Contacts of the helix formed by residues 35 - 51 (chain G) in PDB entry 1N34
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 35 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1240A U 4.7 7.7 + - - -
1241A G 4.1 17.4 + - - -
1289A A 4.1 22.7 - - - +
1290A G 5.2 14.4 - - - -
1351A U 5.7 1.3 - - - +
1371A G 5.8 3.8 - - - +
1372A U 4.4 10.3 - - - +
31G MET* 3.8 3.3 - - - +
32G ARG* 3.4 22.7 + - - +
33G ASP* 3.8 25.7 + - + +
34G GLY* 1.3 72.9 - - - +
36G LYS* 1.3 55.2 + - - +
37G ASN* 2.6 24.6 + - + +
38G LEU* 3.1 42.2 - - + +
39G ALA* 3.4 1.9 + - - +
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Residues in contact with LYS 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372A U 4.9 0.4 + - - -
1373A G 4.2 25.8 + - - +
1374A A 3.4 13.2 + - - -
24G THR* 4.3 13.5 + - + +
27G ILE* 3.6 23.1 - - + -
28G ASN* 3.1 49.5 + - - +
31G MET* 3.8 13.0 - - - -
34G GLY 3.0 9.7 + - - -
35G LYS* 1.3 70.1 - - - +
37G ASN* 1.3 67.8 + - - +
39G ALA* 3.4 6.5 - - + -
40G ALA* 2.6 25.0 + - + +
42I ARG* 5.7 9.4 - - + +
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Residues in contact with ASN 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1290A G 2.9 19.8 + - - +
1291A G 2.7 33.7 + - - +
1373A G 5.6 0.8 + - - -
35G LYS* 2.6 13.2 + - + +
36G LYS* 1.3 81.2 - - - +
38G LEU* 1.3 60.7 + - + +
39G ALA 2.6 9.4 + - - -
40G ALA* 2.6 13.5 + - - +
41G ARG* 3.0 18.9 + - - +
40I LEU* 4.3 20.3 - - - +
41I VAL* 5.8 4.9 - - - +
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Residues in contact with LEU 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1240A U 2.9 61.5 - - - +
1241A G 4.6 4.0 - - - +
1290A G 6.0 1.3 - - - +
1291A G 5.1 4.7 - - - +
32G ARG* 5.1 4.0 - - + +
35G LYS* 3.1 42.2 - - + +
37G ASN* 1.3 80.5 - - + +
39G ALA* 1.3 89.2 + - + +
41G ARG* 3.1 20.5 - - + +
42G ILE* 2.7 28.7 + - + +
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Residues in contact with ALA 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1240A U 4.7 0.7 - - - -
27G ILE* 3.3 19.2 - - + +
30G ILE* 4.6 4.3 - - - +
31G MET* 3.5 36.3 - - + +
35G LYS 3.6 1.8 - - - +
36G LYS* 3.0 17.5 - - - +
37G ASN 2.6 4.0 + - - -
38G LEU* 1.3 84.9 - - + +
40G ALA* 1.3 69.5 + - - +
42G ILE* 2.7 15.1 + - - +
43G PHE* 3.2 7.4 + - - +
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Residues in contact with ALA 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ILE* 3.0 25.4 - - + +
36G LYS* 2.6 21.9 + - + +
37G ASN* 2.6 9.8 + - - +
39G ALA* 1.3 70.3 - - - +
41G ARG* 1.3 66.8 + - - +
43G PHE* 2.9 11.4 + - - +
44G TYR* 2.9 21.6 + - + +
41I VAL* 3.9 28.0 - - + -
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Residues in contact with ARG 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1291A G 3.2 30.4 + - - -
1292A U 2.7 43.4 + - - -
37G ASN* 3.0 11.7 + - - +
38G LEU* 3.1 25.9 - - - +
39G ALA 2.8 2.6 + - - -
40G ALA* 1.3 74.2 - - - +
42G ILE* 1.3 56.8 + - + +
44G TYR* 2.6 30.8 + - - -
45G ASP* 2.7 31.2 + - - +
41I VAL* 5.3 2.4 - - + +
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Residues in contact with ILE 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1240A U 3.3 54.7 - - + +
30G ILE* 3.6 14.1 - - + -
38G LEU* 2.7 22.3 + - + +
39G ALA 2.7 7.9 + - - +
41G ARG* 1.3 72.3 - - + +
43G PHE* 1.3 56.4 + - - +
45G ASP* 3.8 0.6 - - - +
46G ALA* 2.8 32.1 + - - +
116G ALA* 4.0 15.7 - - + -
117G ALA* 4.1 11.6 - - + +
120G ILE* 3.1 40.1 - - + +
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Residues in contact with PHE 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G VAL* 5.6 3.6 - - + -
18G TYR* 5.0 9.6 - + - -
23G VAL* 3.3 50.7 - - + -
26G PHE* 3.3 38.6 - + + -
27G ILE* 3.8 16.4 - - + -
30G ILE* 5.3 0.8 - - + +
39G ALA 3.2 5.3 + - - +
40G ALA 2.9 11.8 + - - +
42G ILE* 1.3 76.0 - - - +
44G TYR* 1.3 73.3 + + - +
46G ALA* 3.7 10.0 - - + +
47G CYS* 3.5 27.4 - - - -
58G PRO 5.8 0.7 - - - -
62G PHE* 4.0 30.1 - + + -
124G LEU* 4.8 8.5 - - + -
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Residues in contact with TYR 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ASP* 2.9 26.9 + - - -
17G VAL* 3.4 28.9 - - + +
27G ILE* 4.0 12.0 - - + +
40G ALA* 2.9 19.0 + - + +
41G ARG* 2.6 14.9 + - - +
43G PHE* 1.3 89.5 - + - +
45G ASP* 1.3 61.7 - - - +
46G ALA 3.1 4.0 - - - -
47G CYS* 2.9 29.2 + - - +
48G LYS* 3.4 7.2 + - - +
41I VAL* 2.9 52.1 - - + +
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Residues in contact with ASP 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G ARG* 2.7 38.6 + - - +
44G TYR* 1.3 72.3 - - - +
46G ALA* 1.3 57.1 + - - +
47G CYS 2.9 5.6 - - - -
48G LYS* 2.8 41.8 + - + +
49G ILE* 3.6 6.1 + - - +
117G ALA* 4.1 23.2 - - + +
121G ALA* 4.7 1.2 - - - +
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Residues in contact with ALA 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ILE 2.8 20.3 + - - +
43G PHE* 3.7 10.3 - - - +
44G TYR 3.1 0.4 - - - -
45G ASP* 1.3 79.2 - - - +
47G CYS* 1.3 58.1 + - - +
48G LYS 3.1 1.0 + - - -
50G ILE* 2.9 16.0 + - - +
117G ALA 3.6 4.0 - - - -
120G ILE* 3.7 13.0 - - + -
121G ALA* 2.8 49.6 - - - +
124G LEU* 4.1 9.6 - - + -
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Residues in contact with CYS 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G VAL* 6.3 2.0 - - - -
18G TYR* 4.2 9.0 - - - -
43G PHE* 3.5 34.8 - - - -
44G TYR* 2.9 14.2 + - - +
46G ALA* 1.3 79.6 - - - +
48G LYS* 1.3 67.0 + - - +
49G ILE 3.3 0.7 - - - -
50G ILE* 3.3 12.2 - - - -
51G GLN* 3.1 24.6 - - - +
58G PRO* 3.6 30.3 - - + -
124G LEU* 6.2 1.3 - - - -
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Residues in contact with LYS 48 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44G TYR 4.2 3.6 - - - +
45G ASP* 2.8 42.7 + - + +
47G CYS* 1.3 88.5 + - - +
49G ILE* 1.3 61.3 + - + +
51G GLN* 3.8 16.4 + - - +
52G GLU* 2.9 30.0 + - + +
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Residues in contact with ILE 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G ASP 3.6 5.5 + - - +
46G ALA 3.9 1.0 + - - -
48G LYS* 1.3 80.5 - - + +
50G ILE* 1.3 59.1 + - - +
51G GLN 3.0 5.6 - - - -
52G GLU* 3.6 10.8 - - + -
53G LYS* 2.9 59.6 + - + +
115G ARG* 4.3 21.8 - - - +
117G ALA* 6.1 0.9 - - + -
118G VAL* 4.3 23.3 - - + +
121G ALA* 4.5 13.9 - - + -
122G HIS* 6.1 2.0 - - - +
125G MET* 4.2 3.3 - - + +
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Residues in contact with ILE 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G ALA 2.9 25.1 - - - +
47G CYS* 3.3 6.7 + - - +
48G LYS 3.3 0.4 - - - -
49G ILE* 1.3 75.8 - - - +
51G GLN* 1.3 62.0 + - - +
54G THR* 3.6 16.3 + - - +
56G GLN 4.0 3.6 - - - +
58G PRO* 3.3 34.3 - - + +
61G VAL* 4.3 16.8 - - + -
121G ALA* 2.9 33.4 - - + +
124G LEU* 3.3 26.5 - - + -
125G MET* 3.3 24.9 - - - -
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Residues in contact with GLN 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G CYS* 3.1 15.0 - - + +
48G LYS* 3.8 15.7 + - - +
49G ILE 3.2 0.4 + - - -
50G ILE* 1.3 78.0 - - - +
52G GLU* 1.3 64.7 + - - +
54G THR 2.8 37.2 + - - +
55G GLY* 2.5 35.9 + - - +
57G GLU* 3.3 33.6 + - - +
58G PRO* 3.6 4.7 - - + +
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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