Contacts of the helix formed by residues 39 - 56 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ASN* 2.7 24.1 + - - +
26I LYS* 3.1 21.1 + - - +
37I ARG* 3.6 12.9 - - - +
38I VAL* 1.3 75.6 - - - +
40I SER* 1.3 62.4 + - - +
41I GLN* 3.3 28.9 + - - -
42I SER* 2.9 29.5 + - - -
43I TRP* 3.5 5.7 + - - +
190I HIS* 3.5 10.1 - - - -
38K G 4.4 0.2 + - - -
39K U 4.0 2.3 + - - -
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Residues in contact with SER 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E ALA* 2.8 21.4 + - - +
38I VAL 3.6 1.2 + - - -
39I SER* 1.3 70.5 - - - +
41I GLN* 1.3 67.3 + - - +
43I TRP 3.5 0.3 + - - -
44I LYS* 2.8 33.5 + - - +
188I PHE* 3.3 43.7 - - - -
189I ALA 4.0 3.1 - - - -
190I HIS* 3.0 31.6 + - - -
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Residues in contact with GLN 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E ASP* 4.2 11.8 + - - +
203E PHE 4.5 2.6 + - - -
204E PHE* 3.5 20.2 - - - +
226E PHE* 6.0 1.0 - - - -
274E ALA* 6.1 0.3 - - - +
26I LYS* 4.8 1.2 - - - +
39I SER* 3.3 19.5 - - - -
40I SER* 1.3 88.8 + - - +
42I SER* 1.3 63.7 + - - +
44I LYS* 3.4 9.8 + - - +
45I ARG* 3.0 23.2 + - - +
190I HIS* 4.1 7.4 + - - -
37K U 3.6 35.5 + - + +
38K G 3.9 10.6 + - - +
39K U 2.8 29.2 + - - +
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Residues in contact with SER 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ASN* 2.9 23.7 + - - -
38I VAL* 3.8 7.4 - - - +
39I SER* 2.9 16.4 + - - -
40I SER 3.3 0.2 - - - -
41I GLN* 1.3 79.9 - - - +
43I TRP* 1.3 71.2 + - - +
45I ARG* 3.0 5.9 + - - +
46I ALA* 2.9 22.3 + - - +
268I PRO* 4.9 9.8 - - - +
38K G 3.0 37.9 - - - -
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Residues in contact with TRP 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I VAL* 5.6 7.0 - - + -
39I SER 3.5 5.3 + - - +
40I SER 3.5 1.4 + - - +
41I GLN 3.5 0.2 - - - -
42I SER* 1.3 83.5 + - - +
44I LYS* 1.3 63.9 + - - +
46I ALA* 4.4 6.5 - - - +
47I VAL* 2.9 32.2 + - + +
188I PHE* 3.4 31.0 - - + -
233I ARG* 5.5 6.7 - - - +
268I PRO* 4.8 14.1 - - + -
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Residues in contact with LYS 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E ASN* 3.5 28.1 + - - +
274E ALA* 4.3 7.0 - - - +
40I SER* 2.8 21.1 + - - +
41I GLN* 3.7 7.6 - - - +
43I TRP* 1.3 76.4 - - - +
45I ARG* 1.3 58.0 + - - +
47I VAL* 3.8 4.6 - - - +
48I ARG* 2.9 31.1 + - + +
170I PHE* 3.4 45.0 + - + -
186I VAL 4.7 4.9 + - - -
188I PHE* 4.0 26.9 - - + -
36K C 6.1 0.2 - - - -
37K U 4.0 31.7 + - - +
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Residues in contact with ARG 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E VAL* 3.4 33.4 - - - +
209E ASP* 4.8 3.4 + - - -
41I GLN 3.0 12.4 + - - +
42I SER 3.0 9.0 + - - +
44I LYS* 1.3 74.6 - - - +
46I ALA* 1.3 66.3 + - - +
48I ARG* 3.0 20.2 - - + +
49I HIS* 2.9 58.2 + - + +
38K G 2.9 74.0 + - - +
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Residues in contact with ALA 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I SER 2.9 14.6 + - - +
43I TRP* 3.9 5.6 - - - +
45I ARG* 1.3 78.9 - - - +
47I VAL* 1.3 64.7 + - + +
49I HIS* 3.2 10.1 + - - +
50I GLU* 3.0 22.7 + - - +
266I THR* 4.4 16.7 - - + +
267I VAL 5.0 0.2 - - - +
268I PRO* 4.1 28.7 - - + +
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Residues in contact with VAL 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I TRP* 2.9 25.2 + - + +
44I LYS* 3.8 5.2 - - - +
46I ALA* 1.3 76.8 - - + +
48I ARG* 1.3 59.2 + - - +
50I GLU* 3.2 7.4 + - - +
51I VAL* 2.9 29.4 + - + +
170I PHE* 4.0 5.8 - - + -
188I PHE* 5.2 3.4 - - + -
233I ARG* 5.8 1.6 - - - +
259I PHE* 3.6 37.5 - - + +
262I ALA* 4.1 15.9 - - + +
263I PHE* 4.1 31.9 - - + +
266I THR* 5.4 4.0 - - - -
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Residues in contact with ARG 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E ASP* 3.9 17.4 + - - -
44I LYS* 2.9 16.9 + - - +
45I ARG* 3.0 29.2 - - - +
47I VAL* 1.3 76.6 - - - +
49I HIS* 1.3 76.9 + - - +
51I VAL* 3.4 5.4 + - - +
52I GLU* 2.9 40.7 + - - +
59I ALA* 3.3 32.5 + - - +
61I ARG* 5.0 10.3 - - - +
118I TYR* 3.1 32.9 + - - -
166I SER* 3.0 24.4 + - - +
170I PHE* 3.6 26.7 - - + -
38K G 5.5 3.4 - - - -
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Residues in contact with HIS 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E ASP* 4.1 17.2 + - - -
45I ARG* 2.9 68.9 + - + +
46I ALA* 3.5 9.4 - - - +
48I ARG* 1.3 86.0 + - + +
50I GLU* 1.3 61.4 + - - +
52I GLU* 2.6 30.7 + - - +
53I ALA* 2.9 30.2 + - - +
59I ALA 6.1 0.2 - - - -
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Residues in contact with GLU 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ALA 3.0 12.8 + - - +
47I VAL* 3.7 7.0 - - - +
49I HIS* 1.3 77.5 - - - +
51I VAL* 1.3 59.2 + - - +
53I ALA* 3.7 6.2 - - + +
54I ARG* 2.9 53.8 + - - +
258I GLU 4.6 1.2 - - - +
261I ARG* 6.1 1.0 - - - +
262I ALA* 3.2 24.8 + - + +
265I SER* 5.9 3.5 - - - -
266I THR* 3.2 29.6 - - + +
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Residues in contact with VAL 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I VAL* 2.9 23.5 + - + +
48I ARG* 3.8 7.2 - - - +
50I GLU* 1.3 77.8 - - - +
52I GLU* 1.3 64.7 + - - +
54I ARG* 3.2 2.8 + - - +
55I LEU* 2.9 25.6 + - + +
165I VAL* 4.1 17.5 - - + -
166I SER* 5.2 7.2 - - - +
169I LEU* 4.7 10.3 - - + -
170I PHE* 5.8 0.2 - - + -
258I GLU* 3.5 28.4 - - + +
259I PHE* 4.0 23.3 - - + +
262I ALA* 3.9 16.8 - - + -
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Residues in contact with GLU 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I ARG* 2.9 24.1 + - - +
49I HIS* 2.6 49.3 + - - +
51I VAL* 1.3 76.9 - - - +
53I ALA* 1.3 61.6 + - - +
55I LEU* 5.3 0.7 - - - -
56I GLY* 3.0 22.3 + - - -
57I ASP 3.1 27.3 - - - +
58I LYS* 3.4 21.0 + - + +
59I ALA 3.1 34.4 + - - +
164I ASN* 5.1 1.6 - - - +
166I SER* 5.4 6.3 - - - -
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Residues in contact with ALA 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I HIS 2.9 19.9 + - - +
50I GLU* 3.7 7.6 - - + +
51I VAL 3.2 0.2 - - - -
52I GLU* 1.3 78.7 - - - +
54I ARG* 1.3 59.2 + - - +
56I GLY* 4.0 5.7 + - - -
58I LYS* 3.9 18.8 + - - +
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Residues in contact with ARG 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLU* 2.9 41.3 + - - +
51I VAL* 4.0 3.4 - - - +
53I ALA* 1.3 78.7 - - - +
55I LEU* 1.3 63.8 + - + +
56I GLY 3.3 0.6 + - - -
258I GLU* 4.7 20.5 - - + +
261I ARG* 3.7 39.4 - - - +
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Residues in contact with LEU 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I VAL* 2.9 13.4 + - + +
52I GLU* 5.3 0.4 - - - -
54I ARG* 1.3 79.0 - - + +
56I GLY* 1.3 56.1 + - - +
57I ASP* 3.2 14.1 + - + +
165I VAL* 3.7 26.2 - - + -
254I THR* 5.0 13.5 - - - +
255I ALA* 5.7 0.9 - - - -
258I GLU* 3.0 41.5 - - - +
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Residues in contact with GLY 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I GLU 3.0 12.4 + - - -
53I ALA 4.0 5.3 + - - -
54I ARG 3.3 3.2 + - - -
55I LEU* 1.3 76.1 - - - +
57I ASP* 1.3 59.0 + - - +
58I LYS* 3.6 13.0 + - - +
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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
------------------------------------------------------------
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