Contacts of the helix formed by residues 38 - 49 (chain X) in PDB entry 1NJI
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 38 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36X PRO* 3.3 20.3 + - - +
37X GLU* 1.3 77.9 + - - +
39X ASP* 1.3 68.7 + - + +
40X ALA* 3.3 10.8 - - + +
41X TYR* 4.0 18.6 - - - +
42X ARG* 2.7 36.9 + - - +
103X GLU* 5.2 1.0 + - - -
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Residues in contact with ASP 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945A U 3.6 2.6 + - - -
946A C 3.5 35.1 + - - +
947A U 5.5 2.6 - - - +
38X THR* 1.3 78.9 - - + +
40X ALA* 1.3 66.0 + - - +
42X ARG* 2.9 29.8 + - - +
43X GLY 3.1 18.9 + - - -
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Residues in contact with ALA 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945A U 2.7 34.4 + - - +
946A C 3.6 16.7 + - - +
1022A A 4.8 6.7 - - + +
1023A C 4.3 20.2 - - - +
38X THR* 4.0 9.0 - - + +
39X ASP* 1.3 80.0 - - - +
41X TYR* 1.3 64.5 + - + +
43X GLY 3.5 0.2 + - - -
44X MET* 3.4 16.4 - - + +
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Residues in contact with TYR 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023A C 3.6 19.1 - - - -
1024A G 2.9 33.9 + - - -
24X LEU* 3.7 17.9 - - + -
35X VAL* 3.2 24.5 - - + -
36X PRO* 3.3 46.7 - - + +
38X THR* 3.4 19.5 + - - +
39X ASP 3.3 0.2 - - - -
40X ALA* 1.3 78.6 - - + +
42X ARG* 1.3 66.8 + - - +
44X MET* 3.2 25.7 + - + +
45X VAL* 3.0 28.6 + - - +
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Residues in contact with ARG 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946A C 6.3 0.2 - - - -
3101B G 4.5 14.1 + - - -
37X GLU* 5.7 4.3 - - - +
38X THR 2.7 24.4 + - - +
39X ASP* 2.9 38.0 + - - +
41X TYR* 1.3 73.1 - - - +
43X GLY* 1.3 63.1 + - - +
45X VAL* 3.1 16.3 - - + +
46X ALA* 3.0 23.5 + - + +
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Residues in contact with GLY 43 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945A U 3.2 32.3 - - - +
946A C 4.5 6.0 - - - -
39X ASP 3.1 11.1 + - - -
40X ALA 3.5 0.2 + - - -
41X TYR 3.3 0.2 - - - -
42X ARG* 1.3 75.5 - - - +
44X MET* 1.3 62.7 + - - +
46X ALA* 3.3 9.2 + - - +
47X LYS* 3.2 22.2 + - - +
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Residues in contact with MET 44 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944A G 3.3 40.4 - - - +
945A U 3.3 22.7 - - - +
1023A C 4.7 2.5 - - - +
1024A G 4.8 7.6 - - - +
20X THR* 3.8 23.1 - - + +
23X MET* 5.1 3.8 - - - -
24X LEU* 3.9 19.7 - - + -
40X ALA* 3.4 9.1 + - + +
41X TYR* 3.2 53.5 + - + +
43X GLY* 1.3 76.5 - - - +
45X VAL* 1.3 62.9 + - - +
47X LYS* 3.2 6.4 + - - +
48X VAL* 3.2 20.8 + - - +
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Residues in contact with VAL 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X HIS* 5.9 7.0 - - + +
4X LEU* 4.7 11.4 - - + -
24X LEU* 4.7 11.9 - - + -
35X VAL* 4.5 24.7 - - + -
41X TYR 3.0 16.0 + - - +
42X ARG* 3.1 21.8 - - + +
44X MET* 1.3 77.0 - - - +
46X ALA* 1.3 63.8 + - + +
48X VAL* 3.3 7.6 + - - +
49X ASN* 2.8 28.1 + - - +
52X VAL* 5.1 0.9 - - - +
54X PHE* 4.8 29.3 - - + -
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Residues in contact with ALA 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3083B G 5.2 7.7 + - - -
3099B U 4.5 5.0 + - - -
3100B G 4.5 27.7 - - - +
42X ARG* 3.0 10.6 + - + +
43X GLY* 3.5 13.2 - - - +
44X MET 3.1 0.2 - - - -
45X VAL* 1.3 84.6 - - + +
47X LYS* 1.3 59.4 + - - +
49X ASN* 3.0 25.4 - - - +
50X ASP* 5.4 1.0 - - - +
54X PHE* 6.3 0.4 - - - -
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Residues in contact with LYS 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944A G 3.4 26.5 - - - +
945A U 3.2 21.9 + - - +
3083B G 6.2 1.3 - - - +
3084B G 4.7 5.4 + - - -
16X ASP* 3.2 47.5 + - - +
17X ILE* 3.8 27.9 - - + +
20X THR* 3.7 14.1 - - - +
43X GLY 3.2 11.2 + - - +
44X MET* 3.5 9.2 - - - +
46X ALA* 1.3 76.0 - - - +
48X VAL* 1.3 61.2 + - + +
49X ASN* 3.7 0.4 + - - -
50X ASP* 5.0 2.1 + - - +
51X PHE* 5.1 0.3 - - - -
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Residues in contact with VAL 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X LEU* 4.9 4.7 - - + -
17X ILE* 3.9 15.9 - - + +
20X THR* 3.8 26.7 - - + -
21X LEU* 3.1 45.5 - - + -
24X LEU* 5.4 0.9 - - + -
44X MET 3.2 8.6 + - - +
45X VAL* 3.9 5.4 - - - +
46X ALA 3.3 0.2 - - - -
47X LYS* 1.3 78.1 - - - +
49X ASN* 1.3 54.4 + - - +
50X ASP 2.7 16.8 + - - -
51X PHE* 2.9 17.1 + - + -
52X VAL* 3.6 25.3 + - + +
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Residues in contact with ASN 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3084B G 4.8 0.2 + - - -
3098B C 5.6 0.9 + - - -
3099B U 3.7 38.0 + - - +
45X VAL 2.8 13.8 + - - +
46X ALA* 3.0 22.9 - - - +
47X LYS 3.3 1.0 - - - -
48X VAL* 1.3 74.4 - - - +
50X ASP* 1.3 76.1 + - - +
51X PHE 3.4 0.6 + - - -
52X VAL* 3.9 9.7 - - - +
54X PHE* 3.8 23.5 - - - -
138X LEU* 4.5 0.3 - - - +
139X GLY* 3.6 29.6 + - - -
140X LYS* 4.5 1.4 - - - +
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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
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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