Contacts of the helix formed by residues 49 - 64 (chain B) in PDB entry 1FR2
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 SER 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ARG 3.5 9.4 - - - -
6B ASN* 3.9 17.9 - - - +
47B PHE* 3.2 2.4 - - - +
48B LYS* 1.3 80.9 - - - +
50B PHE* 1.3 64.7 + - - +
51B ASP* 3.4 9.7 + - - +
52B ASP* 3.0 34.9 + - - +
53B PHE 3.2 9.2 + - - -
114B TYR* 3.0 17.4 + - - -
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Residues in contact with PHE 50 (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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5B ARG* 2.8 43.2 + - + +
49B SER* 1.3 72.5 - - - +
51B ASP* 1.3 59.0 + - - +
53B PHE* 3.1 22.2 + + - +
54B ARG* 2.9 34.3 + - + +
101B LEU* 3.8 44.2 - - + -
103B HIS* 3.4 25.8 - + - -
113B VAL* 3.3 37.7 - - + -
114B TYR* 3.3 9.6 + + - -
119B ILE* 3.9 8.7 - - + -
403B PO4 5.2 2.0 - - - -
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Residues in contact with ASP 51 (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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6B ASN* 5.7 2.2 + - - +
49B SER* 3.2 9.0 + - - +
50B PHE* 1.3 81.9 - - - +
52B ASP* 1.3 59.4 + - - +
54B ARG* 3.3 25.9 + - - +
55B LYS* 3.1 26.0 + - - +
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Residues in contact with ASP 52 (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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47B PHE* 3.7 14.7 - - + -
48B LYS* 3.7 15.9 - - - +
49B SER* 3.0 33.8 + - - +
51B ASP* 1.3 77.1 - - - +
53B PHE* 1.3 66.5 + - - +
55B LYS* 3.5 14.5 + - + +
56B ALA* 3.1 21.8 + - - +
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Residues in contact with PHE 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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11B ALA* 4.1 10.3 - - + -
34B ILE* 5.0 2.9 - - + -
42B LEU* 3.7 18.6 - - + -
47B PHE* 3.6 37.3 - + + -
49B SER 3.2 9.4 + - - +
50B PHE* 3.1 27.0 + + - +
52B ASP* 1.3 76.0 - - - +
54B ARG* 1.3 59.2 + - - +
56B ALA* 3.1 4.3 + - - +
57B VAL* 2.9 51.1 + - + +
101B LEU* 4.0 9.0 - - + -
114B TYR* 4.0 16.8 - + + -
116B MET* 3.7 33.2 - - + -
119B ILE* 3.5 22.9 - - + -
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Residues in contact with ARG 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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30A GLU* 2.7 44.1 + - - -
50B PHE* 2.9 20.7 + - + +
51B ASP* 3.4 27.0 + - - +
53B PHE* 1.3 73.7 - - - +
55B LYS* 1.3 66.8 + - - +
57B VAL* 3.2 11.1 + - - +
58B TRP* 3.2 30.9 + - - +
82B GLY 4.6 5.1 + - - -
84B SER* 3.4 23.5 - - - +
98B VAL* 3.9 7.7 - - - +
99B TYR 4.0 6.7 + - - -
100B GLU* 5.6 2.6 - - - +
101B LEU* 4.0 36.1 - - + +
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Residues in contact with LYS 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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51B ASP* 3.1 14.0 + - - +
52B ASP* 3.6 17.5 - - + +
54B ARG* 1.3 76.4 - - - +
56B ALA* 1.3 63.2 + - - +
58B TRP 3.3 1.4 + - - -
59B GLU* 3.0 53.7 + - - +
81B LYS 3.0 24.4 + - - -
82B GLY* 3.6 22.4 - - - +
83B TYR* 5.7 1.0 - - - -
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Residues in contact with ALA 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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42B LEU* 3.9 11.7 - - + -
45B LYS* 6.0 1.3 - - + +
47B PHE* 3.4 35.2 - - + -
52B ASP 3.1 7.0 + - - +
53B PHE 3.1 10.4 + - - +
55B LYS* 1.3 73.7 - - - +
57B VAL* 1.3 65.1 + - - +
59B GLU* 3.3 13.8 + - - +
60B GLU* 3.0 28.6 + - - +
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Residues in contact with VAL 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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22B TRP* 5.4 4.5 - - + -
34B ILE* 4.7 16.8 - - + -
35B PRO* 6.1 0.2 - - + -
38B ILE* 4.5 13.7 - - + +
42B LEU* 3.7 14.6 - - + +
53B PHE* 2.9 51.8 + - + +
54B ARG* 3.5 8.3 - - - +
56B ALA* 1.3 75.2 - - - +
58B TRP* 1.3 78.7 + - + +
60B GLU* 3.2 5.5 + - - +
61B VAL* 3.0 30.2 + - + +
101B LEU* 4.4 10.3 - - + -
121B VAL* 5.9 0.4 - - + -
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Residues in contact with TRP 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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22B TRP* 3.8 28.5 - + - -
23B LEU* 4.3 4.7 - - + -
54B ARG* 3.2 39.2 + - + +
55B LYS 4.0 0.4 - - - +
57B VAL* 1.3 81.2 - - + +
59B GLU* 1.3 60.6 + - - +
61B VAL* 3.3 19.1 + - + +
62B SER 3.0 22.7 + - - -
79B VAL* 3.4 16.4 - - + +
82B GLY 4.0 12.1 - - - +
83B TYR 3.5 19.1 - - - +
84B SER* 3.4 39.3 - - - -
85B PRO* 3.5 26.9 - - + -
99B TYR* 4.1 13.8 + - + -
101B LEU* 4.5 20.7 - - + +
121B VAL* 4.1 20.4 - - + -
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Residues in contact with GLU 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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55B LYS* 3.0 56.8 + - - +
56B ALA* 3.7 12.7 - - - +
58B TRP* 1.3 77.0 - - - +
60B GLU* 1.3 63.7 + - + +
62B SER* 2.6 26.6 + - - +
63B LYS* 3.1 17.2 - - + +
79B VAL 3.8 3.4 - - - +
80B SER 5.0 5.5 - - - +
81B LYS 4.5 1.6 - - - +
82B GLY* 3.5 14.9 + - - +
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Residues in contact with GLU 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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38B ILE* 3.6 23.0 - - + +
41B LYS* 3.3 33.4 - - + +
42B LEU* 3.6 21.2 - - + +
45B LYS* 4.3 16.6 + - - -
56B ALA 3.0 21.2 + - - +
57B VAL 3.6 3.1 - - - +
59B GLU* 1.3 75.1 - - - +
61B VAL* 1.3 66.1 - - - +
63B LYS* 3.1 45.0 + - - +
64B ASP* 3.1 16.1 + - - +
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Residues in contact with VAL 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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22B TRP* 3.8 27.6 - - + -
23B LEU* 6.2 0.4 - - + -
38B ILE* 4.1 14.1 - - + -
57B VAL* 3.0 22.0 + - + +
58B TRP* 3.4 31.6 - - + +
60B GLU* 1.3 74.3 - - - +
62B SER* 1.3 64.3 + - - +
63B LYS 3.2 0.7 + - - -
64B ASP 3.2 19.8 + - - +
67B LEU* 4.3 18.8 - - + +
68B SER* 3.5 6.9 - - - +
71B LEU* 4.1 25.8 - - + -
79B VAL* 4.5 1.8 - - + -
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Residues in contact with SER 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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58B TRP 3.0 6.3 + - - -
59B GLU* 2.6 23.0 + - - +
61B VAL* 1.3 76.6 - - - +
63B LYS* 1.3 65.5 + - - +
64B ASP 3.7 0.2 + - - -
68B SER* 4.1 14.5 + - - -
76B LYS 4.9 0.7 - - - -
79B VAL* 3.6 41.9 + - - -
80B SER* 3.8 12.3 + - - -
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Residues in contact with LYS 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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41B LYS* 5.1 4.8 - - - +
59B GLU* 3.1 18.4 - - + +
60B GLU* 3.1 42.0 + - - +
62B SER* 1.3 82.8 - - - +
64B ASP* 1.3 57.8 + - - +
65B PRO* 3.3 11.9 - - - +
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Residues in contact with ASP 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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37B ARG* 2.6 58.2 + - - +
38B ILE* 4.7 3.4 - - + +
41B LYS* 4.7 12.5 + - + -
60B GLU 3.1 14.3 + - - +
61B VAL 3.2 3.5 + - - +
63B LYS* 1.3 76.9 - - - +
65B PRO* 1.3 65.1 - - - +
66B GLU 3.1 9.6 + - - -
67B LEU* 2.9 19.0 + - + +
68B SER* 2.8 27.0 + - - -
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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