Contacts of the helix formed by residues 39 - 51 (chain C) in PDB entry 2N9P
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 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ASN* 1.3 80.0 - - - +
40C LYS* 1.3 61.0 + - - +
42C PHE* 3.0 18.1 - - - +
43C LYS* 3.0 35.9 + - - +
59C LEU* 4.4 15.7 - - + -
67C GLN 3.2 25.8 - - - +
68C ASP* 3.7 3.8 - - - -
70C LYS 3.0 24.2 - - - +
72C LEU* 3.4 33.0 - - + +
75C TYR* 4.0 18.2 - - + -
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Residues in contact with LYS 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C MET 4.8 3.1 - - - +
38C ASN* 3.0 32.3 - - - +
39C VAL* 1.3 75.8 - - + +
41C GLU* 1.3 89.0 + - + +
42C PHE 3.0 0.4 - - - -
43C LYS* 3.2 14.2 + - - +
44C GLU* 3.3 10.7 + - - +
54C SER* 4.1 4.0 + - - -
68C ASP* 3.0 38.8 - - + +
70C LYS 3.8 7.9 + - - +
71C LYS* 5.8 4.5 - - + +
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Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C MET 4.7 0.5 - - - +
38C ASN* 2.7 31.0 + - - +
40C LYS* 1.3 101.2 - - + +
42C PHE* 1.3 57.5 + - - +
44C GLU* 3.3 17.4 + - - +
45C HIS* 2.9 46.7 + - + +
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Residues in contact with PHE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 3.5 26.0 - - + -
21C VAL* 4.6 3.6 - - + -
31C PHE* 3.2 42.8 - + + -
33C VAL* 3.8 26.7 - - + -
38C ASN* 3.3 10.8 - - + +
39C VAL* 3.0 35.0 - - - +
40C LYS 3.0 0.2 - - - -
41C GLU* 1.3 78.8 - - - +
43C LYS* 1.3 77.9 + - + +
45C HIS* 3.0 11.9 + - + +
46C ILE* 3.0 42.6 + - + +
59C LEU* 3.8 24.9 - - + -
72C LEU* 4.3 8.3 - - + -
82C ILE* 5.3 1.3 - - + -
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Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C VAL 3.0 22.5 + - - +
40C LYS 3.2 2.2 + - - +
42C PHE* 1.3 83.5 - - + +
44C GLU* 1.3 62.5 + - - +
46C ILE* 3.3 2.4 - - - +
47C ALA* 3.1 20.4 + - - +
54C SER* 3.1 32.9 + - - +
57C GLN* 2.8 71.0 + - - +
58C ARG* 4.2 2.6 - - - +
59C LEU* 3.6 21.4 - - + +
67C GLN* 3.6 10.5 - - - +
68C ASP* 3.3 34.3 - - - +
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LYS 3.3 6.9 + - - +
41C GLU* 3.3 20.9 + - - +
43C LYS* 1.3 77.9 - - - +
45C HIS* 1.3 71.8 + - + +
47C ALA* 3.3 16.9 - - - +
54C SER* 3.7 14.6 - - - -
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Residues in contact with HIS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 6.1 2.2 - - - +
37C MET* 6.2 2.5 - - + -
38C ASN* 5.0 8.6 + - - -
41C GLU* 2.9 36.5 + - + +
42C PHE* 3.3 11.2 - - - +
44C GLU* 1.3 88.0 + - + +
46C ILE* 1.3 63.3 + - + +
47C ALA 3.1 2.4 + - - -
48C ALA* 4.1 6.6 + - - +
49C SER* 3.7 6.6 + - - -
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Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C PHE* 3.4 56.8 - - + -
42C PHE* 3.0 35.7 + - + +
43C LYS 3.3 4.9 - - - +
45C HIS* 1.3 77.1 - - + +
47C ALA* 1.3 64.9 + - - +
48C ALA 3.2 0.4 - - - -
49C SER* 3.0 11.0 + - - -
50C VAL* 3.0 24.1 + - - +
57C GLN* 3.1 35.7 - - - +
59C LEU* 4.2 4.5 - - + -
84C LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LYS 3.1 9.1 + - - +
44C GLU* 3.3 19.1 - - - +
45C HIS 3.1 1.0 - - - -
46C ILE* 1.3 76.3 - - - +
48C ALA* 1.3 58.5 + - + +
51C SER* 2.7 6.1 + - - -
52C ILE 2.7 49.3 + - - +
53C PRO* 3.7 15.9 - - + -
54C SER 4.1 2.0 - - - +
57C GLN* 3.7 1.1 - - - +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLU 4.9 0.2 + - - -
45C HIS 4.1 5.3 + - - +
46C ILE 3.2 0.6 - - - -
47C ALA* 1.3 74.9 - - - +
49C SER* 1.3 66.9 + - - +
50C VAL 3.1 1.8 - - - -
51C SER* 3.1 18.8 + - - +
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Residues in contact with SER 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLN* 4.8 1.6 - - - +
29C ARG* 3.3 34.6 + - - +
31C PHE* 4.1 18.9 - - - -
45C HIS 3.7 4.7 + - - -
46C ILE* 3.1 23.0 + - - -
48C ALA* 1.3 76.2 - - - +
50C VAL* 1.3 59.6 + - - +
51C SER* 4.9 1.1 + - - -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 5.2 0.4 - - + +
23C THR* 4.1 24.2 - - + +
27C GLN* 5.9 0.4 - - - -
29C ARG* 5.5 2.9 - - + -
31C PHE* 3.6 28.3 - - + -
46C ILE* 3.0 16.6 + - + +
47C ALA 3.6 1.1 - - - +
49C SER* 1.3 77.5 - - - +
51C SER* 1.3 70.6 + - - +
52C ILE* 3.2 39.8 + - + +
57C GLN* 4.0 2.5 - - - +
84C LEU* 3.5 31.9 - - + -
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ALA 2.7 10.2 + - - -
48C ALA* 3.1 14.3 + - - +
49C SER 4.9 1.0 + - - -
50C VAL* 1.3 81.2 - - - +
52C ILE* 1.3 63.2 + - - +
53C PRO* 3.8 7.8 - - - +
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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