Contacts of the helix formed by residues 41 - 53 (chain F) in PDB entry 5NSS
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 GLY 41 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLY 3.4 4.2 - - - -
40F THR* 1.3 79.3 - - - +
42F LYS* 1.3 62.0 + - - +
43F GLU* 3.2 4.8 + - - -
44F LEU* 3.4 18.2 + - - +
45F ILE* 3.6 8.3 + - - +
226F ILE* 6.3 0.4 - - - -
227F ARG* 3.5 17.7 - - - +
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Residues in contact with LYS 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ILE* 4.6 21.7 - - + +
35F ILE 5.0 12.1 - - - +
36F GLY* 5.4 1.3 - - - -
40F THR* 3.3 10.8 + - - +
41F GLY* 1.3 74.4 - - - +
43F GLU* 1.3 59.4 + - - +
45F ILE* 3.2 11.0 + - + +
46F ALA* 2.9 29.3 + - - +
147F ALA* 5.7 4.5 - - + -
176F LEU* 6.5 1.1 - - + -
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Residues in contact with GLU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F GLY* 3.2 2.1 - - - -
42F LYS* 1.3 80.0 - - - +
44F LEU* 1.3 57.2 + - - +
46F ALA* 3.8 5.4 - - - +
47F SER* 2.9 31.9 + - - -
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Residues in contact with LEU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F GLY* 3.4 12.8 + - - +
42F LYS 3.3 0.4 - - - -
43F GLU* 1.3 78.7 - - - +
45F ILE* 1.3 57.2 + - - +
47F SER* 4.6 3.6 - - - +
48F ARG* 2.7 33.4 + - - +
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Residues in contact with ILE 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F VAL* 5.3 6.3 - - + +
19F LEU* 5.7 4.9 - - + -
22F VAL* 4.2 21.1 - - + +
41F GLY 3.6 7.1 + - - +
42F LYS* 3.2 15.1 + - + +
44F LEU* 1.3 78.6 - - - +
46F ALA* 1.3 59.1 + - - +
48F ARG* 4.3 2.9 - - - +
49F LEU* 2.9 30.5 + - - +
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Residues in contact with ALA 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ILE* 6.0 5.2 - - + -
42F LYS 2.9 16.5 + - - +
43F GLU* 3.8 6.5 - - - +
45F ILE* 1.3 74.4 - - - +
47F SER* 1.3 60.5 + - - +
49F LEU* 3.3 5.2 + - - +
50F HIS* 2.9 27.9 + - - +
103F THR* 5.6 0.3 - - - -
105F PHE* 4.7 19.5 - - + -
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Residues in contact with SER 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F GLU 2.9 17.3 + - - -
44F LEU* 4.5 2.9 - - - -
46F ALA* 1.3 73.8 - - - +
48F ARG* 1.3 61.0 + - - +
50F HIS* 3.2 7.5 + - - +
51F TYR* 2.9 28.9 + - - +
60F PHE* 5.6 5.2 - - - -
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Residues in contact with ARG 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU 2.7 23.8 + - - +
45F ILE* 4.3 3.6 - - - +
47F SER* 1.3 76.4 - - - +
49F LEU* 1.3 59.0 + - - +
51F TYR* 3.8 6.4 - - - +
52F LEU* 2.9 31.7 + - - +
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F VAL* 3.8 16.6 - - + +
23F SER* 5.6 1.8 - - - +
26F ALA* 3.3 25.3 - - + +
45F ILE 2.9 22.3 + - - +
46F ALA* 3.7 6.3 - - - +
47F SER 3.3 0.2 - - - -
48F ARG* 1.3 76.1 - - - +
50F HIS* 1.3 62.1 + - - +
52F LEU* 4.6 2.2 - - - -
53F SER* 3.2 25.8 + - - -
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Residues in contact with HIS 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ALA 2.9 16.3 + - - +
47F SER* 3.7 5.8 - - - +
49F LEU* 1.3 79.0 - - - +
51F TYR* 1.3 59.9 + - - +
53F SER* 3.7 6.7 + - - +
55F ARG* 3.6 6.2 - - + +
56F TRP* 3.3 23.5 + - - -
60F PHE* 3.9 22.0 - - + -
103F THR* 3.7 31.6 - - - +
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Residues in contact with TYR 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F SER 2.9 16.6 + - - +
48F ARG* 4.0 6.7 - - - +
50F HIS* 1.3 77.3 - - - +
52F LEU* 1.3 59.1 + - - +
53F SER 3.3 1.6 - - - +
56F TRP* 3.3 25.8 - - + +
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F SER* 5.7 9.0 - - - -
26F ALA* 5.2 5.4 - - + -
48F ARG 2.9 18.0 + - - +
49F LEU* 4.3 4.7 - - - +
51F TYR* 1.3 75.6 - - - +
53F SER* 1.3 61.9 + - - +
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Residues in contact with SER 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ALA* 3.3 31.2 - - - -
27F PRO* 4.1 7.6 - - - -
49F LEU 3.2 19.1 + - - -
50F HIS* 3.7 4.2 + - - -
51F TYR 3.3 8.8 - - - +
52F LEU* 1.3 81.5 - - - +
54F SER* 1.3 63.3 + - - +
55F ARG* 3.2 12.9 + - - -
56F TRP* 3.7 7.1 + - - +
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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