Contacts of the helix formed by residues 47 - 63 (chain B) in PDB entry 1F5Q
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 GLN 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B THR 5.1 0.9 - - - +
46B SER* 1.3 73.3 - - - +
48B TYR* 1.3 64.1 + - - +
49B ARG 3.2 0.7 - - - -
50B LYS* 3.2 37.5 + - - +
51B VAL* 3.3 17.0 + - + +
247B TYR* 4.0 13.8 + - + +
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Residues in contact with TYR 48 (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 GLN 5.2 0.2 - - - -
43B HIS* 2.4 48.8 + + - +
46B SER* 3.2 31.4 - - - -
47B GLN* 1.3 77.8 - - - +
49B ARG* 1.3 66.7 + - - +
51B VAL* 3.5 6.8 + - - +
52B LEU* 3.1 38.5 + - + +
81B PHE* 3.6 21.0 - + - -
88B ARG* 6.3 0.4 - - + -
91B TYR* 3.6 36.4 + + + -
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B HIS* 3.5 32.5 - - + +
44B PHE* 3.5 25.4 - - - +
46B SER* 3.3 19.1 + - - +
47B GLN 3.2 0.6 - - - -
48B TYR* 1.3 87.9 - - + +
50B LYS* 1.3 65.4 + - + +
52B LEU* 4.0 4.9 - - + +
53B THR* 3.1 40.5 + - + +
74B VAL* 3.6 12.5 - - - +
77B LEU* 5.9 3.4 - - + -
78B ASP* 3.0 35.5 + - - -
182B LEU 3.0 28.9 + - - -
183B CYS 4.0 12.5 + - - -
185B GLY 4.2 7.3 - - - +
188B ALA* 3.5 12.0 - - - +
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE 5.8 2.2 - - - +
45B THR 3.9 12.0 + - - -
46B SER 3.5 20.4 - - - +
47B GLN* 3.4 26.4 + - - +
48B TYR 3.2 0.4 - - - -
49B ARG* 1.3 79.5 - - + +
51B VAL* 1.3 60.8 + - - +
53B THR* 3.3 4.1 + - - -
54B THR* 2.9 33.6 + - + +
183B CYS 4.7 13.2 - - - +
185B GLY 6.2 1.3 - - - +
186B ARG* 5.9 5.1 - - - +
247B TYR* 3.4 37.9 + - + +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN* 3.3 13.4 + - + +
48B TYR* 3.9 9.2 - - - +
50B LYS* 1.3 77.0 - - - +
52B LEU* 1.3 66.4 + - + +
54B THR* 3.2 7.4 + - - -
55B TRP* 3.0 33.8 + - + +
92B GLN* 5.3 5.4 - - - +
247B TYR* 3.8 17.7 - - + -
248B PHE* 3.3 26.4 - - + +
251B ASN* 4.6 3.4 - - + -
252B ALA* 4.2 25.6 - - + +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B HIS* 6.0 0.2 - - + -
48B TYR* 3.1 34.4 + - + +
49B ARG* 4.0 5.4 - - + +
50B LYS 3.4 0.2 - - - -
51B VAL* 1.3 87.8 - - + +
53B THR* 1.3 57.1 + - - +
55B TRP* 3.6 4.6 - - - +
56B MET* 3.1 35.6 + - - +
77B LEU* 4.1 13.5 - - + -
81B PHE* 3.6 34.5 - - + -
91B TYR* 4.2 13.2 - - + +
92B GLN* 4.4 28.3 - - - +
95B ALA* 3.9 16.4 - - + -
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ARG* 3.1 49.6 + - + +
50B LYS 3.3 4.9 + - - -
52B LEU* 1.3 72.7 - - - +
54B THR* 1.3 63.2 + - - +
55B TRP 3.2 1.6 - - - -
56B MET* 3.6 5.8 + - - -
57B PHE* 3.0 27.2 + - - +
70B PHE* 3.4 7.7 - - - -
74B VAL* 4.4 18.6 - - + -
77B LEU* 4.9 9.9 - - + -
182B LEU 4.3 3.1 - - - +
183B CYS* 3.6 31.0 + - - +
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Residues in contact with THR 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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50B LYS* 2.9 22.4 + - + +
51B VAL 3.2 5.0 + - - -
53B THR* 1.3 78.9 - - - +
55B TRP* 1.3 64.9 + - - +
57B PHE* 3.5 8.1 - - - +
58B CYS* 3.1 28.2 + - - -
183B CYS* 4.6 13.9 - - + +
243B PHE* 4.7 7.6 - - + -
244B ASP 3.9 23.6 - - - +
245B GLU* 4.3 3.4 - - - -
247B TYR* 4.0 7.4 - - + -
248B PHE* 3.3 25.0 + - - +
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Residues in contact with TRP 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 VAL* 3.0 20.3 + - + +
52B LEU* 3.6 4.5 - - - +
54B THR* 1.3 74.4 + - - +
56B MET* 1.3 85.0 + - + +
57B PHE 3.0 0.9 - - - -
58B CYS* 3.0 4.5 + - - +
59B VAL* 2.9 44.9 + - + +
92B GLN* 3.1 36.9 - - - +
95B ALA* 3.9 21.8 - - + -
96B ALA* 4.2 15.3 - - + -
99B LEU* 3.7 26.2 - - + -
116B LEU* 4.5 5.4 - - + -
119B LEU* 4.5 24.7 + - + +
120B CYS* 4.2 10.1 - - - -
248B PHE* 3.6 38.1 - + + -
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Residues in contact with MET 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 LEU 3.1 18.9 + - - +
53B THR* 3.9 7.2 - - - +
55B TRP* 1.3 97.7 - - + +
57B PHE* 1.3 57.3 + - - +
59B VAL* 3.3 2.7 + - - +
60B CYS* 2.9 33.6 + - - -
70B PHE* 4.3 7.9 - - + -
73B ALA* 3.3 44.4 - - + +
74B VAL* 4.8 6.1 - - - -
77B LEU* 3.8 23.6 - - - -
95B ALA* 3.1 24.9 - - + +
98B ALA* 3.8 3.6 - - + -
99B LEU* 3.4 21.5 - - + +
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Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B THR 3.0 19.0 + - - +
54B THR* 3.5 8.7 - - - +
55B TRP 3.0 0.6 - - - -
56B MET* 1.3 75.3 - - - +
58B CYS* 1.3 76.7 + - - +
60B CYS* 3.4 4.6 + - + +
61B LYS* 3.0 37.6 + - + +
70B PHE* 3.6 34.7 - + + -
179B PHE* 3.9 26.5 - + + -
183B CYS* 5.0 0.9 - - - -
243B PHE* 3.8 36.3 - + + -
245B GLU* 4.5 18.4 - - + -
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Residues in contact with CYS 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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54B THR 3.1 9.9 + - - +
55B TRP 3.0 4.8 + - - +
57B PHE* 1.3 83.9 - - - +
59B VAL* 1.3 56.9 + - + +
61B LYS* 3.1 10.7 + - - +
62B ASP* 2.7 48.9 + - - +
245B GLU* 3.3 46.9 - - - -
246B ASN* 5.6 1.8 - - - -
248B PHE* 3.8 16.2 - - + -
249B LYS* 5.7 2.5 - - - -
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Residues in contact with VAL 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 TRP* 2.9 53.6 + - + +
56B MET* 3.5 8.5 - - - +
58B CYS* 1.3 77.6 - - + +
60B CYS* 1.3 58.3 + - - +
62B ASP* 3.8 6.9 - - - +
63B LEU* 2.9 43.0 + - + +
99B LEU* 4.0 17.7 - - + -
116B LEU* 4.3 5.8 - - + -
119B LEU* 4.0 27.6 - - + -
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Residues in contact with CYS 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 MET 2.9 20.5 + - - +
57B PHE* 3.7 5.2 - - + +
59B VAL* 1.3 75.3 - - - +
61B LYS* 1.3 63.4 + - - +
64B ARG* 3.1 2.1 + - - -
65B GLN* 2.9 45.4 + - + +
66B ASP 5.6 1.3 - - - +
69B VAL* 4.1 10.5 - - - -
70B PHE* 3.7 35.7 - - + -
99B LEU* 3.8 22.9 - - - -
111B ILE* 6.0 0.2 - - - -
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Residues in contact with LYS 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 PHE* 3.0 30.0 + - + +
58B CYS* 3.6 16.5 - - - +
60B CYS* 1.3 75.8 - - - +
62B ASP* 1.3 77.8 + - - +
64B ARG* 3.1 18.5 + - - +
245B GLU* 2.9 33.8 + - - +
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Residues in contact with ASP 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 CYS* 2.7 34.2 + - - +
59B VAL* 3.8 6.5 + - - +
61B LYS* 1.3 77.3 - - - +
63B LEU* 1.3 63.3 + - + +
64B ARG* 2.8 23.3 + - - +
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Residues in contact with LEU 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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59B VAL* 2.9 37.5 + - + +
62B ASP* 1.3 76.1 - - + +
64B ARG* 1.3 69.4 + - - +
65B GLN* 3.4 26.8 + - + +
109B MET* 6.0 1.6 - - - +
111B ILE* 4.3 25.1 - - + -
112B LYS 5.8 1.1 - - - +
115B GLN* 3.3 32.5 - - + +
116B LEU* 5.3 2.7 - - + -
119B LEU* 4.5 15.3 - - + -
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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
------------------------------------------------------------
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