Contacts of the helix formed by residues 39 - 56 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ASN* 2.7 26.4 + - - +
26H LYS* 3.2 28.8 + - - +
37H ARG* 3.7 14.6 + - - +
38H VAL* 1.3 75.2 - - - +
40H SER* 1.3 62.6 + - - +
41H GLN* 3.4 14.1 + - - -
42H SER* 3.0 23.6 + - - -
43H TRP* 3.5 5.9 + - - +
190H HIS* 3.3 10.3 - - - -
15K A 3.3 8.3 + - - -
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Residues in contact with SER 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ALA* 2.6 36.4 + - - +
38H VAL 3.5 1.1 + - - -
39H SER* 1.3 70.5 - - - +
41H GLN* 1.3 67.4 + - - +
43H TRP 3.5 0.2 + - - -
44H LYS* 2.9 33.2 + - - +
188H PHE* 3.1 35.9 - - - -
189H ALA 3.9 3.6 - - - -
190H HIS* 3.0 24.1 + - - -
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Residues in contact with GLN 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ASP* 3.4 17.4 + - - +
204D PHE* 3.4 21.8 - - - +
226D PHE* 5.7 1.6 - - - -
274D ALA* 5.4 5.7 - - + +
26H LYS* 3.6 1.6 - - - +
39H SER* 3.4 14.0 - - - -
40H SER* 1.3 88.6 + - - +
42H SER* 1.3 60.5 + - - +
44H LYS* 3.6 8.9 - - - +
45H ARG* 3.0 22.9 + - - +
190H HIS* 4.2 5.4 + - - -
13K U 3.7 44.7 - - + +
14K G 3.6 9.4 + - - +
15K A 2.4 30.2 + - - +
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Residues in contact with SER 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ASN* 2.8 27.5 + - - +
38H VAL* 3.8 4.9 - - - +
39H SER* 3.0 11.6 + - - -
41H GLN* 1.3 81.3 - - - +
43H TRP* 1.3 71.6 + - - +
45H ARG* 3.0 14.0 + - - +
46H ALA* 3.0 12.3 + - - +
268H PRO* 4.4 10.2 - - - +
14K G 3.1 42.8 - - - -
16K U 4.7 0.2 - - - -
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Residues in contact with TRP 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H GLN* 3.8 13.9 - - - -
12H LEU* 5.5 5.4 - - + -
17H ILE* 5.1 5.6 - - + -
38H VAL* 4.4 11.2 - - + -
39H SER 3.5 5.6 + - - +
40H SER 3.5 1.6 + - - +
41H GLN 3.5 0.2 - - - -
42H SER* 1.3 81.3 + - - +
44H LYS* 1.3 62.7 + - - +
46H ALA* 3.1 6.8 + - - +
47H VAL* 2.9 39.8 + - + +
188H PHE* 3.3 33.8 - + + -
191H ALA* 5.4 5.8 - - + -
231H PHE* 5.8 2.5 - + - -
233H ARG* 3.0 56.5 - - - +
263H PHE 3.6 2.4 + - - -
264H LEU 5.2 0.2 - - - -
266H THR* 3.1 32.4 - - + +
267H VAL* 4.6 1.1 - - + -
268H PRO* 3.5 33.7 - - + -
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Residues in contact with LYS 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D ASN* 3.3 29.9 + - - +
274D ALA* 4.4 2.8 - - - +
40H SER* 2.9 23.4 + - - +
41H GLN* 3.6 7.2 - - - +
43H TRP* 1.3 77.8 - - - +
45H ARG* 1.3 57.6 + - - +
47H VAL* 3.4 5.9 + - - +
48H ARG* 2.9 31.0 + - - +
170H PHE* 3.5 42.7 + - + -
186H VAL 4.7 3.8 + - - -
188H PHE* 3.9 27.5 - - + +
13K U 2.7 38.8 + - - +
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Residues in contact with ARG 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D VAL* 3.3 28.8 - - - +
209D ASP* 5.1 2.0 + - - -
41H GLN 3.0 12.4 + - - +
42H SER 3.0 10.6 + - - +
44H LYS* 1.3 74.5 - - - +
46H ALA* 1.3 68.8 + - - +
48H ARG* 3.1 16.9 - - + +
49H HIS* 2.9 55.4 + - + +
268H PRO 5.8 1.4 + - - -
269H SER* 5.7 2.2 + - - -
14K G 3.2 71.6 + - - +
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Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H SER 3.0 11.0 + - - +
43H TRP* 3.1 8.9 + - - +
45H ARG* 1.3 79.6 - - - +
47H VAL* 1.3 63.1 + - - +
49H HIS* 3.3 5.3 + - - +
50H GLU* 3.0 28.6 + - - +
266H THR* 3.2 26.7 + - + +
267H VAL 4.3 1.3 - - - +
268H PRO* 4.1 25.1 - - + +
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Residues in contact with VAL 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H TRP* 2.9 42.7 + - + +
44H LYS* 3.8 5.2 - - - +
46H ALA* 1.3 74.2 - - - +
48H ARG* 1.3 60.1 + - - +
50H GLU* 3.3 3.6 + - - +
51H VAL* 2.9 29.6 + - + +
170H PHE* 4.1 7.0 - - + -
188H PHE* 5.0 2.0 - - + -
259H PHE* 3.6 35.2 - - + +
262H ALA* 4.2 11.7 - - + -
263H PHE* 3.8 19.3 - - + +
266H THR* 3.5 13.5 - - + -
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Residues in contact with ARG 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D VAL* 5.8 2.6 - - - +
209D ASP* 4.6 11.1 + - - -
44H LYS* 2.9 17.3 + - - +
45H ARG* 3.1 30.4 - - - +
47H VAL* 1.3 78.0 - - - +
49H HIS* 1.3 79.8 + - - +
51H VAL* 4.0 4.0 - - - +
52H GLU* 2.8 65.3 + - - +
59H ALA* 3.3 15.2 + - - +
61H ARG* 5.1 10.4 - - - +
118H TYR* 2.9 42.5 + - - -
166H SER* 4.2 4.9 - - - +
170H PHE* 3.6 26.7 - - + -
14K G 5.3 6.0 + - - -
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Residues in contact with HIS 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D ASP* 4.5 12.7 + - - -
45H ARG* 2.9 70.0 + - + +
46H ALA* 3.8 5.8 - - - +
47H VAL 3.2 0.2 - - - -
48H ARG* 1.3 95.8 + - + +
50H GLU* 1.3 63.7 + - - +
52H GLU* 4.1 9.3 + - - +
53H ALA* 2.9 31.7 + - - +
58H LYS* 5.5 8.1 + - - -
59H ALA 6.0 0.7 - - - -
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Residues in contact with GLU 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ALA* 3.0 16.3 + - - +
47H VAL 3.8 3.4 - - - +
49H HIS* 1.3 84.9 - - - +
51H VAL* 1.3 55.9 - - - +
53H ALA* 3.3 5.2 + - + +
54H ARG* 2.9 33.0 + - - +
262H ALA* 4.2 16.4 - - + -
265H SER* 5.2 6.5 - - - +
266H THR* 3.2 33.6 + - - +
267H VAL 5.1 0.5 + - - +
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Residues in contact with VAL 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H VAL* 2.9 24.9 + - + +
48H ARG* 4.0 6.1 - - - +
50H GLU* 1.3 76.4 - - - +
52H GLU* 1.3 58.7 + - + +
54H ARG* 3.2 5.4 + - - +
55H LEU* 2.9 30.9 + - + +
57H ASP* 5.9 0.2 - - - +
165H VAL* 4.6 13.7 - - + -
166H SER* 4.9 7.2 - - - +
169H LEU* 5.2 7.6 - - + -
170H PHE* 6.0 1.3 - - + -
258H GLU* 3.7 35.8 - - + +
259H PHE* 3.9 16.2 - - + +
262H ALA* 3.5 21.1 - - + -
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Residues in contact with GLU 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ARG* 2.8 54.9 + - - +
49H HIS* 4.1 11.0 + - - +
51H VAL* 1.3 76.3 - - + +
53H ALA* 1.3 61.5 + - - +
56H GLY* 3.1 22.3 + - - -
57H ASP* 3.3 27.5 - - - +
58H LYS* 4.3 16.1 + - + +
59H ALA* 3.3 20.9 + - - +
164H ASN* 4.5 2.5 - - - +
165H VAL* 6.3 0.4 - - + -
166H SER* 2.5 37.3 + - - +
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Residues in contact with ALA 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H HIS 2.9 21.4 + - - +
50H GLU* 3.8 6.3 - - + +
52H GLU* 1.3 77.6 - - - +
54H ARG* 1.3 59.4 + - - +
56H GLY* 4.0 6.2 + - - -
58H LYS* 5.6 6.9 - - - +
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Residues in contact with ARG 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G ASP* 6.3 0.4 - - - +
50H GLU 2.9 18.5 + - - +
51H VAL* 3.8 4.3 - - - +
53H ALA* 1.3 78.3 - - - +
55H LEU* 1.3 62.0 + - - +
56H GLY 3.4 0.4 + - - -
258H GLU* 5.0 21.8 - - + +
261H ARG* 3.0 49.5 - - - +
262H ALA* 6.2 3.6 - - - +
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Residues in contact with LEU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H VAL* 2.9 15.3 + - + +
54H ARG* 1.3 77.6 - - - +
56H GLY* 1.3 56.0 + - - +
57H ASP* 3.3 20.3 + - - +
165H VAL* 3.8 26.0 - - + -
254H THR* 5.2 12.8 - - - +
255H ALA* 5.6 0.4 - - - -
258H GLU* 3.0 39.9 - - - +
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Residues in contact with GLY 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H GLU 3.1 12.2 + - - -
53H ALA* 4.0 5.8 + - - -
54H ARG 3.4 3.4 - - - -
55H LEU* 1.3 76.3 - - - +
57H ASP* 1.3 59.9 + - - +
58H LYS* 3.6 10.5 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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