Contacts of the helix formed by residues 55 - 73 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D GLN* 3.3 13.8 - - - +
53D GLU* 2.7 34.1 + - + +
54D LYS* 1.3 74.5 - - - +
56D LEU* 1.3 62.5 + - - +
57D THR* 2.8 29.9 + - - -
58D GLU* 3.1 25.9 + - + +
59D LEU* 3.2 15.2 + - - +
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D LYS 3.6 3.7 + - - +
55D ASN* 1.3 72.6 + - - +
57D THR* 1.3 58.9 + - - +
59D LEU* 3.9 6.1 - - + +
60D ASP* 3.1 24.3 + - - +
89D GLY* 3.4 34.5 - - - +
91D LYS* 4.2 14.8 - - + -
134D ASN* 4.1 31.9 - - + +
137D TYR* 4.5 11.9 - - + -
138D LEU* 3.4 36.1 - - + -
141D ILE* 3.9 19.5 - - + -
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Residues in contact with THR 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ASN* 2.8 14.0 + - - -
56D LEU* 1.3 74.1 - - - +
58D GLU* 1.3 63.0 + - - +
60D ASP* 3.0 12.1 + - + +
61D ASN* 2.9 45.0 + - - +
89D GLY 5.5 0.2 - - - -
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D GLN* 3.5 35.9 + - - +
53D GLU* 4.4 4.0 - - - +
55D ASN* 3.1 26.1 + - - +
57D THR* 1.3 79.3 - - - +
59D LEU* 1.3 57.8 + - - +
61D ASN* 3.0 21.4 + - - +
62D LEU* 2.9 44.4 + - + +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D MET* 3.6 41.7 - - + +
49D GLN* 3.9 16.4 - - + -
50D LEU* 3.8 24.9 - - + +
55D ASN 3.2 15.9 + - - +
56D LEU* 4.1 7.9 - - + +
57D THR 3.4 0.2 - - - -
58D GLU* 1.3 74.4 - - - +
60D ASP* 1.3 56.0 + - - +
62D LEU* 4.2 5.5 - - + +
63D GLY* 3.1 18.4 + - - -
85D ILE* 3.4 20.6 - - + +
89D GLY* 5.8 0.4 - - - -
138D LEU* 3.9 14.6 - - + -
141D ILE* 3.9 33.4 - - + -
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Residues in contact with ASP 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU 3.1 15.0 + - - +
57D THR* 3.0 20.8 + - + +
59D LEU* 1.3 75.7 - - - +
61D ASN* 1.3 61.4 + - - +
63D GLY 3.3 1.0 + - - -
64D HIS* 2.9 25.5 + - - +
85D ILE 5.1 0.7 - - - -
86D GLN* 3.1 34.5 - - - +
89D GLY* 5.0 1.6 - - - +
90D ARG* 2.8 45.2 + - + +
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Residues in contact with ASN 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D THR* 2.9 30.2 + - - +
58D GLU* 3.0 25.6 + - - +
60D ASP* 1.3 78.7 - - - +
62D LEU* 1.3 56.5 + - + +
64D HIS* 3.0 13.4 + - - +
65D PHE* 2.9 28.1 + - - +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D THR* 4.5 14.1 + - + -
45D GLN* 4.0 35.7 - - + +
46D MET* 3.5 50.1 - - + +
49D GLN* 4.8 7.6 - - - +
58D GLU* 2.9 34.6 + - - +
59D LEU* 4.2 4.5 - - + +
61D ASN* 1.3 72.9 - - + +
63D GLY* 1.3 65.0 + - - +
65D PHE* 3.4 9.7 + - + +
66D LEU* 3.2 21.1 + - - +
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Residues in contact with GLY 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D MET* 3.5 13.6 - - - +
59D LEU 3.1 14.3 + - - -
60D ASP 3.7 4.0 - - - -
62D LEU* 1.3 79.3 - - - +
64D HIS* 1.3 59.1 + - - +
67D LYS* 3.2 25.6 + - - +
82D CYS* 3.5 17.4 - - - +
85D ILE* 4.4 3.6 - - - -
86D GLN* 3.9 12.1 - - - -
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Residues in contact with HIS 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ASP* 4.3 4.0 + - - -
26B ASP 5.3 2.2 - - - -
27B PHE* 3.7 40.9 - + - -
30B GLY* 5.3 6.6 - - - -
31B LEU* 5.0 11.8 - - + +
34B GLN* 5.1 10.8 + - - -
60D ASP* 2.9 10.3 + - - +
61D ASN* 3.0 18.1 + - - +
63D GLY* 1.3 76.3 - - - +
65D PHE* 1.3 68.8 + - + +
67D LYS* 3.5 2.6 + - - +
68D GLY* 3.3 15.2 + - - -
86D GLN* 3.2 24.8 + - - +
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Residues in contact with PHE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLN* 5.6 9.9 - - - +
38D GLN* 3.4 40.8 - - + -
42D THR* 3.5 34.1 - - + -
61D ASN 2.9 12.4 + - - +
62D LEU* 3.4 13.4 + - + +
64D HIS* 1.3 81.8 - - + +
66D LEU* 1.3 67.7 + - + +
68D GLY* 3.1 13.2 + - - -
69D SER* 3.2 26.2 + - - -
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PHE* 3.5 29.2 - - + -
38D GLN* 5.7 0.2 - - + -
39D ALA* 4.0 17.3 - - + +
42D THR* 3.0 27.6 - - + +
43D PHE* 3.4 33.4 - - + -
46D MET* 4.5 6.1 - - + -
62D LEU 3.2 12.3 + - - +
65D PHE* 1.3 83.8 - - + +
67D LYS* 1.3 50.9 + - - +
68D GLY 3.3 0.2 - - - -
69D SER* 4.0 5.4 - - - +
70D SER* 2.4 39.2 + - - -
78D ILE* 4.7 4.5 - - + -
82D CYS* 3.8 20.9 - - - -
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B MET* 3.2 34.4 + - + -
24B ASP* 3.1 35.3 + - - +
27B PHE* 3.9 16.6 - - + -
63D GLY 3.2 20.0 + - - +
64D HIS 3.7 3.6 - - - +
65D PHE 3.2 0.2 - - - -
66D LEU* 1.3 75.9 - - - +
68D GLY* 1.3 59.3 + - - +
70D SER* 3.4 5.9 + - - -
71D ALA* 2.9 32.2 + - - +
79D ALA* 4.0 12.1 - - + +
82D CYS* 3.8 10.7 - - + +
83D GLU* 3.0 33.8 + - - +
86D GLN* 3.3 20.3 - - - +
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Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 5.3 0.3 - - - +
27B PHE* 4.1 18.1 - - - -
31B LEU* 4.3 21.7 - - - +
64D HIS 3.3 7.2 + - - -
65D PHE 3.1 7.5 + - - -
67D LYS* 1.3 76.9 - - - +
69D SER* 1.3 63.7 + - - +
71D ALA* 3.5 1.8 + - - +
72D ALA* 3.1 24.4 + - - +
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Residues in contact with SER 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PHE* 3.8 23.1 - - - -
38D GLN* 3.5 20.9 + - - -
65D PHE* 3.2 27.0 + - - -
66D LEU* 4.0 6.7 - - - -
68D GLY* 1.3 74.4 - - - +
70D SER* 1.3 62.5 + - - +
72D ALA* 3.2 19.3 + - - +
73D LEU* 3.4 13.3 + - - +
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Residues in contact with SER 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PHE* 4.0 15.5 - - - -
66D LEU 2.4 25.1 + - - -
67D LYS* 3.4 7.8 + - - -
69D SER* 1.3 80.5 - - - +
71D ALA* 1.3 62.3 + - - +
73D LEU* 3.2 3.0 + - - +
74D GLY 3.2 4.0 + - - -
75D LEU* 2.8 47.2 + - - +
78D ILE* 4.0 20.2 - - - +
79D ALA* 3.6 10.9 + - - -
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLU 5.9 0.2 - - - +
17B ILE* 4.1 13.9 - - + +
20B MET* 3.6 31.2 - - + -
27B PHE* 4.7 1.1 - - + -
13D ILE* 3.6 19.4 - - - +
67D LYS 2.9 22.6 + - - +
68D GLY* 3.9 5.2 - - - +
70D SER* 1.3 77.5 + - - +
72D ALA* 1.3 61.3 + - - +
74D GLY* 3.4 8.8 + - - +
75D LEU 4.7 2.2 - - - +
76D GLN* 5.8 0.9 - - - +
79D ALA* 4.2 7.4 - - + -
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 4.5 9.6 - - + +
31B LEU* 6.5 0.2 - - + -
72B ALA* 3.9 29.5 - - + +
13D ILE* 3.5 16.5 - - - +
17D ILE* 4.2 13.0 - - - +
68D GLY 3.1 14.9 + - - +
69D SER* 3.4 11.7 - - - +
70D SER 3.1 0.4 - - - -
71D ALA* 1.3 78.1 - - - +
73D LEU* 1.3 64.5 + - + +
74D GLY 3.3 1.1 - - - -
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE* 4.3 3.6 - - - -
14D LEU* 3.6 30.7 - - + +
17D ILE* 5.1 9.4 - - + -
31D LEU* 4.0 33.0 - - + +
32D ILE* 4.1 25.4 - - + +
35D PHE* 3.5 40.4 - - + -
69D SER 3.4 9.8 + - - +
70D SER 3.2 7.6 + - - +
72D ALA* 1.3 84.0 - - + +
74D GLY* 1.3 60.9 + - - +
75D LEU* 3.5 18.3 + - + +
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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