Contacts of the helix formed by residues 37 - 49 (chain B) in PDB entry 1F9N
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 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 4.9 2.0 - - - -
30B LYS* 5.1 1.6 - - - +
36B VAL* 1.3 79.1 + - - +
38B GLN* 1.3 87.6 + - + +
39B ALA* 3.0 19.3 - - + +
40B THR* 2.9 25.9 + - - -
41B VAL* 2.9 16.4 + - - +
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Residues in contact with GLN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLN* 4.3 8.5 - - - +
23B ASP* 5.5 4.2 - - - +
26B VAL* 4.5 20.6 - - + +
30B LYS* 4.9 10.7 + - - +
37B THR* 1.3 88.7 - - + +
39B ALA* 1.3 61.5 + - + +
41B VAL* 4.1 1.4 - - - +
42B SER* 3.3 24.4 + - - -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B THR* 3.0 13.2 - - + +
38B GLN* 1.3 80.6 - - + +
40B THR* 1.3 62.4 + - - +
42B SER* 2.7 21.0 + - - -
43B ARG* 3.3 10.6 + - - +
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ASN* 5.0 7.4 - - - +
6B ARG* 3.6 30.1 - - - +
36B VAL* 4.5 10.8 - - + -
37B THR* 2.9 25.5 + - - -
39B ALA* 1.3 78.3 - - - +
41B VAL* 1.3 64.8 + - - +
43B ARG* 3.1 9.7 + - + +
44B ASP* 3.0 23.7 + - - +
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 5.7 0.4 - - + -
22B GLN* 4.2 5.8 - - + +
25B LEU* 3.6 31.0 - - + -
26B VAL* 3.4 34.3 - - + -
29B LEU* 4.1 13.9 - - + -
36B VAL* 3.7 23.1 - - + -
37B THR 2.9 15.2 + - - +
38B GLN 4.3 2.2 - - - +
40B THR* 1.3 73.4 - - - +
42B SER* 1.3 66.0 + - - +
44B ASP* 3.0 11.6 + - + +
45B ILE* 2.9 28.9 + - + +
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Residues in contact with SER 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLN* 3.5 31.3 + - - +
38B GLN 3.3 15.8 + - - -
39B ALA* 2.7 26.0 + - - -
41B VAL* 1.3 79.4 - - - +
43B ARG* 1.3 60.3 + - - +
45B ILE* 3.5 4.7 + - - +
46B LYS* 3.2 22.0 + - - +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ALA 3.6 9.9 - - - +
40B THR* 3.1 13.2 + - + +
41B VAL 3.0 0.2 - - - -
42B SER* 1.3 80.1 + - - +
44B ASP* 1.3 68.1 + - - +
46B LYS* 3.1 8.1 + - - +
47B GLU* 2.9 36.4 + - - +
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 2.9 41.2 + - - -
7B HIS* 2.7 30.6 + - + +
10B ILE* 3.7 22.0 - - + +
29B LEU* 5.3 0.2 - - - +
40B THR* 3.0 20.4 + - - +
41B VAL* 3.0 12.3 + - - +
43B ARG* 1.3 75.2 - - - +
45B ILE* 1.3 58.9 + - - +
47B GLU* 3.0 12.2 + - - +
48B LEU* 2.8 36.1 + - - +
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 5.8 0.7 - - + -
22B GLN* 3.4 41.5 - - + +
25B LEU* 4.1 15.0 - - + -
41B VAL* 2.9 23.9 + - + +
42B SER* 3.5 7.9 - - - +
44B ASP* 1.3 76.9 - - + +
46B LYS* 1.3 57.0 + - - +
48B LEU 3.5 0.5 + - - -
49B HIS* 3.1 21.8 + - - -
50B LEU* 3.2 44.9 + - + +
62B TYR* 3.9 24.5 - - + +
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B SER 3.2 9.9 + - - +
43B ARG* 3.1 11.0 + - - +
45B ILE* 1.3 80.9 - - - +
47B GLU* 1.3 62.5 + - + +
49B HIS* 3.5 23.9 + - - +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B HIS* 3.3 33.1 + - + -
43B ARG* 2.9 33.6 + - + +
44B ASP* 3.5 11.7 - - - +
46B LYS* 1.3 79.0 - - + +
48B LEU* 1.3 64.0 + - - +
49B HIS* 3.3 15.2 + - - -
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B HIS* 3.6 43.7 - - + +
10B ILE* 4.0 39.0 - - + -
11B ARG* 4.3 28.3 + - + +
44B ASP 2.8 19.2 + - - +
47B GLU* 1.3 78.9 - - - +
49B HIS* 1.3 73.9 + - - +
50B LEU* 3.4 21.7 + - + +
64B LEU* 4.9 3.8 - - + +
65B PRO* 4.0 11.4 - - - +
81E MET 5.2 4.5 - - - +
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Residues in contact with HIS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE 3.1 7.3 + - - -
46B LYS* 3.5 20.0 + - - +
47B GLU* 3.3 15.6 + - - -
48B LEU* 1.3 80.6 - - - +
50B LEU* 1.3 67.0 + - - +
51B VAL* 3.7 4.3 - - - +
65B PRO* 2.9 26.6 - - + +
81E MET* 6.0 10.2 - - + -
82E ASP* 5.4 6.3 - - - -
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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