Contacts of the helix formed by residues 44 - 56 (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 VAL 44 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42N GLY* 4.7 4.0 - - - -
43N LEU* 1.3 88.1 - - + +
45N SER* 1.3 70.0 + - - +
46N GLN* 3.5 8.0 - - - +
47N GLN* 3.2 14.2 + - + +
48N LEU* 3.4 26.9 + - + -
175N ARG* 6.1 0.7 - - - +
199N MET* 3.3 51.8 - - + +
200N GLY 3.8 10.3 - - - +
201N GLY* 5.0 3.4 - - - -
492N LEU* 5.3 2.0 - - + -
495N LEU* 3.9 20.4 - - + -
496N ARG* 5.9 0.2 - - + -
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Residues in contact with SER 45 (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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41N LYS* 4.1 31.8 + - - -
42N GLY 3.2 15.2 + - - -
44N VAL* 1.3 82.1 - - - +
46N GLN* 1.3 77.9 + - - +
48N LEU* 2.6 23.4 + - - +
49N ASP* 3.2 20.7 + - - -
496N ARG* 4.9 5.7 + - - -
543N SER 4.6 3.6 + - - -
544N CYS* 4.2 17.4 - - - +
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Residues in contact with GLN 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N LEU 4.1 3.2 + - - -
44N VAL* 3.5 8.9 - - - +
45N SER* 1.3 82.9 + - - +
47N GLN* 1.3 83.2 + - + +
49N ASP* 3.4 4.5 + - - +
50N SER* 2.8 28.1 + - - -
214N ALA* 6.1 0.3 - - - +
408N LEU* 3.8 22.5 - - + +
495N LEU* 3.5 17.2 - - - +
496N ARG* 3.6 37.7 - - - +
497N ARG 5.7 0.3 - - - +
539N LEU* 3.5 30.1 - - + +
544N CYS* 5.4 3.1 - - - +
545N ILE* 4.6 23.6 - - + +
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Residues in contact with GLN 47 (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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44N VAL* 3.7 9.0 - - + +
45N SER 2.9 0.8 + - - -
46N GLN* 1.3 92.3 + - + +
48N LEU* 1.3 67.7 + - - +
50N SER* 4.0 1.4 - - - -
51N PHE 3.2 8.8 + - - -
173N MET* 3.0 23.8 - - + +
201N GLY* 3.2 32.6 - - - +
203N PHE* 5.3 1.0 - - - -
211N VAL* 4.8 3.3 - - - +
212N LEU* 3.4 28.7 + - - +
213N ILE* 5.6 0.2 - - - +
214N ALA 5.1 1.0 - - - +
408N LEU* 3.7 31.2 - - - +
409N ALA* 3.7 17.2 - - - +
495N LEU* 3.8 26.2 + - + +
497N ARG 5.8 0.6 + - - -
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Residues in contact with LEU 48 (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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41N LYS 5.1 6.5 - - - +
42N GLY* 6.3 0.2 - - - -
44N VAL* 3.7 33.7 - - + +
45N SER* 2.6 15.5 + - - +
47N GLN* 1.3 69.1 - - - +
49N ASP* 1.3 58.8 + - - +
51N PHE* 2.6 30.7 + - - +
52N ASN* 3.1 19.9 + - - +
173N MET* 3.9 12.1 - - - -
174N LEU 3.7 17.7 - - - +
175N ARG* 3.3 35.0 - - + +
176N SER* 4.2 2.9 - - - +
199N MET 4.9 1.6 - - - +
201N GLY* 4.1 7.6 - - - +
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Residues in contact with ASP 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41N LYS* 4.0 21.7 + - - -
45N SER* 3.2 20.1 + - - -
46N GLN* 4.0 6.2 + - - +
48N LEU* 1.3 80.5 - - - +
50N SER* 1.3 57.1 + - - +
52N ASN* 3.3 14.7 + - - +
53N GLN* 2.9 32.3 + - - +
547N VAL* 4.9 8.1 - - + -
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Residues in contact with SER 50 (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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46N GLN 2.8 20.6 + - - -
47N GLN 4.0 3.1 - - - -
48N LEU 2.8 2.0 + - - -
49N ASP* 1.3 74.7 - - - +
51N PHE* 1.3 62.0 + - - +
53N GLN* 3.7 2.8 + - - +
54N PHE* 3.2 19.6 + - - +
408N LEU* 4.0 18.6 - - - +
409N ALA 5.1 0.2 - - - -
410N GLY* 3.3 10.4 + - - -
411N PRO* 3.3 27.0 - - - +
547N VAL* 4.5 14.2 - - - +
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Residues in contact with PHE 51 (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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47N GLN 3.2 13.2 + - - +
48N LEU* 2.6 14.7 + - - +
50N SER* 1.3 69.6 - - - +
52N ASN* 1.3 62.1 + - - +
54N PHE* 2.8 36.7 + + + +
55N VAL* 3.0 24.1 + - + +
170N LEU* 4.4 7.4 - - + -
171N PRO 3.8 4.0 - - - -
172N ILE* 3.7 17.7 - - + -
173N MET* 3.2 46.4 - - + -
176N SER* 3.5 22.9 - - - -
178N ASN* 5.4 2.5 - - + -
203N PHE* 3.9 13.0 - + - -
409N ALA 5.5 0.4 - - - -
410N GLY* 4.6 4.7 - - - -
413N LEU* 3.4 34.1 - - + -
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Residues in contact with ASN 52 (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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48N LEU* 3.1 18.3 + - - +
49N ASP* 3.6 20.0 + - - +
51N PHE* 1.3 73.5 - - - +
53N GLN* 1.3 55.1 + - - +
54N PHE 2.6 16.4 + - - -
55N VAL* 2.8 17.4 + - - +
56N ASP* 3.0 29.1 + - - +
176N SER* 3.7 9.0 - - - +
177N LYS* 3.0 50.4 + - + +
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Residues in contact with GLN 53 (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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49N ASP 2.9 14.0 + - - +
50N SER 3.9 3.4 - - - +
52N ASN* 1.3 70.6 - - - +
54N PHE* 1.3 58.1 + - - +
56N ASP* 5.0 4.7 - - - -
57N TYR* 3.0 55.4 + - - +
58N THR* 2.9 28.6 + - - +
547N VAL* 3.1 47.6 - - + +
548N GLY 4.6 10.8 + - - +
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Residues in contact with PHE 54 (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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50N SER 3.2 12.8 + - - +
51N PHE* 2.8 14.4 + + - +
52N ASN 2.6 4.9 + - - -
53N GLN* 1.3 74.2 - - - +
55N VAL* 1.3 68.7 + - + -
58N THR* 3.1 25.5 - - + -
59N LEU* 2.6 65.6 + - + +
62N ILE* 4.3 4.7 - - + -
170N LEU* 3.9 19.1 - - + -
410N GLY* 4.1 14.1 - - - -
411N PRO* 5.9 0.2 - - + -
413N LEU* 3.9 32.3 - - + -
414N ALA* 3.5 33.2 - - + -
417N PHE* 4.4 7.2 - + + -
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Residues in contact with VAL 55 (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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51N PHE* 3.6 35.2 - - + +
52N ASN* 2.8 12.4 + - - +
54N PHE* 1.3 86.5 - - + +
56N ASP* 1.3 78.1 + - - +
59N LEU* 3.0 23.5 + - + +
95N ILE* 6.0 0.3 - - - +
97N VAL* 3.7 37.5 - - + -
170N LEU* 4.1 8.7 - - + -
172N ILE* 6.4 0.2 - - + -
178N ASN* 4.3 12.8 - - - +
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Residues in contact with ASP 56 (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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52N ASN* 3.0 24.4 + - - +
53N GLN* 5.0 1.7 - - - -
55N VAL* 1.3 86.1 - - - +
57N TYR* 1.3 84.5 + - + +
60N GLN* 4.3 8.7 - - - +
95N ILE* 6.1 0.3 - - - +
177N LYS* 3.3 41.7 + - - +
178N ASN* 5.7 0.9 - - - +
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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
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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