Contacts of the helix formed by residues 39 - 56 (chain B) in PDB entry 3ER8
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 GLN 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 3.8 25.6 - - + +
38B GLY* 1.3 95.0 + - - +
40B LEU* 1.3 63.3 + - - +
41B LYS 3.4 0.4 - - - -
42B LEU* 3.9 17.0 - - - +
43B LEU* 2.9 30.7 + - - +
71B PRO* 5.7 7.8 - - - +
72B GLY* 5.7 1.8 - - - +
73B THR* 3.6 17.6 + - - +
74B HIS* 3.5 32.8 + - - +
294B LEU* 3.5 24.2 - - + +
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.7 4.7 - - + -
36B TYR 3.6 9.5 + - - +
37B GLN* 2.8 11.8 + - + +
39B GLN* 1.3 78.7 - - - +
41B LYS* 1.3 64.8 + - - +
43B LEU* 4.7 0.7 - - - -
44B LEU* 2.9 63.5 + - + +
200B PHE* 3.2 41.1 - - + -
290B ILE* 4.0 17.3 - - + -
291B PHE* 3.8 31.2 - - + -
294B LEU* 3.8 8.9 - - + +
296B ILE* 4.4 8.1 - - + -
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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
----------------------------------------------------------
37B GLN 2.7 18.6 + - - +
38B GLY* 4.4 13.9 + - - -
40B LEU* 1.3 75.2 - - - +
42B LEU* 1.3 82.2 + - - +
44B LEU* 4.3 2.1 - - - +
45B GLY* 3.4 15.4 + - - -
175B LYS* 5.4 1.8 - - - +
196B MET* 5.6 0.9 - - - +
198B GLN* 3.5 34.3 - - + +
199B PRO* 3.5 22.3 + - - +
200B PHE 3.7 9.4 - - - +
201B ALA* 3.8 22.0 - - + -
202B PRO* 4.4 10.7 - - + +
207B GLU* 3.6 22.8 + - - +
209B ARG* 5.0 0.6 - - - +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 4.0 14.8 - - - +
39B GLN* 3.7 13.5 + - - +
40B LEU 3.2 0.2 - - - -
41B LYS* 1.3 95.5 - - - +
43B LEU* 1.3 64.1 + - - +
45B GLY* 3.1 2.3 + - - -
46B GLU* 3.0 38.6 + - - +
66B TYR* 5.0 2.5 - - - +
72B GLY* 6.1 0.4 - - - -
74B HIS* 3.8 31.4 - - + +
138B ASP* 4.2 26.2 - - - +
198B GLN* 5.2 0.9 - - - +
209B ARG* 4.2 19.3 - - - +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN 2.9 23.0 + - - +
40B LEU* 4.2 2.2 - - - +
42B LEU* 1.3 73.7 - - - +
44B LEU* 1.3 57.9 + - - +
46B GLU* 4.7 0.9 - - - +
47B LEU* 3.2 29.0 + - + +
74B HIS* 3.8 20.1 - - + +
77B TYR* 3.7 37.9 - - + -
78B LEU* 3.2 30.0 - - + +
290B ILE* 3.5 36.1 - - + +
293B PHE* 5.2 0.2 - - + -
294B LEU* 4.3 12.3 - - + -
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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
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40B LEU* 2.9 50.4 + - + +
41B LYS* 4.4 2.5 - - - +
43B LEU* 1.3 76.9 - - - +
45B GLY* 1.3 60.5 + - - +
47B LEU* 4.3 3.1 - - - +
48B PHE* 3.5 9.9 + - - +
199B PRO* 4.5 9.6 - - + +
200B PHE* 4.2 7.0 - - + -
263B MET* 3.7 34.8 - - + +
266B MET* 2.9 32.6 - - + +
267B LEU* 3.6 36.3 - - + +
290B ILE* 4.1 11.4 - - + -
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Residues in contact with GLY 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS 3.4 10.1 + - - -
42B LEU* 3.1 7.1 + - - -
44B LEU* 1.3 79.3 - - - +
46B GLU* 1.3 59.3 + - - +
47B LEU 3.4 0.2 - - - -
48B PHE* 3.6 2.6 - - - +
49B PHE* 3.1 27.5 + - - +
173B SER* 5.6 1.0 + - - -
196B MET* 3.7 30.4 - - - +
199B PRO* 5.9 0.4 - - - +
209B ARG* 5.9 3.8 - - - +
211B LEU* 5.2 0.3 - - - +
266B MET* 4.2 1.8 - - - -
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Residues in contact with GLU 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 LEU* 3.0 28.5 + - - +
45B GLY* 1.3 74.8 - - - +
47B LEU* 1.3 61.1 + - - +
48B PHE 3.3 0.2 - - - -
49B PHE* 3.9 7.0 - - + -
50B LEU* 3.0 36.6 + - + +
66B TYR* 2.2 40.0 + - - -
74B HIS* 2.8 25.0 + - - -
78B LEU* 3.1 29.6 - - + +
136B ILE* 4.3 19.3 - - + +
173B SER* 5.7 2.5 - - - +
209B ARG* 5.8 0.3 + - - -
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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
----------------------------------------------------------
43B LEU* 3.2 19.3 + - + +
44B LEU* 4.3 4.5 - - - +
46B GLU* 1.3 73.6 - - - +
48B PHE* 1.3 57.9 + - - +
50B LEU* 5.0 0.7 - - - -
51B SER* 2.6 44.7 + - - +
77B TYR* 4.4 9.2 - - + +
78B LEU* 3.6 24.2 - - + +
81B HIS* 3.4 37.5 - - + +
82B PHE* 4.2 7.2 - - + -
267B LEU* 4.0 14.4 - - + -
270B VAL* 4.4 14.6 - - + -
286B LEU* 5.6 3.1 - - + -
290B ILE* 4.0 26.9 - - + -
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B MET* 3.6 24.2 - - + -
12B TYR* 3.1 21.8 - + - -
44B LEU 3.5 5.2 + - - +
45B GLY 3.6 3.6 - - - +
47B LEU* 1.3 78.1 - - - +
49B PHE* 1.3 52.8 + - - +
51B SER* 3.7 4.1 - - - -
52B LYS* 2.7 48.1 + - + +
196B MET* 3.8 23.6 - - + -
211B LEU* 4.1 10.1 - - + -
266B MET* 3.4 40.4 - - + -
269B THR* 3.5 26.7 + - + -
270B VAL* 4.9 4.0 - - - +
376C ASP* 3.0 31.9 - - + -
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY 3.1 15.5 + - - +
46B GLU* 4.1 4.7 - - + +
48B PHE* 1.3 83.3 - - - +
50B LEU* 1.3 83.7 + - + +
52B LYS* 3.0 12.3 + - + +
53B LEU* 2.9 59.6 + - + +
134B ILE* 3.8 14.4 - - + -
136B ILE* 4.0 15.0 - - + -
171B ALA* 4.3 1.6 - - + -
172B SER* 3.6 33.7 - - - -
173B SER* 3.5 23.1 - - - +
211B LEU* 4.1 29.4 - - + -
212B SER 5.1 1.6 - - - -
213B ILE* 5.8 1.6 - - + -
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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
----------------------------------------------------------
46B GLU* 3.0 29.6 + - + +
49B PHE* 1.3 100.8 - - + +
51B SER* 1.3 57.2 + - - +
53B LEU* 3.4 21.5 - - + +
54B GLN* 3.1 21.0 + - - +
59B LEU* 3.2 25.1 - - + +
64B VAL* 4.7 4.9 - - + -
78B LEU* 4.7 2.5 - - + -
82B PHE* 3.5 20.8 - - + -
89B ILE* 6.0 0.2 - - + -
91B TRP* 4.3 20.4 - - + -
134B ILE* 4.0 8.7 - - + -
136B ILE* 3.5 25.1 - - + -
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 2.6 30.5 + - - +
48B PHE* 3.7 3.6 - - - -
50B LEU* 1.3 70.8 - - - +
52B LYS* 1.3 67.0 + - - +
54B GLN* 3.5 16.7 + - - +
55B ARG* 3.0 24.1 + - - +
81B HIS* 4.6 0.5 + - - -
82B PHE* 4.1 9.8 - - - -
269B THR 3.9 20.4 - - - -
270B VAL* 3.7 25.2 - - - +
271B TYR* 4.4 4.2 - - - -
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Residues in contact with LYS 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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12B TYR* 3.6 22.0 + - - -
48B PHE* 2.7 27.3 + - + +
49B PHE* 3.0 13.9 + - + +
51B SER* 1.3 76.5 - - - +
53B LEU* 1.3 70.5 + - + +
55B ARG* 3.1 24.4 + - - +
56B HIS* 3.2 26.3 + - + -
211B LEU* 5.0 6.7 - - + -
213B ILE* 5.4 6.5 - - + -
269B THR* 5.7 1.8 + - - +
371C LEU* 3.5 25.1 - - + +
375C ALA 2.9 28.3 + - - -
376C ASP* 3.2 20.8 + - - +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 2.9 38.0 + - + +
50B LEU* 3.4 32.5 - - + +
52B LYS* 1.3 76.5 - - + +
54B GLN* 1.3 54.9 + - - +
56B HIS* 2.5 33.6 + - - -
57B GLY 3.1 6.1 + - - -
58B ILE* 3.3 30.0 + - + -
59B LEU* 3.7 8.5 - - + -
134B ILE* 3.5 33.4 - - + -
171B ALA* 3.8 12.6 - - + -
213B ILE* 4.7 13.0 - - + -
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Residues in contact with GLN 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 3.1 13.8 + - - +
51B SER* 3.7 10.5 + - - +
53B LEU* 1.3 76.8 - - - +
55B ARG* 1.3 58.9 + - - +
57B GLY* 3.1 17.7 + - - -
59B LEU* 3.2 25.3 - - + +
60B ASP 5.1 0.9 - - - +
82B PHE* 3.4 18.1 - - - -
85B LEU* 4.1 19.9 + - - +
87B VAL* 3.1 31.9 - - + +
271B TYR* 3.7 28.3 + - + +
238C ARG* 5.7 0.3 - - - -
258C ARG* 4.5 18.6 + - - +
380C ASP* 3.9 6.8 - - - +
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Residues in contact with ARG 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 SER 3.0 13.3 + - - +
52B LYS* 3.2 17.9 - - - +
53B LEU 2.6 4.6 + - - -
54B GLN* 1.3 73.8 - - - +
56B HIS* 1.3 67.3 + - + +
57B GLY 3.2 1.1 - - - -
268B ARG 4.8 0.8 + - - -
269B THR* 3.0 44.9 + - - +
271B TYR* 2.9 48.7 + - + +
376C ASP 3.5 17.3 + - - -
377C THR* 3.8 14.9 + - - +
378C SER* 2.8 42.9 + - - +
379C CYS* 4.9 1.2 - - - +
380C ASP* 3.1 29.0 - - + +
388C VAL* 4.2 3.6 - - + +
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Residues in contact with HIS 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 LYS* 3.2 34.9 + - + +
53B LEU* 2.5 12.0 + - - +
55B ARG* 1.3 79.6 + - - +
57B GLY* 1.3 61.3 + - - +
58B ILE* 3.0 16.9 + - + +
213B ILE* 5.5 3.1 - - + -
363C GLU* 4.5 17.0 - - - +
367C SER* 3.7 38.4 + - - +
370C ILE* 3.9 23.6 - - + +
375C ALA 5.3 0.4 + - - -
376C ASP 6.4 0.2 - - - -
378C SER* 3.4 35.6 + - - -
380C ASP* 5.3 0.9 - - - -
388C VAL* 3.5 23.4 - - + +
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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) + - + + + + + -
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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