Contacts of the helix formed by residues 43 - 60 (chain D) in PDB entry 3L49
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 HIS 43 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D UNL 3.1 35.5 + - - -
41D THR 3.2 3.1 + - - +
42D ASP* 1.3 83.2 - - + +
44D ASP* 1.3 67.7 + - - +
45D TRP* 3.9 10.5 + - + +
46D ASP* 2.9 33.8 + - - +
47D LEU* 3.1 21.1 + - - +
71D ARG* 4.0 7.4 + - - -
194D ILE* 5.0 2.2 - - + -
225D TRP* 3.7 28.5 - + + -
227D VAL* 3.9 23.9 - - + +
250D ASP* 3.8 6.2 + - - -
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Residues in contact with ASP 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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43D HIS* 1.3 75.6 - - - +
45D TRP* 1.3 66.2 + - - +
47D LEU* 3.5 6.2 + - - +
48D LYS* 3.0 61.2 + - - +
227D VAL* 6.4 0.4 - - + -
251D GLY 5.2 0.9 - - - +
252D SER* 4.3 18.4 - - - -
253D PRO* 3.8 27.0 - - + +
274D PRO* 5.2 3.1 - - - +
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Residues in contact with TRP 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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1D UNL 3.6 32.5 - - + +
43D HIS* 3.3 8.8 + - + -
44D ASP* 1.3 81.3 + - - +
46D ASP* 1.3 76.2 + - - +
48D LYS 3.3 0.2 + - - -
49D ALA* 3.0 33.8 + - + -
94D GLN* 4.2 4.5 - - - -
95D LEU* 3.8 20.0 - - + -
118D VAL* 3.8 18.2 - - + -
119D ASP* 3.3 21.5 - - - -
250D ASP* 3.9 26.0 - - + +
252D SER* 5.9 0.8 - - - -
272D GLN* 3.3 29.5 - - + +
274D PRO* 3.5 34.9 - - + +
277D ILE* 3.8 24.7 - - + -
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Residues in contact with ASP 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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1D UNL 3.3 9.0 + - - -
39D ILE* 4.4 0.9 - - - +
40D GLY 3.0 27.1 + - - +
41D THR* 3.8 7.1 - - - +
43D HIS* 2.9 39.8 + - + +
45D TRP* 1.3 78.4 - - - +
47D LEU* 1.3 57.7 + - - +
50D TYR* 3.0 20.8 + - - +
71D ARG* 2.7 22.8 + - - -
94D GLN* 3.0 23.9 + - - +
95D LEU* 3.4 19.0 - - - +
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Residues in contact with LEU 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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41D THR* 3.8 35.1 - - + +
43D HIS 3.1 13.8 + - - +
44D ASP* 3.8 7.2 - - - +
46D ASP* 1.3 76.9 - - - +
48D LYS* 1.3 65.2 + - + +
50D TYR* 3.3 6.3 + - + +
51D GLN* 2.9 65.7 + - + +
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Residues in contact with LYS 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 ASP* 3.0 50.8 + - - +
45D TRP 3.6 4.5 - - - +
47D LEU* 1.3 82.7 - - + +
49D ALA* 1.3 56.6 + - - +
51D GLN* 4.1 10.4 - - - +
52D ALA* 3.1 28.9 + - - +
253D PRO* 5.3 5.9 - - - +
274D PRO* 3.7 21.0 - - + +
275D SER* 3.6 22.4 + - - +
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Residues in contact with ALA 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 TRP* 3.0 33.6 + - + +
46D ASP 3.9 1.8 - - - +
47D LEU 3.3 0.2 - - - -
48D LYS* 1.3 73.9 - - - +
50D TYR* 1.3 65.2 + - - +
52D ALA* 3.5 2.3 + - - +
53D GLN* 2.9 32.7 + - - +
94D GLN* 3.7 16.6 - - - +
118D VAL* 4.7 5.4 - - + -
274D PRO* 3.5 22.8 - - + +
277D ILE* 5.3 0.2 - - + -
278D GLY* 3.8 3.5 - - - +
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Residues in contact with TYR 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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36D ILE* 4.0 19.7 - - + -
38D ALA* 3.7 24.0 - - + -
41D THR* 3.5 21.3 - - + -
46D ASP 3.0 18.5 + - - +
47D LEU* 3.3 7.4 + - + +
49D ALA* 1.3 75.2 - - - +
51D GLN* 1.3 68.7 + - + +
53D GLN* 3.4 7.8 + - - +
54D ILE* 3.3 44.8 + - + +
66D ALA* 3.1 35.5 + - + +
67D LEU 3.2 23.9 + - - -
68D ASP* 3.6 10.6 + - + +
94D GLN* 3.5 7.3 + - - +
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Residues in contact with GLN 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 LEU* 2.9 53.5 + - + +
48D LYS* 4.1 9.1 - - - +
50D TYR* 1.3 81.6 - - + +
52D ALA* 1.3 57.8 + - - +
54D ILE* 3.3 9.1 + - + +
55D ALA* 2.9 32.7 + - - +
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Residues in contact with ALA 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 LYS 3.1 20.2 + - - +
49D ALA 3.7 5.2 - - - +
50D TYR 3.3 0.2 - - - -
51D GLN* 1.3 73.3 - - - +
53D GLN* 1.3 64.4 + - - +
55D ALA* 4.0 4.9 - - - +
56D GLU* 3.2 25.8 + - - +
275D SER* 3.2 35.4 - - - +
278D GLY* 4.0 8.1 - - - -
279D LYS* 4.1 3.9 + - + +
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Residues in contact with GLN 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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36D ILE* 3.5 30.7 - - + +
49D ALA* 2.9 18.3 + - - +
50D TYR* 3.6 7.7 - - - +
51D GLN 3.3 0.2 - - - -
52D ALA* 1.3 74.8 - - - +
54D ILE* 1.3 67.1 + - - +
56D GLU 3.1 2.8 + - - -
57D ILE* 2.9 27.0 + - - +
92D ILE* 3.3 26.5 - - + +
94D GLN* 2.8 30.0 + - - +
118D VAL* 3.8 19.4 - - + +
278D GLY* 3.4 20.0 - - - +
281D ALA* 4.8 0.7 - - + -
282D VAL* 3.5 18.3 - - + +
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Residues in contact with ILE 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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36D ILE* 4.0 7.9 - - + -
50D TYR* 3.3 44.5 + - + +
51D GLN* 3.3 9.8 + - + +
53D GLN* 1.3 76.9 - - - +
55D ALA* 1.3 64.6 + - - +
57D ILE* 3.2 5.5 + - - +
58D GLU* 3.1 36.7 + - - +
64D ALA* 3.9 21.5 - - + -
66D ALA* 3.8 22.7 - - + -
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Residues in contact with ALA 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 GLN 2.9 18.2 + - - +
52D ALA* 4.0 6.3 - - - +
54D ILE* 1.3 76.6 - - - +
56D GLU* 1.3 50.8 + - - +
58D GLU* 3.2 8.9 + - - +
59D ARG* 2.8 36.5 + - - +
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Residues in contact with GLU 56 (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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52D ALA 3.2 15.6 + - - +
53D GLN 3.1 4.7 + - - +
55D ALA* 1.3 75.6 - - - +
57D ILE* 1.3 66.1 + - - +
59D ARG* 2.8 48.9 + - - -
60D LEU* 3.2 32.5 + - + +
279D LYS* 3.5 31.2 - - + +
282D VAL* 3.7 20.6 - - + -
283D GLN* 2.9 27.7 + - - +
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Residues in contact with ILE 57 (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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29D LEU* 4.7 4.5 - - + +
34D ILE* 3.9 37.2 - - + +
36D ILE* 3.6 30.5 - - + -
53D GLN 2.9 15.4 + - - +
54D ILE 3.2 6.5 + - - +
56D GLU* 1.3 75.3 - - - +
58D GLU* 1.3 61.5 + - - +
60D LEU* 3.1 11.1 + - - +
61D GLY 3.3 0.2 + - - -
62D GLY* 3.0 44.7 + - - +
63D THR 3.7 3.8 - - - +
64D ALA* 3.7 24.7 - - + +
282D VAL* 3.8 22.4 - - + -
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Residues in contact with GLU 58 (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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54D ILE* 3.1 27.6 + - - +
55D ALA* 3.7 8.4 - - - +
57D ILE* 1.3 75.0 - - - +
59D ARG* 1.3 58.2 + - - +
61D GLY* 3.1 17.3 + - - -
62D GLY 3.6 16.6 - - - +
63D THR* 5.4 0.2 - - - -
64D ALA* 4.5 15.1 + - + +
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Residues in contact with ARG 59 (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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55D ALA 2.8 20.9 + - - +
56D GLU* 2.8 46.0 + - - +
57D ILE 3.3 0.2 - - - -
58D GLU* 1.3 73.1 - - - +
60D LEU* 1.3 81.2 + - - +
61D GLY 3.3 1.0 + - - -
279D LYS* 6.1 1.6 - - - +
283D GLN* 4.6 3.4 - - - +
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Residues in contact with LEU 60 (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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28D SER* 3.4 23.2 + - - +
29D LEU* 2.7 59.7 + - + +
30D GLU* 3.7 1.0 + - - +
56D GLU* 3.2 35.1 + - + +
57D ILE 3.1 2.6 + - - +
59D ARG* 1.3 102.5 - - - +
61D GLY* 1.3 59.5 + - - +
62D GLY 3.4 2.0 - - - -
282D VAL* 4.4 4.0 - - + +
283D GLN* 4.8 7.6 - - + +
286D ALA* 4.3 14.1 - - + -
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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