Contacts of the helix formed by residues 39 - 56 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ASN* 2.6 26.1 + - - +
26G LYS* 3.3 19.0 + - - -
37G ARG* 3.7 15.1 + - - +
38G VAL* 1.3 75.1 - - - +
40G SER* 1.3 63.3 + - - +
41G GLN* 3.5 14.9 + - - -
42G SER* 2.9 23.9 + - - -
43G TRP* 3.5 5.9 + - - +
190G HIS* 3.3 11.0 - - - -
21K G 3.0 15.4 + - - -
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Residues in contact with SER 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G VAL 3.6 0.6 + - - -
39G SER* 1.3 72.1 - - - +
41G GLN* 1.3 65.1 + - - +
44G LYS* 2.9 33.7 + - - +
188G PHE* 3.2 42.8 - - - -
189G ALA 4.0 3.8 - - - -
190G HIS* 3.0 24.8 + - - -
274H ALA* 2.6 26.8 + - - +
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Residues in contact with GLN 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LYS* 3.8 0.2 - - - +
39G SER* 3.5 12.1 - - - -
40G SER* 1.3 90.0 + - - +
42G SER* 1.3 56.8 + - - +
44G LYS* 3.5 11.3 - - - +
45G ARG* 2.9 26.5 + - - +
190G HIS* 4.2 6.8 + - - -
202H ASP* 3.3 24.9 + - - +
204H PHE* 3.5 11.0 - - - +
226H PHE* 5.7 3.3 - - - -
274H ALA* 5.7 3.3 - - - +
19K G 3.4 46.0 + - + +
20K U 3.9 8.9 + - - +
21K G 2.5 31.5 + - - +
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Residues in contact with SER 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ASN* 3.0 19.2 + - - +
38G VAL* 3.7 6.4 - - - +
39G SER* 2.9 19.7 + - - -
40G SER 3.2 0.2 - - - -
41G GLN* 1.3 78.7 - - - +
43G TRP* 1.3 76.4 + - - +
45G ARG* 2.9 14.7 + - - +
46G ALA* 3.0 12.1 + - - +
268G PRO* 4.5 10.6 - - - +
20K U 3.2 41.0 + - - -
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Residues in contact with TRP 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G GLN* 3.6 15.9 - - - -
12G LEU* 5.3 11.0 - - + -
38G VAL* 4.5 15.0 - - + +
39G SER 3.5 7.6 + - - +
42G SER* 1.3 82.9 + - - +
44G LYS* 1.3 63.1 + - - +
46G ALA* 3.1 3.4 + - - +
47G VAL* 2.9 38.1 + - + +
188G PHE* 3.1 32.5 - + + -
191G ALA* 5.4 6.5 - - + -
231G PHE* 5.7 3.4 - + - -
233G ARG* 3.0 56.6 - - - +
263G PHE 3.7 2.0 + - - -
266G THR* 3.2 30.2 - - + +
267G VAL* 4.7 2.2 - - + -
268G PRO* 3.6 34.5 - - + -
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Residues in contact with LYS 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G SER* 2.9 22.1 + - - +
41G GLN* 3.5 8.7 - - - +
42G SER 3.1 0.2 - - - -
43G TRP* 1.3 76.2 - - - +
45G ARG* 1.3 59.1 + - - +
47G VAL* 3.4 6.1 + - - +
48G ARG* 2.9 30.4 + - + +
170G PHE* 3.6 41.8 + - + +
186G VAL 4.7 2.5 + - - -
188G PHE* 3.8 29.1 - - + -
273H ASN* 2.9 28.5 + - - +
274H ALA* 4.3 7.4 - - - +
19K G 3.4 33.6 + - - +
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Residues in contact with ARG 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G GLN 2.9 11.5 + - - +
42G SER* 2.9 11.0 + - - +
44G LYS* 1.3 75.3 - - - +
46G ALA* 1.3 67.3 - - - +
48G ARG* 3.0 18.7 - - + +
49G HIS* 2.9 53.3 + - + +
268G PRO 5.4 5.5 + - - -
269G SER* 5.8 1.2 + - - -
207H VAL* 3.3 34.1 - - - +
209H ASP* 5.2 1.4 + - - -
20K U 3.3 59.9 + - - +
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Residues in contact with ALA 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G SER 3.0 9.1 + - - +
43G TRP* 3.5 8.7 - - - +
45G ARG* 1.3 78.0 - - - +
47G VAL* 1.3 62.7 + - - +
49G HIS* 3.1 8.6 + - - +
50G GLU* 3.1 18.9 + - - +
266G THR* 3.4 29.8 + - + +
267G VAL 4.2 1.1 - - - +
268G PRO* 3.8 29.6 - - + +
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Residues in contact with VAL 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G TRP* 2.9 42.1 + - + +
44G LYS* 3.8 6.3 - - - +
46G ALA* 1.3 75.4 - - - +
48G ARG* 1.3 64.4 + - - +
50G GLU* 3.2 2.8 + - - +
51G VAL* 2.9 27.9 + - + +
170G PHE* 4.1 7.0 - - + -
188G PHE* 5.0 2.2 - - + -
259G PHE* 3.5 35.9 - - + -
262G ALA* 4.2 7.0 - - + +
263G PHE* 3.9 18.6 - - + +
266G THR* 3.5 13.9 - - + -
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Residues in contact with ARG 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G LYS* 2.9 17.3 + - - +
45G ARG* 3.0 33.4 - - - +
47G VAL* 1.3 77.5 - - - +
49G HIS* 1.3 83.3 + - - +
51G VAL* 3.9 3.8 - - - +
52G GLU* 2.9 38.4 + - - +
59G ALA* 3.5 29.7 + - - +
61G ARG* 5.3 10.0 - - - +
118G TYR* 3.2 40.6 + - - -
166G SER* 4.0 9.3 + - - +
170G PHE* 3.7 26.0 - - + -
207H VAL* 5.4 3.2 - - - +
209H ASP* 4.1 14.7 + - - -
20K U 5.2 6.7 + - - -
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Residues in contact with HIS 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ARG* 2.9 68.1 + - + +
46G ALA* 3.1 7.2 + - - +
48G ARG* 1.3 94.9 + - - +
50G GLU* 1.3 61.9 + - - +
52G GLU* 3.3 22.4 + - - +
53G ALA* 2.9 33.5 + - - +
209H ASP* 4.6 10.0 + - - -
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Residues in contact with GLU 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F ASP 5.4 3.3 - - - +
46G ALA 3.1 14.0 + - - +
47G VAL 3.2 4.2 + - - +
49G HIS* 1.3 79.2 - - - +
51G VAL* 1.3 57.0 + - - +
53G ALA* 4.4 3.8 - - + -
54G ARG* 2.8 48.0 + - + +
258G GLU* 4.2 1.1 - - - -
261G ARG* 4.6 10.3 + - - +
262G ALA* 4.2 14.8 - - + -
265G SER* 3.8 23.6 + - - -
266G THR* 3.8 22.3 + - - -
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Residues in contact with VAL 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G VAL* 2.9 26.6 + - + +
48G ARG* 3.9 5.6 - - - +
50G GLU* 1.3 75.3 - - - +
52G GLU* 1.3 58.6 + - - +
54G ARG* 4.0 0.3 - - - +
55G LEU* 2.9 36.7 + - + +
165G VAL* 4.1 27.6 - - + -
166G SER* 4.8 4.3 - - - +
169G LEU* 4.6 11.2 - - + -
170G PHE* 5.9 1.1 - - + -
255G ALA 5.6 0.9 - - - +
258G GLU* 3.0 29.4 - - - +
259G PHE* 3.9 16.2 - - + -
262G ALA* 3.6 17.7 - - + -
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Residues in contact with GLU 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ARG* 2.9 32.9 + - - +
49G HIS* 3.3 31.4 + - - +
51G VAL* 1.3 78.8 - - - +
53G ALA* 1.3 68.1 + - - +
56G GLY 3.1 17.2 + - - -
57G ASP 3.0 28.5 + - - +
58G LYS* 3.0 45.8 + - - +
59G ALA 4.6 8.3 - - - +
165G VAL* 4.8 3.1 - - - -
166G SER* 3.6 16.4 - - - +
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Residues in contact with ALA 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G HIS* 2.9 22.8 + - + +
50G GLU* 3.9 4.9 - - + +
52G GLU* 1.3 86.4 - - - +
54G ARG* 1.3 59.4 + - - +
56G GLY* 4.0 5.7 + - - -
58G LYS* 4.5 13.2 + - - +
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Residues in contact with ARG 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G GLU* 2.8 30.0 + - + +
53G ALA* 1.3 75.8 - - - +
55G LEU* 1.3 62.4 + - - +
56G GLY 3.3 1.5 + - - -
258G GLU* 3.3 32.2 - - + +
261G ARG* 3.1 48.8 - - - +
262G ALA* 6.1 0.4 - - - -
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Residues in contact with LEU 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G VAL* 2.9 17.9 + - + +
54G ARG* 1.3 77.0 - - - +
56G GLY* 1.3 56.1 + - - +
57G ASP* 3.3 18.0 + - - +
165G VAL* 3.6 38.1 - - + -
254G THR* 5.1 13.9 - - - +
255G ALA* 4.7 12.1 - - + +
258G GLU* 4.6 25.1 - - + +
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Residues in contact with GLY 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G GLU 3.1 9.4 + - - -
53G ALA 4.0 5.7 + - - -
54G ARG 3.3 3.6 + - - -
55G LEU* 1.3 76.2 - - - +
57G ASP* 1.3 63.4 + - - +
58G LYS* 3.6 12.0 + - - +
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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
------------------------------------------------------------
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