Contacts of the helix formed by residues 36 - 48 (chain B) in PDB entry 4RN1
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 LYS 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASP* 3.2 36.5 + - + +
34B ILE 3.2 1.8 + - - -
35B PRO* 1.3 79.3 - - + +
37B ARG* 1.3 64.5 + - - +
38B ALA 3.3 2.5 - - - -
39B ASP* 3.3 7.2 + - + +
40B MET* 3.0 27.7 + - + +
336B PHE* 4.7 20.2 - - + -
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Residues in contact with ARG 37 (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 ASP* 3.7 0.4 + - - +
34B ILE* 3.2 47.9 + - + +
35B PRO 3.1 3.1 + - - -
36B LYS* 1.3 79.1 - - - +
38B ALA* 1.3 59.2 + - - +
40B MET* 3.3 5.5 + - + +
41B VAL* 2.9 43.1 + - + +
137B TRP 4.4 5.3 + - - -
138B SER* 5.0 5.1 - - - +
141B TRP* 3.6 11.3 - - - -
303B GLY 2.8 31.1 + - - +
304B GLY* 3.7 8.3 + - - -
305B GLY 3.0 29.2 + - - +
306B TYR* 5.1 0.4 - - - -
308B LEU* 3.6 29.4 - - + +
311B THR* 4.0 11.9 - - + -
315B TRP* 3.6 22.1 - - - -
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 3.9 16.5 - - + +
28B CYS* 3.6 30.9 + - + -
29B ASP* 3.2 11.1 + - - +
34B ILE 5.0 0.2 + - - -
37B ARG* 1.3 79.7 - - - +
39B ASP* 1.3 57.3 + - - +
41B VAL* 3.5 6.7 + - - +
42B HIS* 3.0 29.6 + - - +
138B SER* 3.7 15.3 - - - +
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Residues in contact with ASP 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 3.7 13.3 - - - +
29B ASP* 2.8 28.3 + - - +
36B LYS* 3.6 8.7 - - + +
37B ARG 3.2 0.2 - - - -
38B ALA* 1.3 74.8 - - - +
40B MET* 1.3 54.3 + - - +
42B HIS* 3.4 6.6 + - - +
43B SER* 2.7 49.0 + - - -
335B GLU* 5.9 0.9 - - - +
336B PHE* 3.3 25.3 - - + -
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Residues in contact with MET 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PRO 5.1 0.7 - - - +
36B LYS* 3.0 23.3 + - + +
37B ARG* 3.7 4.7 - - - +
39B ASP* 1.3 76.0 - - - +
41B VAL* 1.3 63.9 + - - +
43B SER* 4.0 0.5 - - - -
44B LEU* 3.1 26.0 + - - +
308B LEU* 3.8 28.7 - - + +
309B ALA* 3.9 28.0 - - - +
312B ALA* 4.0 8.9 - - + +
334B HIS* 5.0 0.7 + - - -
336B PHE* 3.7 39.0 - - + -
339B ALA* 3.9 27.6 - - + -
340B TYR* 4.0 12.2 + - + +
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 5.5 0.9 - - - +
37B ARG* 2.9 29.2 + - + +
38B ALA* 3.8 7.0 - - - +
40B MET* 1.3 77.5 - - - +
42B HIS* 1.3 63.2 + - + +
44B LEU* 3.9 1.6 - - - +
45B ILE* 3.1 45.2 + - + +
137B TRP* 4.2 15.3 - - + -
311B THR* 4.7 0.2 - - + -
312B ALA* 4.0 24.0 - - + +
315B TRP* 3.7 42.8 - - + -
316B THR* 4.0 1.6 + - - +
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Residues in contact with HIS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 2.9 38.5 + + - +
20B TYR* 3.3 50.4 + + - -
25B VAL* 4.3 11.2 - - + -
38B ALA 3.0 16.8 + - - +
39B ASP* 4.0 7.4 - - - +
41B VAL* 1.3 78.6 - - + +
43B SER* 1.3 62.8 + - - +
45B ILE* 3.3 2.1 + - - +
46B GLU* 2.8 50.7 + - + +
51B HIS* 5.1 10.8 - + + -
56B ILE* 6.1 0.9 - - + -
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASP* 2.7 40.6 + - - -
40B MET 4.0 2.5 - - - -
42B HIS* 1.3 75.1 - - - +
44B LEU* 1.3 59.8 + - - +
46B GLU* 3.6 15.1 + - - +
47B ALA* 2.9 28.4 + - - +
334B HIS* 3.9 21.8 - - - +
335B GLU* 4.9 5.6 - - - +
336B PHE* 3.7 13.7 - - - -
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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
----------------------------------------------------------
40B MET 3.1 18.8 + - - +
41B VAL 3.9 0.2 - - - +
43B SER* 1.3 73.0 - - - +
45B ILE* 1.3 66.2 + - - +
47B ALA* 3.2 4.0 + - + +
48B TYR* 3.1 48.9 + - + -
312B ALA* 3.6 17.0 - - + +
313B ARG* 4.0 5.2 - - - +
316B THR* 3.4 25.4 - - + +
331B ILE* 4.1 14.4 - - + -
332B PRO* 4.3 3.4 - - + -
334B HIS* 3.7 27.5 - - + +
340B TYR* 3.5 24.7 - - + +
346B LEU* 4.5 8.3 - - + -
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 3.9 21.8 - - + +
41B VAL* 3.1 24.1 + - + +
42B HIS* 3.6 4.9 - - - +
44B LEU* 1.3 76.3 - - - +
46B GLU* 1.3 61.1 + - - +
48B TYR* 3.3 3.1 + - - -
49B ALA 3.2 3.5 + - - -
50B LEU* 3.1 44.9 + - + +
51B HIS* 4.1 11.0 - - + +
54B MET* 4.4 11.0 - - + -
137B TRP* 3.8 22.7 - - + +
315B TRP 4.7 1.3 - - - +
316B THR* 3.6 26.2 - - + +
319B THR* 3.7 20.2 - - + +
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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
----------------------------------------------------------
42B HIS* 2.8 38.1 + - + +
43B SER* 3.6 14.3 + - - +
45B ILE* 1.3 74.5 - - - +
47B ALA* 1.3 60.4 + - - +
49B ALA* 2.9 19.8 + - - +
51B HIS* 3.6 34.6 + - + +
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B SER 2.9 18.8 + - - +
44B LEU* 3.2 10.5 + - + +
46B GLU* 1.3 77.8 - - - +
48B TYR* 1.3 59.4 + - - +
49B ALA* 3.2 1.8 + - - +
332B PRO* 4.0 31.7 - - + +
333B ASP 4.8 1.6 - - - +
334B HIS* 4.0 22.4 - - + +
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Residues in contact with TYR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.1 41.8 + - + +
45B ILE 3.3 5.1 + - - +
46B GLU 3.2 0.2 - - - -
47B ALA* 1.3 75.0 - - - +
49B ALA* 1.3 70.3 + - - +
50B LEU* 3.2 23.9 + - + +
53B GLN* 5.4 0.7 + - - -
316B THR* 3.7 15.5 - - + -
327B LEU* 3.9 20.4 - - + +
328B SER* 3.1 41.5 + - - -
330B GLU 3.3 12.0 + - - -
331B ILE* 3.9 3.3 - - - +
332B PRO* 3.4 31.4 - - + +
346B LEU* 3.8 25.6 - - + +
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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