Contacts of the helix formed by residues 26 - 41 (chain N) in PDB entry 2JA7
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 THR 26 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N PRO* 4.3 2.6 - - + -
25N ILE* 1.3 77.8 - - - +
27N ALA* 1.3 69.7 + - - +
28N GLU* 4.6 5.8 + - - +
29N ASP* 2.7 37.5 + - - +
30N SER* 3.9 2.6 + - - -
655N LYS* 4.2 14.1 + - + +
707N PRO* 4.3 4.8 - - - +
708N GLU* 3.5 17.5 - - + +
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Residues in contact with ALA 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N THR* 1.3 71.5 - - - +
28N GLU* 1.3 55.0 + - - +
29N ASP 2.4 19.6 + - - -
30N SER* 2.5 29.1 + - - -
31N TRP* 4.3 2.2 + - - -
706N GLN* 5.5 6.5 - - - +
707N PRO* 4.9 6.5 - - + -
708N GLU* 3.4 20.3 + - + +
744N HIS* 6.0 6.5 - - + -
1049N ASP* 5.8 4.3 - - - +
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Residues in contact with GLU 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N THR* 3.7 5.7 + - - +
27N ALA* 1.3 75.5 - - - +
29N ASP* 1.3 61.0 + - - +
30N SER 3.6 0.2 - - - -
31N TRP* 3.9 19.9 + - - +
32N ALA* 4.4 1.9 + - - +
807N ARG* 3.3 31.5 + - - -
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Residues in contact with ASP 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N ILE* 3.1 18.2 - - + +
26N THR* 2.7 43.3 + - - +
27N ALA 2.4 14.5 + - - -
28N GLU* 1.3 66.4 - - - +
30N SER* 1.3 67.3 + - - +
31N TRP 2.7 4.5 + - - -
32N ALA* 2.7 24.6 + - - +
33N VAL 3.8 1.0 + - - -
655N LYS* 4.1 22.3 - - - +
658N ILE* 3.2 34.6 - - + +
662N MET* 5.1 2.9 - - - +
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Residues in contact with SER 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N ILE* 4.7 2.1 - - - +
26N THR 3.9 2.0 + - - -
27N ALA* 2.5 29.5 + - - -
29N ASP* 1.3 71.9 - - - +
31N TRP* 1.3 63.3 + - - -
33N VAL* 2.9 28.9 + - - +
34N ILE* 3.1 9.8 + - - +
638N PHE* 5.0 9.0 - - - -
707N PRO* 4.9 9.1 - - - +
743N ILE* 2.9 32.5 + - - +
744N HIS* 4.5 14.0 + - - -
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Residues in contact with TRP 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N ALA 4.9 2.2 - - - -
28N GLU* 3.9 25.1 + - - +
29N ASP 2.7 4.6 + - - -
30N SER* 1.3 73.8 - - - +
32N ALA* 1.3 53.4 + - - +
34N ILE* 2.8 36.0 + - + +
35N SER* 2.6 36.1 + - - -
744N HIS* 3.7 37.1 - + - -
746N SER* 3.5 21.8 - - - -
747N MET* 4.7 5.8 - - + -
806N THR* 5.8 0.7 - - + -
807N ARG* 3.3 71.3 - - + +
808N ALA* 4.5 8.5 - - + -
811N TYR* 4.0 24.7 + + - +
1045N SER* 5.0 3.8 - - - -
1046N PRO* 6.0 0.4 - - + -
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Residues in contact with ALA 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N GLU 4.4 1.5 + - - +
29N ASP* 2.7 17.4 + - - +
31N TRP* 1.3 72.3 - - - +
33N VAL* 1.3 62.9 + - - +
35N SER* 3.2 11.0 + - - -
36N ALA* 3.0 20.6 + - - +
658N ILE* 4.4 17.0 - - + +
661N LEU* 4.8 8.4 - - + +
662N MET* 4.1 27.8 - - + -
665N GLU* 4.2 7.8 - - - +
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Residues in contact with VAL 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N ASP 4.6 0.2 - - - +
30N SER* 2.9 16.4 + - - +
32N ALA* 1.3 76.9 - - - +
34N ILE* 1.3 64.4 + - - +
36N ALA* 2.9 23.2 + - - +
37N PHE 3.0 4.7 + - - -
638N PHE* 3.6 39.5 - - + -
653N VAL* 5.3 2.7 - - + -
658N ILE* 4.6 20.9 - - + -
661N LEU* 4.5 10.3 - - + -
681N TRP* 3.6 26.5 - - + -
684N LEU* 4.6 13.7 - - + -
743N ILE* 4.4 6.7 - - + -
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Residues in contact with ILE 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N SER 3.1 5.1 + - - +
31N TRP* 2.8 42.1 + - + +
33N VAL* 1.3 70.1 - - - +
35N SER* 1.3 58.2 + - - +
37N PHE* 2.5 36.2 + - + +
38N PHE* 3.3 31.8 + - + -
542N MET* 4.2 9.0 - - + -
743N ILE* 3.3 28.7 - - + -
744N HIS* 4.2 8.5 - - + -
747N MET* 3.8 28.5 - - + -
811N TYR* 4.1 9.9 - - + -
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Residues in contact with SER 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N TRP 2.6 13.4 + - - -
32N ALA* 3.2 12.7 - - - -
34N ILE* 1.3 72.1 - - - +
36N ALA* 1.3 59.6 + - - +
38N PHE* 3.7 2.8 + - - +
39N ARG* 2.8 35.9 + - - +
665N GLU* 3.7 23.1 + - - -
810N GLU* 3.4 15.2 + - - -
811N TYR* 3.0 30.3 + - - -
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Residues in contact with ALA 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N ALA 3.0 10.7 + - - +
33N VAL* 2.9 14.6 + - - +
34N ILE 2.9 0.4 - - - -
35N SER* 1.3 76.4 - - - +
37N PHE* 1.3 64.3 + - - +
39N ARG* 3.3 28.6 + - - +
40N GLU* 3.6 3.6 + - - +
661N LEU* 4.2 24.9 - - + -
680N THR* 5.0 1.5 - - - -
681N TRP* 3.9 18.5 + - + +
684N LEU* 4.4 11.0 - - + -
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Residues in contact with PHE 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N VAL 3.0 4.4 + - - -
34N ILE* 2.5 24.9 + - + +
36N ALA* 1.3 74.5 - - - +
38N PHE* 1.3 70.7 + + - +
40N GLU* 3.2 1.7 + - - +
41N LYS* 2.9 59.6 + - + +
541N LEU 4.5 4.0 - - - -
542N MET* 3.1 74.3 - - + -
544N CYS* 4.0 10.8 - - - -
636N PRO* 4.2 8.1 - - + -
681N TRP* 3.7 31.8 - + + +
692N TYR* 5.0 2.7 - + - -
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Residues in contact with PHE 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N ILE* 3.3 25.5 + - + -
35N SER 4.5 1.1 - - - +
37N PHE* 1.3 91.9 - + - +
39N ARG* 1.3 66.9 + - - +
40N GLU 3.2 0.4 + - - -
41N LYS* 3.8 1.6 - - + -
42N GLY* 3.4 31.6 + - - +
43N LEU* 3.4 30.5 - - + -
541N LEU* 3.8 31.9 - - + -
747N MET* 3.9 20.4 - - + -
811N TYR* 3.0 49.6 - + + +
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Residues in contact with ARG 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ALA 5.4 0.2 + - - -
35N SER* 2.8 33.4 + - - +
36N ALA* 3.3 20.0 - - - +
37N PHE 3.1 0.8 - - - -
38N PHE* 1.3 79.3 - - - +
40N GLU* 1.3 59.8 + - + +
661N LEU* 6.4 0.2 - - - -
664N THR* 5.9 1.8 - - - -
665N GLU* 2.6 56.4 + - - +
668N ASP* 4.1 18.2 + - - +
810N GLU* 5.5 2.0 + - - -
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Residues in contact with GLU 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N ALA 4.3 5.4 - - - +
37N PHE 3.2 5.6 + - - +
39N ARG* 1.3 82.3 - - + +
41N LYS* 1.3 74.9 + - + +
680N THR* 3.5 17.6 + - + +
681N TRP* 3.8 24.0 - - + +
682N SER* 3.4 37.3 + - - -
692N TYR* 5.3 0.3 + - - -
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Residues in contact with LYS 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N PHE* 2.9 54.0 + - + +
38N PHE* 4.5 1.8 - - + -
40N GLU* 1.3 97.2 - - - +
42N GLY* 1.3 66.1 + - - +
45N SER* 4.1 20.2 + - - -
48N LEU* 5.1 6.8 - - - +
49N ASP* 4.0 20.4 + - - -
544N CYS* 4.3 18.1 - - - +
634N TYR* 4.9 8.5 + - - -
681N TRP* 4.9 2.5 - - + -
692N TYR* 4.2 20.0 + - - +
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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
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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