Contacts of the helix formed by residues 52 - 63 (chain D) in PDB entry 1FBA
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 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D THR* 1.3 73.2 - - - +
53D ASP* 1.3 58.7 + - + +
55D ARG* 3.5 30.7 + - - +
56D ARG* 3.1 27.5 + - - +
81D GLU* 4.5 5.8 - - - +
85D GLN* 3.4 26.1 - - - +
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Residues in contact with ASP 53 (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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51D THR* 3.1 5.6 + - - +
52D GLU* 1.3 79.3 - - + +
54D ASN* 1.3 57.1 + - - +
55D ARG 3.2 1.3 - - - -
56D ARG* 2.9 42.4 + - - +
57D ALA* 2.7 35.3 + - - +
88D ASP* 4.6 2.4 - - - +
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Residues in contact with ASN 54 (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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43D LEU* 4.4 5.5 - - + +
48D VAL* 3.8 22.4 - - + +
49D GLU* 2.8 36.0 + - - +
51D THR* 2.8 26.4 + - - +
53D ASP* 1.3 79.4 - - - +
55D ARG* 1.3 59.5 + - - +
57D ALA* 3.4 9.4 + - - +
58D TYR* 3.0 27.7 + - - +
313D TRP* 4.2 6.0 - - + -
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Residues in contact with ARG 55 (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 SER 5.2 0.2 - - - -
36D GLY* 3.9 18.5 - - - +
39D MET* 3.5 37.5 - - + -
43D LEU* 3.8 7.2 - - + -
50D ASN* 3.0 37.8 + - - +
51D THR* 3.1 28.1 + - - +
52D GLU* 3.5 27.8 - - - +
54D ASN* 1.3 77.4 - - - +
56D ARG* 1.3 59.7 + - - +
58D TYR* 3.5 6.0 + - - +
59D ARG* 3.0 41.2 + - - +
81D GLU* 3.1 39.3 + - - +
85D GLN* 5.4 1.1 - - - +
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Residues in contact with ARG 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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52D GLU* 3.1 18.9 + - - +
53D ASP* 2.9 46.2 + - - +
54D ASN 3.1 0.4 - - - -
55D ARG* 1.3 76.5 - - - +
57D ALA* 1.3 55.7 - - - +
59D ARG* 3.2 1.6 + - - -
60D GLN* 2.7 39.5 + - - +
85D GLN* 3.9 33.7 - - - +
86D LYS* 2.6 27.9 + - - +
87D ALA* 2.9 3.6 + - - +
88D ASP* 2.7 51.2 + - - +
93D PHE* 3.5 14.7 - - + -
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Residues in contact with ALA 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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53D ASP* 2.7 21.4 + - - +
54D ASN* 3.5 12.8 - - - +
56D ARG* 1.3 74.8 - - - +
58D TYR* 1.3 57.7 + - - +
60D GLN* 3.4 12.4 + - - +
61D LEU* 3.1 25.8 + - - +
313D TRP* 4.6 13.9 - - + -
317D LYS* 4.8 19.4 + - - +
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Residues in contact with TYR 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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34D GLU* 5.8 0.2 - - - -
39D MET* 3.7 26.5 - - + -
43D LEU* 4.6 4.3 - - + -
54D ASN 3.0 16.3 + - - +
55D ARG* 3.8 6.1 - - - +
56D ARG 3.2 0.2 - - - -
57D ALA* 1.3 74.9 - - - +
59D ARG* 1.3 77.4 + - - +
61D LEU* 3.2 17.0 + - + +
62D LEU* 3.2 31.8 + - + +
306D GLN* 2.8 45.7 + - - +
309D VAL* 4.2 18.6 - - + +
310D LEU* 3.5 26.7 - - + +
313D TRP* 3.7 36.1 - + + -
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Residues in contact with ARG 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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32D ALA* 3.4 16.4 + - - +
34D GLU* 3.0 51.1 + - - +
39D MET* 3.8 21.5 - - - +
55D ARG* 3.0 30.4 + - - +
56D ARG* 3.2 4.2 + - - +
58D TYR* 1.3 85.1 - - - +
60D GLN* 1.3 66.1 + - - +
62D LEU* 3.3 13.1 + - - +
63D PHE* 2.9 51.4 + - + -
79D PHE* 5.2 0.6 - - - +
81D GLU* 4.4 10.9 + - - -
82D THR* 3.1 32.0 + - + -
85D GLN* 4.9 2.5 - - - +
93D PHE* 4.0 11.4 - - + -
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Residues in contact with GLN 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 ARG* 2.7 21.3 + - - +
57D ALA* 3.5 9.5 - - - +
59D ARG* 1.3 78.3 - - - +
61D LEU* 1.3 51.4 + - - +
63D PHE* 3.9 0.6 - - - +
64D SER* 2.8 47.7 + - - +
87D ALA* 3.4 11.2 - - + -
88D ASP* 2.8 54.3 + - - +
93D PHE* 3.8 17.0 - - + -
317D LYS* 3.9 18.4 - - - +
320D ILE* 6.1 1.0 - - - +
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Residues in contact with LEU 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 ALA 3.1 12.6 + - - +
58D TYR* 3.2 12.3 + - + +
60D GLN* 1.3 75.7 - - - +
62D LEU* 1.3 72.3 + - + +
64D SER* 3.5 5.0 + - - -
65D THR* 3.2 4.9 + - - +
309D VAL* 4.1 25.8 - - + -
313D TRP* 3.1 47.8 - - + +
319D ASN 4.9 0.2 - - - +
320D ILE* 4.1 26.7 - - + +
323D GLY* 4.3 0.7 - - - -
324D GLN* 2.8 49.9 + - + +
327D LEU* 6.2 0.4 - - + -
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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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30D LEU* 4.9 8.3 - - + -
32D ALA* 4.6 13.9 - - + -
58D TYR* 3.2 49.9 + - + +
59D ARG* 3.5 17.5 - - - +
61D LEU* 1.3 81.4 - - + +
63D PHE* 1.3 69.4 + - + +
65D THR* 2.7 29.9 + - - -
69D LEU* 4.4 5.2 - - - +
306D GLN* 3.7 17.5 - - + +
309D VAL* 4.2 16.6 - - + -
327D LEU* 4.0 29.0 - - + +
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Residues in contact with PHE 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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30D LEU* 4.9 4.7 - - + -
32D ALA* 4.4 13.5 - - + -
59D ARG* 2.9 40.6 + - + +
60D GLN 4.4 1.6 - - - +
62D LEU* 1.3 85.2 - - + +
64D SER* 1.3 50.2 + - - +
65D THR* 3.1 5.8 - - - -
69D LEU* 6.1 1.1 - - - -
76D VAL* 3.9 22.4 - - + -
78D LEU* 3.6 22.9 - - + -
82D THR* 3.8 16.8 - - + -
93D PHE* 3.8 30.1 - + + +
96D ILE* 3.4 18.2 - - + +
97D LEU* 3.6 32.9 - - + +
100D LYS* 2.7 27.4 + - - +
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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
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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