Contacts of the helix formed by residues 40 - 50 (chain F) in PDB entry 1NTZ
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 ASN 40 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F ILE* 5.6 1.4 - - - +
38F HIS* 3.2 18.6 + - + +
39F GLU* 1.3 73.8 - - - +
41F ASP* 1.3 53.0 + - - +
42F ASP* 2.8 41.6 + - - +
43F VAL* 3.1 19.2 + - - +
44F LYS* 2.7 37.3 + - - +
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Residues in contact with ASP 41 (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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40F ASN* 1.3 75.5 + - - +
42F ASP* 1.4 67.7 + - - +
44F LYS* 3.0 13.4 + - - +
45F GLU* 2.9 24.9 + - - +
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Residues in contact with ASP 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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40F ASN* 2.8 19.2 + - - +
41F ASP* 1.4 74.4 - - - +
43F VAL* 1.3 56.9 + - - +
45F GLU* 3.3 3.9 + - - +
46F ALA* 3.0 25.6 + - - +
94F LEU* 3.7 20.1 - - + +
97F VAL* 3.5 23.9 - - + +
98F ILE* 3.8 11.6 - - + +
101F ARG* 2.9 51.9 + - - +
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Residues in contact with VAL 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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37F ILE* 3.6 40.8 - - + -
38F HIS 3.6 13.5 - - - +
39F GLU* 3.8 21.1 - - + -
40F ASN* 3.1 23.2 + - - +
42F ASP* 1.3 76.3 - - - +
44F LYS* 1.3 65.5 + - - +
46F ALA* 3.1 3.5 + - - +
47F ILE* 2.9 29.4 + - + +
90F LEU* 4.5 4.3 - - + -
94F LEU* 3.9 24.0 - - + -
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Residues in contact with LYS 44 (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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39F GLU* 3.5 42.4 + - + +
40F ASN 2.7 25.3 + - - +
41F ASP* 3.0 13.7 + - - +
43F VAL* 1.3 73.8 - - - +
45F GLU* 1.3 56.7 + - - +
47F ILE* 3.5 9.5 + - - +
48F ARG* 3.1 25.3 + - - +
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Residues in contact with GLU 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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41F ASP 2.9 11.1 + - - +
42F ASP 3.5 8.7 - - - +
44F LYS* 1.3 76.4 - - - +
46F ALA* 1.3 59.6 + - - +
48F ARG* 3.0 42.2 + - - +
49F ARG* 2.9 61.7 + - - +
97F VAL* 3.7 17.5 - - + -
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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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42F ASP 3.0 13.5 + - - +
43F VAL* 3.1 10.1 + - - +
45F GLU* 1.3 73.1 - - - +
47F ILE* 1.3 66.0 + - - +
49F ARG* 3.0 15.1 + - - +
50F LEU* 3.2 14.6 + - - +
90F LEU* 3.8 19.9 - - + +
93F TYR* 3.9 9.9 - - + +
94F LEU* 3.9 28.9 - - + +
97F VAL* 4.2 5.6 - - + +
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Residues in contact with ILE 47 (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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39F GLU* 4.5 10.3 - - - +
43F VAL* 2.9 26.3 + - + +
44F LYS* 3.5 9.9 - - - +
46F ALA* 1.3 74.6 - - - +
48F ARG* 1.3 64.0 + - - +
50F LEU* 3.1 25.6 + - + +
55F TYR* 3.8 32.9 - - + -
58F ARG* 3.5 46.7 - - - +
90F LEU* 3.8 27.1 - - + -
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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 LYS 3.1 11.1 + - - +
45F GLU* 3.0 44.3 + - - +
46F ALA 3.1 0.2 - - - -
47F ILE* 1.3 80.9 - - - +
49F ARG* 1.3 71.8 + - - +
50F LEU 3.2 7.3 + - - +
55F TYR* 5.7 3.2 - - - -
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Residues in contact with ARG 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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45F GLU* 2.9 44.5 + - - +
46F ALA* 3.0 8.5 + - - +
48F ARG* 1.3 82.0 - - - +
50F LEU* 1.3 64.9 + - - +
51F PRO* 3.7 1.2 - - - +
93F TYR* 3.9 27.5 - - + -
96F GLU* 4.2 13.1 - - - +
97F VAL* 3.7 21.3 - - - +
100F GLU* 2.6 39.9 + - - -
104F ARG* 5.8 1.6 - - - +
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Residues in contact with LEU 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 3.2 9.2 + - - +
47F ILE* 3.1 30.5 + - + +
48F ARG 3.7 6.6 - - - +
49F ARG* 1.3 80.3 - - - +
51F PRO* 1.3 79.8 - - + +
52F GLU 3.9 0.3 + - - -
54F LEU* 4.5 4.9 - - + -
55F TYR* 4.2 26.9 - - + +
58F ARG* 4.2 11.4 - - - -
89F TYR* 4.2 31.0 - - + +
90F LEU* 3.9 12.6 - - + -
93F TYR* 3.6 32.3 - - + -
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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