Contacts of the helix formed by residues 55 - 73 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B GLN* 3.3 14.6 - - - +
53B GLU* 2.7 33.8 + - + +
54B LYS* 1.3 75.2 - - - +
56B LEU* 1.3 63.6 + - - +
57B THR* 2.8 29.8 + - - -
58B GLU* 3.1 26.3 + - + +
59B LEU* 3.2 15.2 + - - +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LYS 3.6 3.9 + - - +
55B ASN* 1.3 73.1 + - - +
57B THR* 1.3 58.3 + - - +
59B LEU* 3.8 6.8 + - + +
60B ASP* 3.1 23.9 + - - +
89B GLY* 3.4 32.7 - - - +
91B LYS* 4.2 14.6 - - + -
134B ASN* 4.1 31.2 - - + +
137B TYR* 4.5 12.1 - - + -
138B LEU* 3.5 36.8 - - + -
141B ILE* 3.9 19.3 - - + -
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Residues in contact with THR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN* 2.8 14.3 + - - -
56B LEU* 1.3 74.4 - - - +
58B GLU* 1.3 61.8 + - - +
60B ASP* 3.0 12.4 + - + +
61B ASN* 2.9 45.1 + - - +
89B GLY 5.5 0.2 - - - -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLN* 3.5 37.1 + - - +
53B GLU* 4.4 4.3 - - - +
55B ASN* 3.1 25.1 + - + +
57B THR* 1.3 78.6 - - - +
59B LEU* 1.3 58.5 + - - +
61B ASN* 3.0 21.2 + - - +
62B LEU* 2.9 43.4 + - + +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B MET* 3.6 41.5 - - + +
49B GLN* 3.9 16.2 - - + -
50B LEU* 3.8 24.7 - - + -
55B ASN 3.2 15.5 + - - +
56B LEU* 4.1 8.7 - - + +
58B GLU* 1.3 74.6 - - - +
60B ASP* 1.3 55.5 + - - +
62B LEU* 4.2 6.4 - - + +
63B GLY* 3.1 19.0 + - - -
85B ILE* 3.4 20.9 - - + +
89B GLY* 5.9 0.2 - - - -
138B LEU* 3.9 14.6 - - + -
141B ILE* 3.9 33.7 - - + -
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Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU 3.1 14.9 + - - +
57B THR* 3.0 17.5 + - + +
59B LEU* 1.3 75.4 - - - +
61B ASN* 1.3 63.5 + - - +
63B GLY 3.4 0.9 + - - -
64B HIS* 2.9 25.1 + - - +
85B ILE 5.1 0.4 - - - -
86B GLN* 3.1 34.7 - - - +
89B GLY* 5.0 1.5 - - - +
90B ARG* 2.8 45.6 + - + +
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Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B THR* 2.9 30.8 + - - +
58B GLU* 3.0 26.4 + - - +
60B ASP* 1.3 80.0 - - - +
62B LEU* 1.3 57.9 + - + +
64B HIS* 2.9 13.6 + - + +
65B PHE* 2.9 27.9 + - - +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B THR* 4.5 14.4 + - + -
45B GLN* 4.0 35.2 - - + +
46B MET* 3.5 51.2 - - + +
49B GLN* 4.8 6.7 - - - +
58B GLU* 2.9 35.3 + - - +
59B LEU* 4.2 4.5 - - + +
61B ASN* 1.3 73.9 - - + +
63B GLY* 1.3 64.6 + - - +
65B PHE* 3.4 9.6 + - + +
66B LEU* 3.2 21.1 + - - +
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Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B MET* 3.5 13.8 - - - +
59B LEU 3.1 14.3 + - - -
60B ASP 3.7 3.8 - - - -
62B LEU* 1.3 80.1 - - - +
64B HIS* 1.3 61.0 + - - +
67B LYS* 3.2 24.8 + - - +
82B CYS* 3.5 18.0 - - - +
85B ILE* 4.5 3.1 - - - -
86B GLN* 3.9 11.7 - - - -
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Residues in contact with HIS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP* 2.9 9.9 + - - +
61B ASN* 2.9 17.5 + - + +
63B GLY* 1.3 75.6 - - - +
65B PHE* 1.3 68.8 + - - +
67B LYS* 3.4 2.9 + - - +
68B GLY* 3.3 15.2 + - - -
86B GLN* 3.2 24.7 + - - +
90B ARG* 5.8 0.6 + - - -
24D ASP* 4.3 4.6 + - - -
26D ASP 5.3 2.2 - - - -
27D PHE* 3.8 40.1 - + - -
30D GLY* 5.4 6.7 - - - -
31D LEU* 5.0 10.8 - - + +
34D GLN* 5.0 12.8 + - - -
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLN* 3.4 39.9 - - + -
42B THR* 3.5 34.3 - - + -
61B ASN 2.9 11.8 + - - +
62B LEU* 3.7 12.6 - - + +
64B HIS* 1.3 80.0 - - + +
66B LEU* 1.3 68.4 - - + +
68B GLY* 3.1 12.5 + - - -
69B SER* 3.2 26.9 + - - -
34D GLN* 5.6 9.4 - - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 3.5 29.2 - - + -
38B GLN* 5.7 0.2 - - + -
39B ALA* 4.0 17.5 - - + +
42B THR* 3.1 27.4 - - + +
43B PHE* 3.4 33.7 - - + -
46B MET* 4.5 5.4 - - + -
62B LEU 3.2 12.7 + - - +
65B PHE* 1.3 83.9 - - + +
67B LYS* 1.3 50.0 + - - +
69B SER* 4.0 5.2 - - - +
70B SER* 2.5 38.3 + - - -
78B ILE* 4.7 5.4 - - + -
82B CYS* 3.7 21.3 - - - -
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLY 3.2 18.3 + - - +
64B HIS* 3.7 4.3 - - - +
65B PHE 3.2 0.8 - - - -
66B LEU* 1.3 76.6 - - - +
68B GLY* 1.3 58.5 + - - +
70B SER* 3.3 5.9 + - - -
71B ALA* 2.9 31.7 + - - +
79B ALA* 4.0 11.1 - - + +
82B CYS* 3.8 11.0 - - + +
83B GLU* 3.0 34.4 + - + +
86B GLN* 3.3 20.4 - - - +
20D MET* 3.3 34.4 + - + -
24D ASP* 3.0 34.8 + - - +
27D PHE* 3.9 16.8 - - + -
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B HIS 3.3 6.8 + - - -
65B PHE 3.1 7.0 + - - -
67B LYS* 1.3 78.2 - - - +
69B SER* 1.3 64.7 + - - +
71B ALA* 3.5 1.8 + - - +
72B ALA* 3.1 23.9 + - - +
17D ILE* 5.4 0.3 - - - +
27D PHE* 4.1 18.3 - - - -
31D LEU* 4.3 20.8 - - - +
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 3.8 22.9 - - - -
38B GLN* 3.5 21.4 + - - -
65B PHE* 3.2 27.8 + - - -
66B LEU* 4.0 6.7 - - - -
68B GLY* 1.3 73.5 - - - +
70B SER* 1.3 63.1 + - - +
72B ALA* 3.2 19.7 + - - +
73B LEU* 3.4 13.0 + - - +
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 4.1 15.9 - - - -
66B LEU 2.5 22.7 + - - -
67B LYS* 3.3 9.0 + - - -
69B SER* 1.3 79.4 - - - +
71B ALA* 1.3 61.5 + - - +
73B LEU* 3.2 3.2 + - - +
74B GLY 3.2 4.5 + - - -
75B LEU* 2.8 47.9 + - - +
78B ILE* 4.0 19.6 - - - +
79B ALA* 3.6 10.9 + - - -
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 3.6 19.4 - - - +
67B LYS 2.9 23.5 + - - +
68B GLY* 3.9 4.9 - - - +
70B SER* 1.3 76.8 + - - +
72B ALA* 1.3 60.3 + - - +
74B GLY* 3.4 9.4 + - - +
75B LEU 4.8 2.2 - - - +
76B GLN* 5.8 0.7 - - - +
79B ALA* 4.3 7.6 - - + +
17D ILE* 4.1 12.9 - - + +
20D MET* 3.7 30.3 - - + -
27D PHE* 4.7 1.8 - - + -
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 3.4 16.4 - - - +
17B ILE* 4.2 13.3 - - - +
68B GLY 3.1 13.9 + - - +
69B SER* 3.3 12.6 - - - +
70B SER 3.1 0.2 - - - -
71B ALA* 1.3 78.5 - - - +
73B LEU* 1.3 64.0 + - + +
74B GLY 3.3 0.9 - - - -
17D ILE* 4.6 10.1 - - + +
31D LEU* 6.5 0.4 - - + -
72D ALA* 3.9 28.8 - - + +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.3 4.0 - - - -
14B LEU* 3.5 30.9 - - + +
17B ILE* 5.1 8.3 - - + -
31B LEU* 4.0 33.2 - - + +
32B ILE* 4.1 24.7 - - + +
35B PHE* 3.5 40.6 - - + -
69B SER 3.4 9.4 + - - +
70B SER 3.2 7.3 + - - +
72B ALA* 1.3 83.3 - - + +
74B GLY* 1.3 60.8 + - - +
75B LEU* 3.3 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
------------------------------------------------------------
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