Contacts of the helix formed by residues 55 - 73 (chain D) in PDB entry 1F2L
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 55 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D MET* 5.4 2.6 - - - +
16D THR 4.7 5.5 - - - +
17D SER* 5.7 0.7 - - - -
52D ASP* 2.9 38.0 + - - +
53D PRO 3.6 3.6 - - - +
54D LYS* 1.3 79.5 - - - +
56D GLN* 1.3 68.9 + - - +
57D TRP* 3.5 33.1 + - + -
58D VAL* 3.0 16.4 + - + +
59D LYS* 3.1 10.0 + - - +
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Residues in contact with GLN 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LYS 3.5 4.0 + - - -
55D GLU* 1.3 71.7 - - - +
57D TRP* 1.3 52.6 + - - +
59D LYS* 3.1 29.7 + - - +
60D ASP* 2.7 71.9 + - - +
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Residues in contact with TRP 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D THR* 3.4 23.5 + - + -
17D SER* 3.9 4.1 - - - +
18D LYS* 3.3 58.4 - - + +
19D ILE* 3.5 30.5 - - + -
21D VAL* 5.1 3.5 - - + +
24D LEU* 4.5 6.1 - - + -
41D LEU* 3.4 33.7 - - + -
51D ALA* 3.9 4.9 - - + -
55D GLU* 3.2 34.1 + - + -
56D GLN* 1.3 78.6 - - - +
58D VAL* 1.3 72.2 + - + +
60D ASP* 3.4 10.8 + - - +
61D ALA* 2.9 32.2 + - + +
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Residues in contact with VAL 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ILE* 3.8 39.9 - - + -
41D LEU* 5.0 4.0 - - + -
51D ALA* 3.6 13.2 - - + -
52D ASP 3.3 27.6 - - - +
53D PRO* 4.0 4.5 - - + -
55D GLU* 3.0 5.2 + - + +
57D TRP* 1.3 113.2 - - + +
59D LYS* 1.3 60.5 + - - +
61D ALA* 3.2 3.5 + - - +
62D MET* 2.8 32.8 + - + +
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Residues in contact with LYS 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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53D PRO 3.1 26.2 - - - +
54D LYS* 3.8 18.7 + - - +
55D GLU 3.1 5.4 + - - +
56D GLN* 3.1 33.5 + - - +
58D VAL* 1.3 75.0 - - - +
60D ASP* 1.3 64.4 + - - +
62D MET* 3.2 16.1 + - + +
63D GLN* 3.0 29.9 + - + +
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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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21D VAL* 5.1 4.7 - - + -
56D GLN* 2.7 57.8 + - - +
57D TRP* 3.7 9.6 - - - +
59D LYS* 1.3 74.0 - - - +
61D ALA* 1.3 56.6 + - - +
63D GLN* 3.2 7.5 + - - +
64D HIS* 2.9 30.1 + - - +
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Residues in contact with ALA 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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21D VAL* 4.1 15.2 - - + +
24D LEU* 3.7 30.7 - - + -
41D LEU* 5.1 7.0 - - + -
57D TRP* 2.9 24.5 + - + +
58D VAL* 3.6 7.6 - - - +
60D ASP* 1.3 77.2 - - - +
62D MET* 1.3 64.0 + - - +
64D HIS* 3.4 3.8 + - - +
65D LEU* 3.1 28.7 + - + +
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Residues in contact with MET 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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27D TYR* 3.4 54.7 - - + +
37D ARG* 6.2 0.7 - - - -
39D ILE* 3.8 29.8 - - + -
41D LEU* 5.3 1.1 - - + -
53D PRO* 4.6 7.9 - - + -
58D VAL* 2.8 36.0 + - + +
59D LYS* 3.2 21.1 + - + +
61D ALA* 1.3 76.2 - - + +
63D GLN* 1.3 57.8 + - + +
65D LEU* 3.6 1.2 - - - +
66D ASP* 2.8 36.6 + - - +
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Residues in contact with GLN 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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59D LYS* 3.0 21.9 + - + +
60D ASP* 3.7 6.3 - - - +
62D MET* 1.3 76.1 - - + +
64D HIS* 1.3 53.5 + - - +
66D ASP* 3.2 13.4 + - - +
67D ARG* 2.7 64.3 + - - +
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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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21D VAL* 4.5 33.9 + - + +
22D ALA* 5.9 1.4 - - - -
24D LEU 5.8 0.2 - - - -
60D ASP 2.9 17.9 + - - +
61D ALA* 3.6 8.3 - - - +
63D GLN* 1.3 75.8 - - - +
65D LEU* 1.3 71.5 + - + +
67D ARG* 3.1 10.4 + - - +
68D GLN* 2.9 54.4 + - + +
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Residues in contact with LEU 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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24D LEU* 3.4 41.7 - - + +
25D ILE 4.1 6.7 - - - +
26D HIS* 3.9 34.3 - - - +
27D TYR* 4.1 18.2 - - + -
41D LEU* 5.3 2.2 - - + -
61D ALA* 3.1 20.6 + - + +
62D MET 3.6 3.4 - - - +
64D HIS* 1.3 85.5 - - + +
66D ASP* 1.3 64.7 + - - +
68D GLN* 3.1 25.7 + - - +
69D ALA* 3.0 22.2 + - - +
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Residues in contact with ASP 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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27D TYR* 2.7 36.8 + - - -
62D MET* 2.8 25.5 + - - +
63D GLN* 3.8 15.5 + - - +
65D LEU* 1.3 73.6 - - - +
67D ARG* 1.3 58.7 + - + +
69D ALA* 3.3 7.0 + - - +
70D ALA* 2.9 29.7 + - - +
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Residues in contact with ARG 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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63D GLN* 2.7 49.5 + - + +
64D HIS* 3.1 8.7 + - - +
66D ASP* 1.3 71.2 - - + +
68D GLN* 1.3 66.4 + - - +
70D ALA* 3.2 7.2 + - - +
71D ALA* 3.0 24.3 + - - +
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Residues in contact with GLN 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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23C LEU* 5.3 15.5 - - + +
24D LEU 5.0 4.0 + - - +
25D ILE* 5.4 4.2 + - - +
64D HIS* 2.9 47.3 + - + +
65D LEU* 3.4 22.7 - - - +
67D ARG* 1.3 79.4 - - + +
69D ALA* 1.3 65.1 + - - +
71D ALA* 3.1 11.5 + - - +
72D LEU* 3.4 19.9 + - + +
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Residues in contact with ALA 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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47C ARG* 3.1 42.0 + - - +
65D LEU 3.0 9.6 + - - +
66D ASP* 3.9 9.4 - - - +
68D GLN* 1.3 80.2 - - - +
70D ALA* 1.3 62.8 + - - +
72D LEU* 3.4 11.3 + - - +
73D THR* 3.4 2.9 - - - +
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Residues in contact with ALA 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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66D ASP 2.9 18.6 + - - +
67D ARG* 3.5 8.7 - - - +
68D GLN 3.1 0.2 - - - -
69D ALA* 1.3 78.3 - - - +
71D ALA* 1.3 57.7 + - - +
73D THR* 2.6 40.2 + - - -
74D ARG* 4.0 3.7 + - - +
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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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67D ARG 3.0 12.0 + - - +
68D GLN* 3.1 11.9 + - - +
70D ALA* 1.3 75.7 - - - +
72D LEU* 1.3 63.1 + - + +
74D ARG* 3.1 36.0 + - - +
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Residues in contact with LEU 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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16C THR* 4.4 5.5 - - - +
18C LYS 5.9 1.1 - - - +
19C ILE* 4.5 14.4 - - + -
20C PRO* 4.9 10.8 - - + -
23C LEU* 4.0 29.2 - - + -
43C THR* 4.5 11.0 - - + -
47C ARG* 3.7 22.9 - - - +
49C PHE* 3.4 34.1 - - + -
68D GLN* 3.5 16.8 - - + +
69D ALA* 3.4 13.7 + - - +
70D ALA 3.1 0.4 - - - -
71D ALA* 1.3 75.8 - - + +
73D THR* 1.3 61.1 + - - +
74D ARG 3.0 14.0 + - - +
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Residues in contact with THR 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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14C LYS* 5.8 3.5 + - - -
47C ARG* 3.9 11.4 - - - +
49C PHE* 5.3 1.3 - - - -
69D ALA 3.4 13.5 - - - +
70D ALA* 2.6 26.9 + - - +
72D LEU* 1.3 75.9 - - - +
74D ARG* 1.3 67.6 + - - +
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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
------------------------------------------------------------
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