GLN* 3.9 16.6 - - + -
50A LEU* 3.9 22.9 - - + -
54A LYS 5.1 0.2 - - - -
55A ASN 3.2 14.4 + - - +
56A LEU* 3.9 9.0 - - + +
57A THR 3.4 0.2 - - - -
58A GLU* 1.3 74.4 - - - +
60A ASP* 1.3 57.1 + - - +
62A LEU* 4.2 5.8 - - + +
63A GLY* 3.1 19.3 + - - -
85A ILE* 3.4 20.4 - - + +
138A LEU* 3.9 14.1 - - + -
141A ILE* 3.8 36.6 - - + -
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Residues in contact with ASP 60 (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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56A LEU 3.1 14.9 + - - +
57A THR* 3.0 17.1 + - + +
59A LEU* 1.3 76.9 - - - +
61A ASN* 1.3 64.4 + - - +
63A GLY 3.4 0.7 + - - -
64A HIS* 2.9 24.6 + - - +
85A ILE 5.1 0.4 - - - -
86A GLN* 3.1 35.2 - - - +
89A GLY* 4.9 1.8 - - - +
90A ARG* 2.8 45.1 + - - +
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Residues in contact with ASN 61 (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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57A THR* 2.9 31.6 + - - +
58A GLU* 3.0 25.3 + - - +
60A ASP* 1.3 79.9 - - - +
62A LEU* 1.3 56.5 + - + +
64A HIS* 2.9 14.6 + - + +
65A PHE* 2.9 28.6 + - - +
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Residues in contact with LEU 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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42A THR* 4.5 13.7 + - + -
45A GLN* 4.0 35.7 - - + +
46A MET* 3.5 50.2 - - + +
49A GLN* 4.8 7.6 - - - +
58A GLU* 2.9 34.4 + - - +
59A LEU* 4.2 4.7 - - + +
61A ASN* 1.3 72.0 - - + +
63A GLY* 1.3 65.3 + - - +
65A PHE* 3.4 9.7 + - + +
66A LEU* 3.2 21.3 + - - +
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Residues in contact with GLY 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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46A MET* 3.5 14.2 - - - +
59A LEU 3.1 14.2 + - - -
60A ASP 3.7 4.3 - - - -
62A LEU* 1.3 79.3 - - - +
64A HIS* 1.3 60.9 + - - +
67A LYS* 3.2 25.1 + - - +
82A CYS* 3.5 17.0 - - - +
85A ILE* 4.5 3.4 - - - -
86A GLN* 3.9 12.1 - - - -
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Residues in contact with HIS 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 ASP* 2.9 9.7 + - - +
61A ASN* 2.9 17.7 + - - +
63A GLY* 1.3 75.0 - - - +
65A PHE* 1.3 68.5 + - + +
67A LYS* 3.5 2.7 + - - +
68A GLY* 3.3 15.6 + - - -
86A GLN* 3.2 25.3 + - - +
90A ARG* 5.8 0.4 + - - -
24C ASP* 4.4 3.4 + - - -
26C ASP 5.4 2.5 - - - -
27C PHE* 3.8 40.7 - + - -
30C GLY* 5.4 6.5 - - - -
31C LEU* 5.0 11.0 - - + +
34C GLN* 5.0 12.9 + - - -
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Residues in contact with PHE 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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38A GLN* 3.4 40.2 - - + -
42A THR* 3.5 34.3 - - + -
61A ASN 2.9 11.2 + - - +
62A LEU* 3.6 13.2 - - + +
64A HIS* 1.3 80.4 - - - +
66A LEU* 1.3 67.1 + - + +
68A GLY* 3.1 12.8 + - - -
69A SER* 3.2 25.9 + - - -
34C GLN* 5.6 9.2 - - - +
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Residues in contact with LEU 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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35A PHE* 3.5 28.9 - - + -
38A GLN* 5.7 0.2 - - + -
39A ALA* 4.0 18.2 - - + +
42A THR* 3.0 27.6 - - + +
43A PHE* 3.4 33.7 - - + -
46A MET* 4.5 5.2 - - + -
62A LEU 3.2 12.7 + - - +
65A PHE* 1.3 84.2 - - + +
67A LYS* 1.3 51.7 + - - +
69A SER* 4.0 5.4 - - - +
70A SER* 2.5 39.2 + - - -
78A ILE* 4.7 4.9 - - + -
82A CYS* 3.7 21.5 - - - -
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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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63A GLY 3.2 18.5 + - - +
64A HIS* 3.7 4.5 - - - +
65A PHE 3.2 1.0 - - - -
66A LEU* 1.3 75.2 - - - +
68A GLY* 1.3 58.7 + - - +
70A SER* 3.4 5.0 + - - -
71A ALA* 2.9 31.9 + - - +
79A ALA* 4.0 11.5 - - + +
82A CYS* 3.8 11.4 - - + +
83A GLU* 3.0 38.9 + - + +
86A GLN* 3.4 17.0 - - - +
20C MET* 3.2 32.8 + - + -
24C ASP* 3.0 35.3 + - - +
27C PHE* 3.9 16.7 - - + -
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Residues in contact with GLY 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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64A HIS 3.3 6.8 + - - -
65A PHE 3.1 7.3 + - - -
67A LYS* 1.3 77.3 - - - +
69A SER* 1.3 64.2 + - - +
71A ALA* 3.5 1.4 + - - +
72A ALA* 3.1 25.0 + - - +
17C ILE* 5.4 0.3 - - - +
27C PHE* 4.2 17.6 - - - -
31C LEU* 4.3 21.9 - - - +
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Residues in contact with SER 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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35A PHE* 3.8 23.1 - - - -
38A GLN* 3.5 21.5 + - - -
65A PHE* 3.2 23.7 + - - -
66A LEU* 3.9 8.7 - - - -
68A GLY* 1.3 74.6 - - - +
70A SER* 1.3 63.3 + - - +
72A ALA* 3.2 19.5 + - - +
73A LEU* 3.4 13.2 + - - +
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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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35A PHE* 4.1 12.8 - - - -
66A LEU 2.5 22.7 + - - -
67A LYS* 3.4 8.8 + - - -
69A SER* 1.3 79.6 - - - +
71A ALA* 1.3 63.1 + - - +
73A LEU* 3.2 3.0 + - - +
74A GLY 3.2 4.0 + - - -
75A LEU* 2.9 50.2 + - - +
78A ILE* 4.0 19.3 - - - +
79A ALA* 3.6 11.4 + - - -
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Residues in contact with ALA 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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13A ILE* 3.6 19.9 - - - +
67A LYS 2.9 23.6 + - - +
68A GLY* 3.9 4.7 - - - +
70A SER* 1.3 76.4 + - - +
72A ALA* 1.3 60.3 + - - +
74A GLY* 3.5 9.5 + - - +
75A LEU 4.7 2.5 - - - +
76A GLN* 5.8 0.7 - - - +
79A ALA* 4.3 7.6 - - + +
17C ILE* 4.1 14.7 - - + +
20C MET* 3.7 30.5 - - + -
27C PHE* 4.7 1.3 - - + -
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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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13A ILE* 3.5 16.1 - - - +
17A ILE* 4.2 13.2 - - - +
68A GLY 3.1 14.0 + - - +
69A SER* 3.3 12.6 - - - +
70A SER 3.1 0.4 - - - -
71A ALA* 1.3 78.8 - - - +
73A LEU* 1.3 64.2 + - + +
74A GLY 3.3 0.7 - - - -
13C ILE* 6.0 0.2 - - - +
17C ILE* 4.6 9.6 - - + +
31C LEU* 6.5 0.4 - - + -
72C ALA* 3.9 29.8 - - + +
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Residues in contact with LEU 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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13A ILE* 4.3 4.3 - - - -
14A LEU* 3.5 31.1 - - + +
17A ILE* 5.1 9.0 - - + -
28A SER 5.7 0.2 - - - +
31A LEU* 4.0 32.8 - - + +
32A ILE* 4.1 25.1 - - + +
35A PHE* 3.5 40.6 - - + -
69A SER 3.4 9.8 + - - +
70A SER 3.2 6.9 + - - +
72A ALA* 1.3 84.1 - - + +
74A GLY* 1.3 61.8 + - - +
75A LEU* 3.3 17.3 + - + +
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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