Contacts of the helix formed by residues 39 - 56 (chain F) in PDB entry 5U07
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 39 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ASN* 2.7 26.7 + - - +
26F LYS* 3.3 11.8 + - - -
37F ARG* 3.6 17.0 - - - +
38F VAL* 1.3 74.7 - - - +
40F SER* 1.3 63.8 + - - +
41F GLN* 3.4 23.1 + - - -
42F SER* 2.9 26.3 + - - -
43F TRP* 3.5 4.7 + - - +
190F HIS* 3.2 10.3 - - - -
27K C 3.1 14.0 + - - -
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Residues in contact with SER 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F VAL 3.5 1.1 + - - -
39F SER* 1.3 69.2 - - - +
41F GLN* 1.3 67.7 + - - +
43F TRP 3.6 0.3 + - - -
44F LYS* 2.8 34.7 + - - +
188F PHE* 3.3 32.9 - - - -
189F ALA 4.1 1.8 - - - -
190F HIS* 2.9 26.5 + - - -
274G ALA* 2.7 35.7 + - - +
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Residues in contact with GLN 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LYS* 3.7 0.8 - - - +
39F SER* 3.4 15.8 - - - -
40F SER* 1.3 87.9 + - - +
42F SER* 1.3 59.4 + - - +
44F LYS* 3.6 10.3 - - - +
45F ARG* 2.9 27.2 + - - +
190F HIS* 4.2 6.8 + - - -
202G ASP* 3.7 11.4 + - - +
204G PHE* 3.4 26.5 - - - +
226G PHE* 5.8 2.3 - - - -
274G ALA* 5.6 3.5 - - - +
25K U 3.7 41.1 - - + +
26K G 3.7 18.9 + - - +
27K C 3.1 18.5 + - - +
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Residues in contact with SER 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ASN* 2.9 19.1 + - - -
38F VAL* 3.6 6.1 - - - +
39F SER* 2.9 25.0 + - - -
41F GLN* 1.3 78.0 - - - +
43F TRP* 1.3 76.6 + - - +
45F ARG* 3.0 14.4 + - - +
46F ALA* 3.0 11.6 + - - +
268F PRO* 4.3 12.4 - - - +
26K G 2.9 35.9 - - - -
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Residues in contact with TRP 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F GLN* 3.7 14.6 - - - -
12F LEU* 5.2 7.2 - - + -
17F ILE* 5.0 6.3 - - + -
38F VAL* 4.5 13.0 - - + +
39F SER 3.5 6.5 + - - +
40F SER 4.2 0.2 - - - +
42F SER* 1.3 83.1 + - - +
44F LYS* 1.3 62.7 + - - +
46F ALA* 3.1 4.0 + - + +
47F VAL* 2.9 38.6 + - + +
188F PHE* 3.3 31.6 - + + -
191F ALA* 5.4 5.8 - - + -
231F PHE* 5.7 2.7 - + - -
233F ARG* 3.1 56.3 - - - +
263F PHE 3.7 2.0 + - - -
266F THR* 2.9 33.1 + - - -
267F VAL* 4.4 2.9 - - + -
268F PRO* 3.6 32.1 - - + -
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Residues in contact with LYS 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F SER* 2.8 22.8 + - - +
41F GLN* 3.6 7.4 - - - +
43F TRP* 1.3 76.9 - - - +
45F ARG* 1.3 58.4 + - - +
47F VAL* 3.4 6.2 + - - +
48F ARG* 2.9 31.4 + - + +
170F PHE* 3.6 42.1 + - + +
186F VAL 4.7 3.0 + - - -
188F PHE* 3.8 28.2 - - + -
273G ASN* 2.9 29.9 + - - +
274G ALA* 4.4 4.8 - - - +
25K U 3.0 31.0 + - - +
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Residues in contact with ARG 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F GLN 2.9 13.8 + - - +
42F SER 3.0 8.9 + - - +
44F LYS* 1.3 77.9 - - - +
46F ALA* 1.3 64.6 + - - +
48F ARG* 3.1 18.4 - - + +
49F HIS* 2.9 54.9 + - + +
268F PRO 5.6 4.0 + - - -
269F SER* 5.8 1.0 + - - -
207G VAL* 3.3 33.0 - - - +
209G ASP* 4.9 2.6 + - - -
26K G 3.1 63.7 + - - +
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Residues in contact with ALA 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F SER 3.0 8.5 + - - +
43F TRP* 3.6 8.3 - - + +
45F ARG* 1.3 78.3 - - - +
47F VAL* 1.3 62.4 + - - +
49F HIS* 3.1 8.9 + - - +
50F GLU 3.0 18.5 + - - -
266F THR* 3.7 18.6 - - - +
267F VAL 4.1 9.4 - - - +
268F PRO* 3.9 32.1 - - + +
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Residues in contact with VAL 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F TRP* 2.9 35.3 + - + +
44F LYS* 3.8 5.8 - - - +
46F ALA* 1.3 74.8 - - - +
48F ARG* 1.3 64.2 - - - +
50F GLU* 3.2 3.6 + - - +
51F VAL* 2.9 23.4 + - + +
170F PHE* 4.3 5.4 - - + -
188F PHE* 4.8 2.5 - - + -
259F PHE* 3.7 35.4 - - + -
262F ALA* 4.0 11.4 - - + +
263F PHE* 3.8 19.5 - - + +
266F THR* 3.3 23.8 - - - +
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Residues in contact with ARG 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F LYS* 2.9 17.3 + - - +
45F ARG* 3.1 32.2 - - - +
47F VAL* 1.3 77.4 - - - +
49F HIS* 1.3 79.5 + - + +
51F VAL* 3.3 5.3 + - - +
52F GLU* 2.5 60.2 + - - +
59F ALA 3.5 16.6 + - - -
61F ARG* 5.3 8.4 - - - +
118F TYR* 2.9 46.1 + - - -
166F SER* 4.1 3.6 - - - +
170F PHE* 3.6 25.8 - - + -
207G VAL* 5.8 1.8 - - - +
209G ASP* 4.3 14.1 + - - -
26K G 5.2 7.0 + - - -
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Residues in contact with HIS 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F ARG* 2.9 69.4 + - + +
46F ALA* 3.1 6.9 + - - +
48F ARG* 1.3 99.1 + - + +
50F GLU* 1.3 58.0 + - - +
52F GLU* 4.0 7.4 + - - +
53F ALA* 2.9 30.7 + - - +
59F ALA 6.0 1.6 - - - -
209G ASP* 4.7 9.3 + - - -
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Residues in contact with GLU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E ASP 5.5 2.6 - - - +
46F ALA 3.0 7.7 + - - +
47F VAL 3.2 3.3 + - - +
49F HIS* 1.3 78.3 - - - +
51F VAL* 1.3 56.1 + - - +
53F ALA* 3.6 6.7 - - + +
54F ARG* 2.8 39.5 + - + +
261F ARG* 4.4 12.2 + - - +
262F ALA* 4.1 10.8 - - + -
265F SER* 3.7 22.6 + - - -
266F THR* 2.9 35.5 - - + +
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Residues in contact with VAL 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F VAL* 2.9 23.8 + - + +
48F ARG* 3.7 6.3 - - - +
50F GLU* 1.3 75.1 - - - +
52F GLU* 1.3 65.5 + - - +
54F ARG* 4.8 2.9 - - - -
55F LEU* 3.0 26.3 + - + +
165F VAL* 3.9 22.0 - - + -
166F SER* 4.7 7.4 - - - +
169F LEU* 5.0 6.3 - - + -
170F PHE* 5.9 2.0 - - + -
258F GLU* 3.6 25.4 - - + +
259F PHE* 4.0 24.7 - - + +
262F ALA* 3.8 18.4 - - + -
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Residues in contact with GLU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F ARG* 2.5 56.8 + - - +
49F HIS* 3.9 10.2 + - - +
51F VAL* 1.3 77.1 - - + +
53F ALA* 1.3 62.1 + - - +
55F LEU* 5.4 0.2 - - - -
56F GLY* 3.2 21.8 + - - -
57F ASP 3.0 26.8 - - - +
58F LYS* 3.6 15.7 + - + +
59F ALA* 3.0 32.8 - - - +
164F ASN* 3.9 1.9 + - - +
166F SER* 2.4 36.5 + - - +
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Residues in contact with ALA 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F HIS 2.9 19.3 + - - +
50F GLU* 3.6 9.4 - - + +
52F GLU* 1.3 79.1 - - - +
54F ARG* 1.3 59.6 + - - +
56F GLY* 4.0 5.2 + - - -
58F LYS* 4.4 13.9 - - - +
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Residues in contact with ARG 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLU* 2.8 29.2 + - + +
51F VAL* 4.1 3.6 - - - +
53F ALA* 1.3 73.4 - - - +
55F LEU* 1.3 63.2 + - - +
56F GLY 3.4 0.4 + - - -
258F GLU* 4.7 24.2 - - + +
261F ARG* 3.1 51.7 - - - +
262F ALA* 6.4 1.6 - - - +
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F VAL* 3.0 13.4 + - + +
52F GLU* 5.4 0.2 - - - -
54F ARG* 1.3 78.8 - - - +
56F GLY* 1.3 57.2 + - - +
57F ASP* 3.2 13.5 + - + +
165F VAL* 3.5 26.9 - - + -
254F THR* 4.9 16.4 - - - +
255F ALA* 5.5 1.6 - - + -
258F GLU* 3.0 40.6 - - - +
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Residues in contact with GLY 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F GLU 3.2 11.9 + - - -
53F ALA 4.0 4.6 + - - -
54F ARG 3.4 3.2 - - - -
55F LEU* 1.3 76.5 - - - +
57F ASP* 1.3 60.1 + - - +
58F LYS* 3.6 13.1 + - - +
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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