Contacts of the helix formed by residues 39 - 56 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ASN* 3.6 8.1 - - - +
26E LYS* 3.0 19.6 + - - +
37E ARG* 2.6 27.5 + - - +
38E VAL* 1.3 77.6 - - - +
40E SER* 1.3 64.7 + - - +
41E GLN* 3.3 25.8 + - - -
42E SER* 3.0 19.3 + - - -
43E TRP* 3.5 5.7 + - - +
190E HIS* 3.3 9.8 - - - -
202F ASP* 5.2 0.5 - - - +
33K G 3.3 10.8 - - - -
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Residues in contact with SER 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E VAL 3.5 0.6 + - - -
39E SER* 1.3 73.8 - - - +
41E GLN* 1.3 65.1 + - - +
44E LYS* 2.9 33.8 + - - +
188E PHE* 3.2 46.1 - - - -
189E ALA 4.2 1.3 - - - -
190E HIS* 3.1 24.8 + - - -
274F ALA* 2.7 26.1 + - - +
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Residues in contact with GLN 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LYS* 3.9 1.8 - - - +
39E SER* 3.3 15.5 + - - -
40E SER* 1.3 90.2 + - - +
42E SER* 1.3 59.2 + - - +
44E LYS* 3.3 8.8 + - - +
45E ARG 2.9 22.2 + - - -
190E HIS* 4.3 8.0 + - - -
202F ASP* 5.4 6.2 + - - +
203F PHE 4.8 0.2 + - - -
204F PHE* 3.5 24.8 - - - +
226F PHE* 5.6 2.6 - - - -
274F ALA* 5.6 3.5 - - + +
31K G 3.8 40.6 - - + +
32K U 3.4 17.6 + - - +
33K G 2.7 28.6 + - - +
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Residues in contact with SER 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ASN* 2.4 35.0 + - - -
38E VAL* 3.7 3.3 - - - +
39E SER 3.0 9.8 + - - -
41E GLN* 1.3 78.6 - - - +
43E TRP* 1.3 71.3 + - - +
45E ARG* 2.9 19.6 + - - +
46E ALA* 3.0 11.8 + - - +
268E PRO* 4.3 8.8 - - - +
32K U 3.1 39.6 + - - -
33K G 4.1 1.1 - - - -
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Residues in contact with TRP 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLN* 3.8 12.8 - - - -
12E LEU* 5.3 10.8 - - + -
38E VAL* 4.4 14.4 - - + -
39E SER 3.5 6.7 + - - +
42E SER* 1.3 81.3 + - - +
44E LYS* 1.3 63.8 + - - +
46E ALA* 3.1 3.0 + - - +
47E VAL* 2.9 40.1 + - + +
188E PHE* 3.4 36.3 - + + -
191E ALA* 5.5 5.2 - - + -
231E PHE* 5.6 2.9 - + - -
233E ARG* 3.0 55.1 - - + +
263E PHE* 3.7 1.7 + - - -
266E THR* 3.1 32.7 - - + +
267E VAL* 4.6 2.5 - - + -
268E PRO* 3.5 35.7 - - + -
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Residues in contact with LYS 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E SER* 2.9 21.7 + - - +
41E GLN* 3.5 5.8 - - - +
42E SER 3.1 0.2 - - - -
43E TRP* 1.3 77.9 - - - +
45E ARG* 1.3 59.1 + - - +
47E VAL* 3.4 7.1 + - - +
48E ARG* 2.9 29.8 + - + +
170E PHE* 3.4 46.1 + - + +
186E VAL 4.6 3.9 + - - -
188E PHE* 4.1 24.1 - - + -
273F ASN* 3.4 27.3 + - - +
274F ALA* 4.4 6.1 - - - +
31K G 4.3 34.7 + - - +
32K U 6.0 0.2 - - - +
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Residues in contact with ARG 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E GLN 2.9 5.9 + - - +
42E SER* 2.9 11.4 + - - +
44E LYS* 1.3 74.1 - - - +
46E ALA* 1.3 66.9 + - - +
48E ARG* 3.0 22.9 - - + +
49E HIS* 2.9 55.8 + - + +
268E PRO 5.7 3.0 + - - -
269E SER* 5.9 1.0 + - - -
207F VAL* 4.1 23.4 - - - +
209F ASP* 5.1 3.0 + - - -
32K U 3.2 73.6 + - - +
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Residues in contact with ALA 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E SER 3.0 8.4 + - - +
43E TRP* 3.1 8.2 + - - +
45E ARG* 1.3 78.3 - - - +
47E VAL* 1.3 61.5 + - - +
49E HIS* 3.2 9.9 + - - +
50E GLU* 3.0 19.4 + - - +
266E THR* 3.3 29.2 + - + +
267E VAL 4.1 2.0 - - - +
268E PRO* 3.8 29.8 - - + +
269E SER* 5.8 0.2 - - - +
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Residues in contact with VAL 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E TRP* 2.9 43.4 + - + +
44E LYS* 3.7 7.0 - - - +
46E ALA* 1.3 75.2 - - - +
48E ARG* 1.3 59.4 + - - +
50E GLU* 3.2 3.8 + - - +
51E VAL* 2.9 34.5 + - + +
170E PHE* 4.1 6.5 - - + -
188E PHE* 5.6 1.3 - - + -
259E PHE* 3.7 36.3 - - + +
262E ALA* 4.2 7.1 - - + +
263E PHE* 3.9 17.0 - - + -
266E THR* 3.5 13.2 - - + -
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Residues in contact with ARG 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LYS* 2.9 17.1 + - - +
45E ARG* 3.0 34.7 + - - +
47E VAL* 1.3 77.8 - - - +
49E HIS* 1.3 75.6 + - - +
51E VAL* 4.4 4.3 - - - -
52E GLU* 2.9 42.0 + - - +
59E ALA* 3.5 29.7 + - - +
61E ARG* 5.1 9.6 - - - +
118E TYR* 3.2 41.8 + - - -
166E SER* 3.8 10.6 + - - +
170E PHE* 3.7 24.5 - - + -
209F ASP* 3.9 21.4 + - - -
32K U 5.2 6.9 + - - -
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Residues in contact with HIS 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ARG* 2.9 72.4 + - + +
46E ALA* 3.2 7.2 + - - +
48E ARG* 1.3 87.5 + - + +
50E GLU* 1.3 59.8 + - - +
52E GLU* 2.7 28.8 + - - +
53E ALA* 2.9 32.3 + - - +
209F ASP* 4.7 8.3 + - - -
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Residues in contact with GLU 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E ALA 3.0 15.0 + - - +
47E VAL 3.9 3.1 - - - +
49E HIS* 1.3 78.8 - - - +
51E VAL* 1.3 57.1 + - - +
53E ALA* 3.8 4.4 - - + +
54E ARG* 2.9 42.3 + - + +
261E ARG* 4.7 8.7 + - - +
262E ALA* 4.1 16.4 - - + -
265E SER* 3.3 24.5 + - - -
266E THR* 3.6 26.4 + - - +
291I ASP 5.6 1.4 - - - +
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Residues in contact with VAL 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E VAL* 2.9 25.7 + - + +
48E ARG* 3.9 5.8 - - - +
50E GLU* 1.3 76.0 - - - +
52E GLU* 1.3 61.3 + - - +
54E ARG* 4.0 2.9 - - - +
55E LEU* 2.9 37.0 + - + +
165E VAL* 3.9 28.5 - - + -
166E SER* 4.7 7.2 - - - +
169E LEU* 4.9 8.3 - - + -
170E PHE* 5.9 1.3 - - + -
255E ALA 5.6 1.6 - - - +
258E GLU* 4.0 10.0 - - + +
259E PHE* 3.9 24.2 - - + +
262E ALA* 3.8 19.1 - - + -
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Residues in contact with GLU 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ARG* 2.9 39.1 + - - +
49E HIS* 2.7 43.7 + - - +
51E VAL* 1.3 77.6 - - - +
53E ALA* 1.3 57.6 + - - +
56E GLY* 3.0 27.2 + - - -
57E ASP* 3.1 27.4 - - - +
58E LYS* 3.4 23.5 - - + +
59E ALA* 3.1 32.7 + - - +
164E ASN* 5.7 0.2 - - - -
165E VAL* 6.4 0.2 - - - -
166E SER* 4.1 9.2 - - - +
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Residues in contact with ALA 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E HIS 2.9 21.4 + - - +
50E GLU* 3.8 6.5 - - + +
52E GLU* 1.3 79.3 - - + +
54E ARG* 1.3 59.6 + - - +
56E GLY* 4.0 5.7 + - - -
58E LYS* 5.4 6.3 - - - +
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Residues in contact with ARG 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLU* 2.9 26.6 + - + +
51E VAL* 4.0 2.9 - - - +
53E ALA* 1.3 76.2 - - - +
55E LEU* 1.3 62.5 + - + +
56E GLY 3.3 0.4 + - - -
258E GLU* 3.8 37.4 + - + +
261E ARG* 3.0 50.8 - - - +
262E ALA* 6.2 2.7 - - - +
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Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL* 2.9 20.8 + - + +
54E ARG* 1.3 77.7 - - + +
56E GLY* 1.3 56.0 + - - +
57E ASP* 3.3 16.6 + - - +
165E VAL* 3.5 41.3 - - + -
254E THR* 5.0 13.9 - - - +
255E ALA* 4.9 11.9 - - - -
258E GLU* 4.8 24.2 - - + -
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Residues in contact with GLY 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E GLU 3.0 12.5 + - - -
53E ALA 4.0 5.1 + - - -
54E ARG 3.3 3.6 - - - -
55E LEU* 1.3 75.1 - - - +
57E ASP* 1.3 59.6 + - - +
58E LYS* 3.6 9.6 + - - +
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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
------------------------------------------------------------
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