Contacts of the helix formed by residues 39 - 55 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D ASN* 2.9 12.4 - - - +
26D LYS* 3.9 4.7 - - - +
37D ARG* 3.5 19.2 + - - +
38D VAL* 1.3 75.4 - - - +
40D SER* 1.3 64.1 + - - +
41D GLN* 2.2 45.7 + - - -
42D SER* 2.8 19.5 + - - -
43D TRP* 3.5 5.2 + - - +
190D HIS* 3.2 18.2 - - - -
9K C 3.7 9.4 - - - -
72N ASP* 4.5 1.6 + - - -
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Residues in contact with SER 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D VAL 3.6 1.5 + - - -
39D SER* 1.3 78.4 + - - +
41D GLN* 1.3 62.9 + - - -
42D SER 3.3 0.2 + - - -
43D TRP* 3.4 5.1 + - - +
44D LYS* 2.9 26.0 + - - +
188D PHE* 3.0 42.2 + - - +
189D ALA 4.2 2.2 - - - -
190D HIS* 3.0 34.7 + - - +
142N ALA* 4.2 7.1 - - - +
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Residues in contact with GLN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LYS* 4.3 1.8 - - - +
39D SER* 2.2 33.9 + - - -
40D SER* 1.3 77.1 + - - +
42D SER* 1.3 57.4 + - - +
44D LYS* 3.7 8.5 - - - +
45D ARG* 2.8 32.2 + - - +
190D HIS* 4.0 5.5 - - - -
7K C 3.4 37.1 - - + +
8K G 3.5 11.4 + - - +
9K C 2.8 25.5 + - - -
72N ASP* 4.8 1.3 + - - +
73N PHE 4.5 2.4 + - - -
74N HIS* 2.9 38.4 + - + -
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Residues in contact with SER 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASN* 4.0 10.9 + - - +
38D VAL* 4.3 3.3 - - - +
39D SER 2.8 21.1 + - - -
40D SER 3.2 0.2 - - - -
41D GLN* 1.3 80.3 - - - +
43D TRP* 1.3 75.9 + - - +
45D ARG* 3.0 25.9 - - - +
46D ALA* 3.1 7.6 + - - +
268D PRO* 4.5 16.0 - - - +
8K G 2.9 34.5 - - - -
9K C 4.3 5.6 - - - -
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Residues in contact with TRP 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D VAL* 5.1 11.2 - - + +
39D SER 4.1 7.0 - - - +
40D SER* 3.4 7.2 + - - +
41D GLN 3.3 0.2 - - - -
42D SER* 1.3 83.2 + - - +
44D LYS* 1.3 57.9 + - - +
46D ALA* 3.1 4.8 + - + +
47D VAL* 2.9 44.1 + - + +
188D PHE* 3.0 41.1 - + - -
233D ARG* 2.7 34.9 - - - +
263D PHE* 2.9 53.4 - + - -
266D THR* 3.3 34.1 + - + +
267D VAL* 4.0 1.2 - - - +
268D PRO* 3.1 38.4 - - + +
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Residues in contact with LYS 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D SER* 2.9 22.3 + - - +
41D GLN* 3.7 7.2 - - - +
43D TRP* 1.3 74.7 - - - +
45D ARG* 1.3 65.5 + - - +
47D VAL* 3.0 2.6 + - - +
48D ARG* 2.8 28.8 + - + +
170D PHE* 3.4 29.1 - - + +
171D GLY 5.2 2.2 - - - +
184D GLY* 6.4 0.2 - - - -
186D VAL* 3.9 21.8 + - - +
188D PHE* 3.5 35.4 - - + +
6K C 3.3 25.5 + - - -
7K C 3.3 35.6 + - + +
141N ARG* 5.2 2.8 - - - +
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Residues in contact with ARG 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D GLN 2.8 16.9 + - - +
42D SER* 3.0 20.4 - - - +
44D LYS* 1.3 72.4 - - - +
46D ALA* 1.3 83.9 + - - +
48D ARG* 3.1 14.7 + - - +
49D HIS* 3.0 58.4 + - - +
269D SER* 6.2 0.2 - - - -
7K C 5.1 4.4 - - - -
8K G 2.5 101.1 + - - +
77N GLY 5.6 0.4 + - - -
78N GLY 4.4 10.7 + - - -
79N GLY 5.0 2.8 + - - -
80N LEU* 4.5 18.8 - - - +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D SER 3.1 12.4 + - - +
43D TRP* 3.1 9.4 + - - +
45D ARG* 1.3 84.6 - - - +
47D VAL* 1.3 52.6 + - - +
49D HIS* 2.8 23.1 + - - +
50D GLU* 2.3 27.8 + - - +
266D THR* 4.0 17.5 - - + +
267D VAL 4.5 1.1 - - - +
268D PRO* 4.1 22.7 - - + -
269D SER 5.3 1.1 - - - +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D TRP* 2.9 52.8 + - + +
44D LYS* 3.0 8.7 + - - +
46D ALA* 1.3 74.8 - - - +
48D ARG* 1.3 57.5 + - - +
50D GLU* 3.3 7.7 + - - +
51D VAL* 2.9 38.0 + - + +
170D PHE* 3.9 6.7 - - + -
188D PHE* 3.9 2.9 - - + -
259D PHE* 3.9 28.3 - - + -
262D ALA* 4.4 8.7 - - + -
263D PHE* 4.6 4.5 - - - +
266D THR* 3.6 10.5 - - + -
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Residues in contact with ARG 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LYS* 2.8 19.1 + - - +
45D ARG* 3.1 14.1 + - - +
47D VAL* 1.3 77.5 - - - +
49D HIS* 1.3 62.9 + - + +
51D VAL 4.7 0.2 - - - +
52D GLU* 2.8 63.6 + - - +
166D SER* 3.4 7.5 + - - -
170D PHE* 3.9 40.0 - - + +
172D ARG 3.0 20.2 + - - -
173D MET* 3.0 30.5 - - - +
174D LEU* 4.3 3.6 - - - +
7K C 2.3 52.3 + - - -
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Residues in contact with HIS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ARG* 3.0 52.7 + - - +
46D ALA* 2.8 11.0 + - - +
48D ARG* 1.3 81.5 - - + +
50D GLU* 1.3 65.5 + - - +
52D GLU* 4.8 4.7 - - - -
53D ALA* 2.9 32.3 + - - +
80N LEU* 4.7 15.8 - - + +
84N ARG* 4.9 18.3 + - - -
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ALA* 2.3 33.9 + - - +
47D VAL* 3.6 3.0 - - - +
49D HIS* 1.3 80.0 - - - +
51D VAL* 1.3 57.4 + - - +
53D ALA* 3.8 5.0 - - - +
54D ARG* 2.8 33.9 + - + +
262D ALA* 4.5 15.5 - - + -
265D SER* 5.2 4.5 - - - +
266D THR* 2.9 34.9 + - - +
267D VAL 5.4 0.3 - - - +
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D VAL* 2.9 33.0 + - + +
48D ARG 4.2 2.2 - - - +
50D GLU* 1.3 71.3 - - - +
52D GLU* 1.3 61.8 + - + +
54D ARG* 3.4 2.9 + - - -
55D LEU* 2.8 55.9 + - + +
166D SER* 6.0 2.7 - - - +
169D LEU* 5.9 3.1 - - + -
170D PHE* 4.5 14.8 - - + -
255D ALA* 5.6 2.5 - - - +
258D GLU* 3.6 6.0 - - + +
259D PHE* 4.0 25.4 - - + +
262D ALA* 3.5 24.0 - - + -
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ARG* 2.8 46.6 + - - +
49D HIS* 4.3 5.5 - - - +
51D VAL* 1.3 79.5 - - + +
53D ALA* 1.3 61.3 + - - +
55D LEU* 3.5 7.2 + - + +
56D GLY 3.4 24.3 + - - +
166D SER* 2.3 40.5 + - - +
170D PHE* 5.9 0.4 - - + -
173D MET* 3.3 13.6 - - - +
84N ARG* 3.9 20.1 + - - -
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Residues in contact with ALA 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D HIS 2.9 22.3 + - - +
50D GLU* 3.8 5.2 - - - +
52D GLU* 1.3 78.7 - - - +
54D ARG* 1.3 62.4 + - - +
56D GLY* 3.2 13.5 + - - -
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Residues in contact with ARG 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLU* 2.8 18.0 + - + +
51D VAL* 6.0 0.2 - - - +
53D ALA* 1.3 72.6 - - - +
55D LEU* 1.3 59.9 + - - +
56D GLY* 3.1 6.1 + - - -
258D GLU* 2.9 42.0 - - + +
261D ARG* 3.0 47.3 - - - +
262D ALA* 6.3 1.8 - - - -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL* 2.8 39.1 + - + +
52D GLU* 3.5 8.3 + - + +
53D ALA 3.3 0.2 - - - -
54D ARG* 1.3 75.6 - - - +
56D GLY* 1.3 64.6 + - - +
165D VAL* 4.5 25.1 - - + +
166D SER* 5.1 11.0 - - - +
254D THR* 5.1 5.2 - - - +
255D ALA* 5.5 5.6 - - - -
258D GLU* 3.0 41.2 + - + +
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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
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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