Contacts of the helix formed by residues 52 - 63 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B THR* 1.3 72.8 - - - +
53B ASP* 1.3 58.7 + - - +
55B ARG* 3.3 22.8 + - - +
56B ARG* 2.9 28.6 + - + +
81B GLU* 4.0 15.0 - - - +
85B GLN* 3.8 22.3 - - - +
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Residues in contact with ASP 53 (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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51B THR* 3.1 6.6 + - - +
52B GLU* 1.3 79.6 - - - +
54B ASN* 1.3 63.7 + - - +
56B ARG* 3.3 34.2 + - - +
57B ALA* 2.9 28.2 + - - +
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Residues in contact with ASN 54 (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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43B LEU* 4.4 5.2 - - + +
48B VAL* 3.4 23.8 - - + +
49B GLU* 2.9 36.0 + - - +
51B THR* 3.0 22.6 + - - +
53B ASP* 1.3 80.3 - - - +
55B ARG* 1.3 60.1 + - - +
57B ALA* 3.3 8.9 + - - +
58B TYR* 3.0 30.1 + - - +
313B TRP* 4.2 5.8 - - + -
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Residues in contact with ARG 55 (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 SER 5.1 0.2 - - - -
36B GLY* 3.8 20.6 - - - +
39B MET* 3.8 33.7 - - + -
43B LEU* 4.0 7.4 - - + -
50B ASN* 2.7 46.1 + - - +
51B THR 2.9 21.2 + - - +
52B GLU* 3.6 25.9 - - - +
54B ASN* 1.3 76.3 - - - +
56B ARG* 1.3 62.7 + - - +
58B TYR* 3.4 5.0 + - - +
59B ARG* 3.0 39.4 + - - +
81B GLU* 2.9 42.9 + - - +
85B GLN* 5.0 0.4 - - - -
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Residues in contact with ARG 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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52B GLU* 2.9 19.4 + - + +
53B ASP* 3.3 32.6 + - - +
55B ARG* 1.3 76.9 - - - +
57B ALA* 1.3 57.8 + - - +
59B ARG* 3.4 0.7 + - - -
60B GLN* 2.8 54.7 + - - +
85B GLN* 3.7 32.5 - - - +
86B LYS 2.8 35.5 + - - +
87B ALA* 3.5 4.0 - - - +
88B ASP* 2.7 23.7 + - - +
93B PHE* 3.3 20.4 - - + -
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Residues in contact with ALA 57 (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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53B ASP* 2.9 20.8 + - - +
54B ASN* 3.4 13.0 - - - +
56B ARG* 1.3 82.0 - - - +
58B TYR* 1.3 65.1 - - - +
60B GLN* 3.1 12.8 + - - +
61B LEU* 3.1 20.8 + - - +
313B TRP* 4.4 15.1 - - + -
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Residues in contact with TYR 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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39B MET* 3.7 27.4 - - + -
43B LEU* 4.8 4.7 - - + -
54B ASN 3.0 16.0 + - - +
55B ARG* 3.4 5.4 + - - +
57B ALA* 1.3 75.6 - - - +
59B ARG* 1.3 74.3 + - - +
61B LEU* 3.1 25.3 + - + +
62B LEU* 3.2 26.9 + - + +
306B GLN* 2.7 46.4 + - - +
309B VAL* 3.9 19.9 - - + +
310B LEU* 3.4 30.7 - - + +
313B TRP* 3.8 31.1 - + + -
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Residues in contact with ARG 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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32B ALA* 3.2 19.6 + - + +
34B GLU* 3.0 53.3 + - - +
39B MET* 3.8 17.2 - - - +
55B ARG* 3.0 31.8 + - - +
56B ARG* 3.8 4.3 - - - +
58B TYR* 1.3 86.9 - - - +
60B GLN* 1.3 57.7 + - - +
62B LEU* 3.2 10.2 + - + +
63B PHE* 2.9 50.0 + - + -
79B PHE* 4.9 1.0 - - - +
81B GLU* 4.2 14.1 + - - -
82B THR* 3.5 34.6 + - + -
85B GLN* 5.0 1.2 - - - +
93B PHE* 4.0 15.5 - - + -
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Residues in contact with GLN 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 ARG* 2.8 23.8 + - - +
57B ALA* 3.1 14.2 + - - +
59B ARG* 1.3 78.9 - - - +
61B LEU* 1.3 50.9 + - - +
63B PHE* 3.3 2.2 + - - +
64B SER* 2.7 48.8 + - - +
87B ALA* 3.0 13.6 - - + -
88B ASP* 2.5 56.1 + - - +
93B PHE* 3.7 19.7 - - + -
96B ILE* 5.8 1.1 - - + -
320B ILE* 5.8 5.9 - - - +
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Residues in contact with LEU 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 ALA 3.1 11.9 + - - +
58B TYR* 3.2 13.9 - - + +
60B GLN* 1.3 76.3 - - - +
62B LEU* 1.3 71.2 + - + +
63B PHE 3.4 0.5 + - - -
64B SER* 3.5 5.4 + - - -
65B THR* 3.1 6.6 + - - +
309B VAL* 3.8 25.8 - - + -
313B TRP* 3.3 51.1 - - + +
320B ILE* 4.1 30.5 - - + +
323B GLY* 4.4 1.6 - - - -
324B GLN* 2.8 41.1 + - + +
327B LEU* 5.7 0.7 - - + -
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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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30B LEU* 4.8 9.1 - - + +
32B ALA* 4.3 19.7 - - + -
58B TYR* 3.6 39.9 - - + +
59B ARG* 3.2 15.1 + - - +
61B LEU* 1.3 80.5 - - + +
63B PHE* 1.3 71.1 + - + +
65B THR* 3.0 21.5 + - - -
69B LEU* 4.2 8.0 - - - +
97B LEU* 5.7 0.2 - - - +
306B GLN* 3.7 28.7 - - + +
309B VAL* 4.1 17.3 - - + -
327B LEU* 3.9 25.6 - - + +
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Residues in contact with PHE 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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30B LEU* 5.1 4.0 - - + -
32B ALA* 4.6 8.7 - - + -
59B ARG* 2.9 28.2 + - + +
60B GLN* 4.0 4.5 - - - +
62B LEU* 1.3 90.8 - - + +
64B SER* 1.3 58.5 + - - +
65B THR 3.4 1.8 - - - -
76B VAL* 3.8 20.4 - - + -
78B LEU* 3.6 24.7 - - + -
82B THR* 3.6 28.0 - - + -
93B PHE* 3.6 32.5 - + + -
96B ILE* 3.0 22.3 - - + +
97B LEU* 3.8 34.4 - - + +
100B LYS* 2.8 18.6 + - - +
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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
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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