Contacts of the helix formed by residues 43 - 60 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B UNL 3.0 29.2 + - - -
41B THR 3.2 1.9 + - - -
42B ASP* 1.3 95.7 + - - +
44B ASP* 1.3 66.9 + - + +
45B TRP* 3.8 11.9 - - + -
46B ASP* 3.1 29.5 + - - +
47B LEU* 3.1 24.0 + - - +
71B ARG* 3.6 15.9 - - - -
225B TRP* 3.7 29.2 - + + -
227B VAL* 4.3 19.7 - - + -
250B ASP* 5.0 1.1 - - - -
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B HIS* 1.3 75.3 - - + +
45B TRP* 1.3 63.6 + - - +
47B LEU* 3.6 7.5 + - - +
48B LYS* 2.9 65.7 + - - +
251B GLY 5.2 0.5 - - - +
252B SER* 4.5 14.6 - - - -
253B PRO* 3.4 27.8 - - + +
274B PRO* 5.6 0.7 - - - +
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Residues in contact with TRP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B UNL 3.6 39.9 - - + +
43B HIS* 3.4 7.9 - - + -
44B ASP* 1.3 78.5 - - - +
46B ASP* 1.3 66.3 + - - +
49B ALA* 3.0 37.3 + - + -
94B GLN* 4.9 0.9 - - - -
95B LEU* 3.7 19.7 - - + -
118B VAL* 4.0 16.2 - - + -
119B ASP* 3.3 24.2 - - - -
250B ASP* 3.5 31.9 - - + -
252B SER* 5.9 0.2 - - - -
272B GLN* 3.5 25.7 - - - +
274B PRO* 3.4 33.8 - - + +
277B ILE* 3.7 26.9 - - + -
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Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B UNL 3.4 10.9 + - - +
39B ILE* 4.3 2.8 - - - +
40B GLY 3.2 25.6 - - - +
41B THR* 3.9 7.6 - - - -
43B HIS* 3.1 34.2 + - + +
45B TRP* 1.3 74.0 - - - +
47B LEU* 1.3 60.8 + - - +
49B ALA 3.4 0.3 + - - -
50B TYR* 3.0 27.3 + - - +
71B ARG* 2.7 23.7 + - - -
94B GLN* 3.1 16.3 + - - +
95B LEU* 3.4 19.1 - - - +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 3.8 35.4 - - + +
43B HIS 3.1 14.9 + - - +
44B ASP* 4.0 7.0 - - - +
46B ASP* 1.3 78.3 - - - +
48B LYS* 1.3 61.2 + - + +
50B TYR* 3.2 4.6 + - + +
51B GLN* 2.9 64.7 + - + +
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Residues in contact with LYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASP* 2.9 50.8 + - - +
45B TRP 3.8 3.4 - - - +
47B LEU* 1.3 79.7 - - + +
49B ALA* 1.3 57.8 + - - +
51B GLN* 4.2 10.8 - - - +
52B ALA* 3.2 28.4 + - - +
253B PRO* 4.4 12.5 - - - +
274B PRO* 3.8 25.3 - - + +
275B SER* 3.8 18.7 + - - +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TRP* 3.0 38.0 + - + +
46B ASP 3.8 2.0 - - - +
47B LEU 3.2 0.4 - - - -
48B LYS* 1.3 75.6 - - - +
50B TYR* 1.3 62.9 + - - +
53B GLN* 3.2 30.0 + - - +
94B GLN* 3.5 15.7 - - - +
118B VAL* 4.7 4.9 - - + -
274B PRO* 3.4 21.1 + - + +
278B GLY* 3.7 6.0 - - - +
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Residues in contact with TYR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 3.8 23.7 - - + +
38B ALA* 3.7 21.8 - - + -
41B THR* 3.6 19.5 - - + -
46B ASP 3.0 18.1 + - - +
47B LEU* 3.5 7.0 - - + +
49B ALA* 1.3 75.4 - - - +
51B GLN* 1.3 68.4 + - + +
53B GLN* 3.4 8.1 + - - +
54B ILE* 3.3 42.4 + - + +
66B ALA* 3.2 34.4 + - + +
67B LEU 3.3 21.8 + - - -
68B ASP* 3.6 13.5 + - + +
94B GLN* 3.6 7.6 + - - +
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Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 2.9 52.8 + - + +
48B LYS* 4.2 10.1 - - - +
50B TYR* 1.3 81.5 - - + +
52B ALA* 1.3 60.0 + - - +
54B ILE* 3.4 10.0 + - + +
55B ALA* 2.9 31.0 + - - +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LYS 3.2 19.6 + - - +
49B ALA 3.9 4.7 - - - +
50B TYR 3.3 0.2 - - - -
51B GLN* 1.3 75.5 - - - +
53B GLN* 1.3 64.1 + - - +
55B ALA* 4.0 6.5 - - - +
56B GLU* 3.2 25.5 + - - +
275B SER* 3.2 34.8 - - - +
278B GLY* 4.1 4.8 - - - +
279B LYS* 4.1 7.5 - - + +
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Residues in contact with GLN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 3.7 24.4 - - + +
49B ALA 3.2 12.2 + - - +
50B TYR* 3.4 10.6 + - - +
51B GLN 3.2 0.4 - - - -
52B ALA* 1.3 76.2 - - - +
54B ILE* 1.3 59.2 + - - +
56B GLU 3.4 0.9 + - - -
57B ILE* 2.9 37.3 + - - +
92B ILE* 3.3 33.9 - - + +
94B GLN* 2.8 33.3 + - - +
118B VAL* 3.5 18.7 - - - +
278B GLY* 3.4 23.5 - - - +
281B ALA* 5.1 0.7 - - + -
282B VAL* 3.5 10.3 - - + +
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 3.9 7.2 - - + -
50B TYR* 3.3 43.4 + - + +
51B GLN* 3.8 9.9 - - + +
53B GLN* 1.3 78.5 - - - +
55B ALA* 1.3 63.4 + - - +
57B ILE* 3.3 7.4 + - - +
58B GLU* 3.3 35.5 + - - +
64B ALA* 4.0 20.9 - - + +
66B ALA* 3.7 22.4 - - + -
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLN 2.9 18.7 + - - +
52B ALA* 4.1 7.4 - - - +
54B ILE* 1.3 77.6 - - - +
56B GLU* 1.3 56.8 - - - +
58B GLU* 3.7 8.1 + - - +
59B ARG* 3.1 28.8 + - - +
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA 3.2 18.3 + - - +
53B GLN 3.9 3.1 - - - +
54B ILE 3.3 0.2 - - - -
55B ALA* 1.3 76.0 - - - +
57B ILE* 1.3 64.6 + - - +
59B ARG* 2.8 48.5 + - - +
60B LEU* 3.2 31.6 + - + +
279B LYS* 3.4 50.0 - - + +
282B VAL* 3.8 16.6 - - + -
283B GLN* 3.2 12.7 + - - +
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 4.1 4.2 - - + +
34B ILE* 3.8 37.0 - - + +
36B ILE* 3.6 27.8 - - + -
53B GLN 2.9 21.5 + - - +
54B ILE 3.3 4.9 + - - +
56B GLU* 1.3 75.6 - - - +
58B GLU* 1.3 61.2 + - - +
60B LEU* 3.2 10.6 + - - +
62B GLY* 2.9 34.2 + - - -
63B THR 3.8 4.9 - - - +
64B ALA* 3.7 33.0 - - + +
92B ILE* 4.9 0.2 - - + -
282B VAL* 3.8 23.6 - - + -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 3.3 35.0 - - - +
55B ALA* 3.9 8.3 - - - +
57B ILE* 1.3 74.6 - - - +
59B ARG* 1.3 59.4 + - - +
61B GLY* 3.1 16.4 + - - -
62B GLY 3.6 17.8 - - - +
63B THR* 5.3 0.5 - - - -
64B ALA* 4.0 15.2 + - - +
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA 3.1 18.5 + - - +
56B GLU* 2.8 43.8 + - - +
57B ILE 3.3 0.4 - - - -
58B GLU* 1.3 76.9 - - - +
60B LEU* 1.3 77.4 + - - +
61B GLY 3.3 1.2 + - - -
279B LYS* 5.0 7.4 - - - +
283B GLN* 4.7 3.8 - - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B SER* 3.5 22.0 + - - +
29B LEU* 3.0 43.9 + - + +
30B GLU* 3.3 5.9 + - - +
56B GLU* 3.2 25.3 + - + +
57B ILE 3.2 4.0 + - - +
58B GLU 3.2 0.6 - - - -
59B ARG* 1.3 99.9 - - - +
61B GLY* 1.3 57.2 + - - +
62B GLY 3.3 2.0 - - - -
282B VAL* 4.2 9.9 - - + +
283B GLN* 5.0 6.5 - - + +
286B ALA* 3.8 28.3 - - + -
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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