Contacts of the helix formed by residues 39 - 56 (chain N) in PDB entry 3V3K
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 SER 39 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37N PHE 3.7 1.6 + - - -
38N LEU* 1.3 75.3 - - - +
40N PRO* 1.4 70.3 - - - +
41N GLU* 3.6 11.1 + - - +
42N LEU* 3.1 35.6 + - - +
43N GLN* 2.8 29.1 + - - +
112N ARG* 4.9 15.4 + - - +
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Residues in contact with PRO 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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38N LEU 4.6 1.1 - - - +
39N SER* 1.4 86.5 - - - +
41N GLU* 1.3 61.1 + - + +
43N GLN* 4.0 6.5 - - + +
44N ASP* 3.1 29.3 + - - +
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Residues in contact with GLU 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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39N SER* 3.2 9.1 + - - +
40N PRO* 1.3 81.5 - - + +
42N LEU* 1.3 63.2 + - + +
44N ASP* 3.9 4.6 - - - +
45N LYS* 3.3 21.0 + - - +
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Residues in contact with LEU 42 (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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38N LEU* 4.2 18.6 - - + -
39N SER* 3.1 31.3 + - - +
41N GLU* 1.3 73.8 - - + +
43N GLN* 1.3 61.7 + - - +
45N LYS* 3.3 13.5 + - + +
46N LEU* 3.0 27.2 + - - +
72N PHE* 4.7 17.5 - - + -
112N ARG* 4.0 31.0 - - + +
113N ASP* 3.9 23.8 - - - +
116N PHE* 3.8 17.6 - - + -
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Residues in contact with GLN 43 (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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38N LEU* 3.7 28.2 - - + +
39N SER 2.8 22.1 + - - +
40N PRO* 4.0 7.4 - - + +
42N LEU* 1.3 72.0 - - - +
44N ASP* 1.3 57.5 + - - +
46N LEU* 3.3 15.9 + - - +
47N ASP* 3.0 62.7 + - - +
123N LYS* 4.6 4.9 - - - +
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Residues in contact with ASP 44 (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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40N PRO 3.1 19.5 + - - +
41N GLU* 3.9 6.1 - - - +
43N GLN* 1.3 76.4 - - - +
45N LYS* 1.3 61.1 + - - +
47N ASP* 3.6 6.9 + - - +
48N VAL* 3.1 41.0 + - - +
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Residues in contact with LYS 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 GLU 3.3 12.6 + - - +
42N LEU* 3.3 19.1 + - + +
44N ASP* 1.3 78.3 + - - +
46N LEU* 1.3 61.4 + - - +
48N VAL* 3.7 7.5 + - + +
49N MET* 3.3 49.9 + - + +
68N GLU* 3.9 17.1 + - - +
72N PHE* 3.6 32.8 - - + +
116N PHE* 4.1 10.5 - - + -
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Residues in contact with LEU 46 (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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38N LEU* 3.9 15.7 - - + -
42N LEU 3.0 12.6 + - - +
43N GLN* 3.5 14.4 - - - +
44N ASP 3.3 0.2 - - - -
45N LYS* 1.3 75.2 - - - +
47N ASP* 1.3 66.0 + - - +
49N MET* 3.2 4.9 + - - +
50N VAL* 3.0 46.9 + - + +
116N PHE* 3.6 19.9 - - + +
119N SER* 3.2 34.1 - - - +
120N LEU* 4.1 13.9 - - + +
123N LYS* 3.2 34.1 - - + +
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Residues in contact with ASP 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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43N GLN* 3.0 41.3 + - - +
44N ASP* 4.0 7.9 - - - +
46N LEU* 1.3 85.4 - - - +
48N VAL* 1.3 58.2 + - + +
50N VAL* 4.3 4.1 - - - +
51N SER* 3.1 26.3 + - - -
123N LYS* 4.1 6.8 + - - +
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Residues in contact with VAL 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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44N ASP* 3.1 31.5 + - - +
45N LYS* 3.8 7.9 - - - +
46N LEU 3.2 0.2 - - - -
47N ASP* 1.3 75.9 - - + +
49N MET* 1.3 63.0 + - + +
51N SER* 2.9 19.2 + - - -
52N ILE* 3.2 37.7 + - + +
65N ILE* 5.6 0.7 - - + -
68N GLU* 5.9 4.7 - - - +
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Residues in contact with MET 49 (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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45N LYS* 3.3 40.6 + - + +
46N LEU 3.2 5.4 + - - +
48N VAL* 1.3 78.5 - - + +
50N VAL* 1.3 59.7 + - - +
52N ILE* 3.9 0.7 - - - +
53N TYR* 2.9 32.3 + - - +
65N ILE* 3.6 40.4 - - + +
68N GLU* 3.3 28.7 - - + +
69N LEU* 3.9 23.1 - - + +
72N PHE* 6.4 0.7 - - + -
116N PHE* 3.7 12.8 - - + -
120N LEU* 3.7 25.4 - - + -
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Residues in contact with VAL 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 LEU* 3.0 30.1 + - + +
47N ASP* 4.3 4.7 - - - +
48N VAL 3.4 0.2 - - - -
49N MET* 1.3 75.9 - - - +
51N SER* 1.3 60.6 + - - +
53N TYR* 3.9 4.1 - - - +
54N SER* 3.0 29.0 + - - +
120N LEU* 5.2 10.5 - - + +
123N LYS* 3.5 50.0 - - + +
124N ILE* 6.1 3.8 - - + -
127N SER* 4.9 8.0 + - - +
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Residues in contact with SER 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 ASP 3.1 13.9 + - - -
48N VAL* 2.9 23.4 + - - -
50N VAL* 1.3 78.9 - - - +
52N ILE* 1.3 64.0 + - - +
54N SER* 3.2 16.1 + - - -
55N CYS* 3.2 24.4 + - - +
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Residues in contact with ILE 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 VAL* 3.2 38.9 + - + +
49N MET 4.1 0.2 - - - +
51N SER* 1.3 81.6 + - - +
53N TYR* 1.3 62.9 + - - +
55N CYS* 4.6 2.6 - - - +
56N ALA* 3.2 28.5 + - + +
61N GLU 5.4 5.2 - - - +
62N LEU* 4.3 1.7 - - + +
64N GLU* 5.8 7.4 - - + +
65N ILE* 3.6 34.3 - - + -
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Residues in contact with TYR 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 MET 2.9 19.9 + - - +
50N VAL* 3.9 5.6 - - - +
51N SER 3.3 0.2 - - - -
52N ILE* 1.3 79.8 - - - +
54N SER* 1.3 63.1 + - - +
56N ALA* 3.7 13.2 + - - +
62N LEU* 3.9 27.7 - - + +
65N ILE* 5.2 7.6 - - + -
124N ILE* 3.6 42.0 - - + +
127N SER* 4.2 21.5 - - - -
128N ARG* 3.4 27.1 + - + -
136N CYS* 3.4 33.1 - - - +
138N VAL* 4.2 21.3 - - + -
139N TYR* 4.5 0.5 - - - +
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Residues in contact with SER 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 VAL* 3.0 17.9 + - - +
51N SER* 3.2 9.5 + - - -
53N TYR* 1.3 82.6 - - - +
55N CYS* 1.3 67.9 + - - +
56N ALA 3.6 5.7 + - - +
127N SER* 3.9 21.3 - - - -
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Residues in contact with CYS 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 SER* 3.2 23.1 + - - +
52N ILE* 4.6 2.9 - - - +
54N SER* 1.3 83.0 + - - +
56N ALA* 1.3 63.0 + - - +
57N ARG* 3.9 21.7 + - - +
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Residues in contact with ALA 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 ILE* 3.2 24.1 + - + +
53N TYR 3.7 6.6 - - - +
54N SER 3.4 8.6 - - - +
55N CYS* 1.3 79.8 - - - +
57N ARG* 1.3 60.8 + - - +
61N GLU* 3.7 24.5 - - + +
62N LEU* 3.7 26.0 - - + -
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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
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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