Contacts of the helix formed by residues 37 - 55 (chain B) in PDB entry 3R2W
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 PHE 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.2 44.6 - - + -
30B THR* 5.2 6.3 - - + -
32B ALA* 3.9 10.8 - - + +
34B SER 3.5 13.5 - - - +
35B HIS 3.4 1.2 + - - -
36B GLU* 1.3 75.4 - - - +
38B GLU* 1.3 75.0 + - - +
39B HIS 3.6 1.7 - - - +
40B THR* 4.1 9.3 + - - -
41B LYS* 3.3 27.6 + - + +
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Residues in contact with GLU 38 (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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35B HIS 4.3 8.8 + - - +
37B PHE* 1.3 87.8 - - - +
39B HIS* 1.3 66.5 + - + +
40B THR 3.2 0.2 + - - -
41B LYS* 3.3 10.8 + - - +
42B LYS* 3.4 21.8 + - - +
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Residues in contact with HIS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLU* 3.2 44.7 + - + +
38B GLU* 1.3 79.6 + - + +
40B THR* 1.3 61.6 + - + +
42B LYS* 3.2 17.8 + - + +
43B ASP* 2.8 45.0 + - - +
180B SER* 6.5 0.7 - - - -
181B ARG* 6.2 1.8 - - - -
221B ASN* 5.7 1.8 - - - +
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.4 9.5 - - + +
32B ALA* 4.5 12.2 - - + +
36B GLU* 2.8 29.4 + - - +
37B PHE* 4.1 14.8 + - - -
38B GLU 3.2 1.0 + - - -
39B HIS* 1.3 75.3 - - - +
41B LYS* 1.3 66.3 + - - +
43B ASP* 3.3 19.1 + - + +
44B LEU* 3.5 24.2 + - + +
181B ARG* 6.0 7.6 - - + -
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.7 23.1 - - + +
37B PHE* 3.3 21.5 + - + +
38B GLU* 3.3 11.6 + - - +
40B THR* 1.3 77.9 - - - +
42B LYS* 1.3 61.7 + - + +
43B ASP 3.5 0.2 + - - -
44B LEU* 3.8 2.1 + - - +
45B ASP* 3.0 30.0 + - - +
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Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLU* 3.4 23.1 - - - +
39B HIS* 3.3 16.2 - - + +
40B THR 3.2 0.4 - - - -
41B LYS* 1.3 78.2 - - + +
43B ASP* 1.3 66.6 + - - +
45B ASP* 3.5 20.2 + - - +
46B GLY* 3.6 4.5 + - - -
221B ASN* 3.2 41.7 + - - +
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Residues in contact with ASP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B HIS* 2.8 31.6 + - - +
40B THR* 3.6 14.8 - - + +
41B LYS 3.3 0.6 - - - -
42B LYS* 1.3 80.0 - - - +
44B LEU* 1.3 69.3 + - + +
46B GLY* 3.2 12.3 + - - -
47B PHE* 3.2 8.3 + - - +
180B SER* 3.8 17.1 - - - -
181B ARG* 3.1 44.5 + - - +
182B TYR* 3.8 14.5 + - + -
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.8 48.4 - - + +
28B ILE* 5.4 3.6 - - + -
29B LEU* 4.2 20.2 - - + +
40B THR* 3.5 22.0 + - + +
41B LYS 3.8 4.0 + - - +
42B LYS 3.5 0.2 - - - -
43B ASP* 1.3 84.1 - - + +
45B ASP* 1.3 55.4 + - - +
47B PHE* 2.8 12.3 + - + +
48B ARG* 2.7 46.3 + - - +
181B ARG 5.5 0.9 - - - +
183B PRO* 4.3 30.3 - - + -
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Residues in contact with ASP 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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41B LYS* 3.0 21.8 - - - +
42B LYS* 3.6 9.9 - - - +
43B ASP 3.2 0.4 - - - -
44B LEU* 1.3 77.5 - - - +
46B GLY* 1.3 51.6 + - - +
48B ARG* 3.4 30.3 + - - +
49B LYS* 2.8 49.8 + - - +
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Residues in contact with GLY 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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42B LYS 3.6 5.1 + - - -
43B ASP 3.2 4.7 + - - -
45B ASP* 1.3 77.4 - - - +
47B PHE* 1.3 53.8 + - - +
49B LYS* 3.1 14.6 + - - +
50B LEU* 2.7 37.6 + - - +
182B TYR* 3.4 18.4 - - - -
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Residues in contact with PHE 47 (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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21B VAL* 6.0 0.2 - - + -
25B LEU* 5.3 16.2 - - + -
43B ASP 3.2 4.6 + - - +
44B LEU* 2.8 23.8 + - + +
46B GLY* 1.3 75.0 - - - +
48B ARG* 1.3 49.1 + - + +
50B LEU* 2.7 8.6 + - + +
51B PHE* 2.6 64.6 + + + -
182B TYR* 3.2 36.6 + + + -
183B PRO* 3.0 45.1 - - + -
185B ILE* 4.5 20.6 - - + -
192B PRO* 6.1 1.6 - - + -
208B TYR* 4.0 9.2 - + - -
357B LEU* 4.2 17.7 - - + -
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Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU 6.0 0.7 - - - +
21B VAL* 6.0 1.6 - - + -
22B LYS* 3.8 44.8 + - + +
25B LEU* 5.1 17.1 - - + +
26B GLU* 5.7 0.4 - - - +
29B LEU* 4.5 18.4 - - - +
44B LEU* 2.7 24.5 + - + +
45B ASP* 3.6 29.8 + - - +
47B PHE* 1.3 73.1 - - + +
49B LYS* 1.3 62.2 + - - +
51B PHE* 4.0 9.4 - - + -
52B HIS* 3.0 27.9 + - - +
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 2.8 26.5 + - - +
46B GLY* 3.3 15.7 - - - +
47B PHE 3.1 0.2 - - - -
48B ARG* 1.3 78.3 - - - +
50B LEU* 1.3 60.1 + - + +
52B HIS* 4.6 4.5 - - - +
53B ARG* 3.3 23.3 + - - +
335B ASN* 3.4 28.2 + - - +
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Residues in contact with LEU 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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46B GLY 2.7 10.8 + - - +
47B PHE* 2.7 13.9 + - + +
49B LYS* 1.3 72.0 - - + +
51B PHE* 1.3 58.9 + - - +
53B ARG* 3.5 17.8 - - - +
54B PHE* 2.9 23.4 + - - +
182B TYR* 3.6 34.5 - - + +
210B PRO* 5.2 4.0 - - + -
214B ASP* 5.5 3.6 - - - +
339B MET* 6.3 0.2 - - + -
341B ILE* 3.3 34.9 - - + +
357B LEU* 4.5 27.1 - - + +
358B GLU* 5.6 0.7 - - - -
359B THR* 4.0 22.9 - - + +
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Residues in contact with PHE 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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17B LEU* 5.1 2.9 - - + -
18B GLU* 5.0 10.3 - - + -
21B VAL* 4.3 22.7 - - + -
47B PHE* 2.6 39.9 + + + +
48B ARG* 3.8 11.4 - - + +
50B LEU* 1.3 69.6 - - - +
52B HIS* 1.3 57.4 + - - +
53B ARG 2.8 3.8 - - - -
54B PHE* 2.4 38.8 + + + +
55B LEU* 3.2 44.1 + - + +
185B ILE* 3.7 28.5 - - + -
190B LEU* 4.3 28.0 - - + -
357B LEU* 4.5 9.4 - - + +
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Residues in contact with HIS 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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18B GLU* 5.7 7.8 - - + +
48B ARG 3.0 13.8 + - - +
49B LYS* 4.6 3.8 - - - +
51B PHE* 1.3 78.5 - - - +
53B ARG* 1.3 63.1 + - + +
55B LEU* 3.6 12.9 + - - +
56B GLN* 3.5 30.5 + - + +
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Residues in contact with ARG 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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49B LYS* 3.3 22.1 + - - +
50B LEU* 3.5 19.4 - - - +
51B PHE 2.8 0.4 - - - -
52B HIS* 1.3 84.2 - - + +
54B PHE* 1.3 62.0 + - - +
55B LEU 3.3 0.8 + - - -
56B GLN* 3.7 17.7 + - - +
337B ILE 4.6 3.2 + - - -
338B ASP* 3.0 29.9 + - - +
339B MET* 3.8 35.2 + - - +
341B ILE* 4.4 24.9 - - + +
359B THR* 5.6 1.0 - - - +
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Residues in contact with PHE 54 (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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50B LEU 2.9 12.4 + - - +
51B PHE* 2.4 29.6 + + - +
53B ARG* 1.3 74.5 - - - +
55B LEU* 1.3 68.8 + - + -
56B GLN 3.7 3.0 + - - +
185B ILE* 6.3 1.6 - - + -
190B LEU* 4.4 20.0 - - + -
341B ILE* 4.7 13.2 - - + -
343B VAL* 3.9 35.9 - - + -
355B ILE* 4.7 18.6 - - + -
357B LEU* 4.3 28.3 - - + -
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Residues in contact with LEU 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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14B ARG* 4.3 28.4 - - + +
17B LEU* 5.4 6.5 - - + -
18B GLU* 4.2 20.6 - - + +
51B PHE* 3.2 48.2 + - + +
52B HIS* 3.6 9.4 + - - +
53B ARG 3.3 0.4 - - - -
54B PHE* 1.3 91.8 - - + +
56B GLN* 1.3 60.2 + - - +
190B LEU* 4.9 8.1 - - + -
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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