Contacts of the helix formed by residues 44 - 50 (chain F) in PDB entry 3LNX
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 44 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F ASN* 4.8 6.5 - - - -
19F GLY* 4.5 8.7 - - - -
41F ILE* 2.9 20.3 + - - -
42F PRO 3.0 2.5 - - - -
43F GLN* 1.3 82.4 - - - +
45F ALA* 1.3 66.4 - - - -
46F ALA 3.4 1.8 - - - -
47F GLU* 3.4 3.3 + - - +
48F SER* 3.1 23.5 + - - -
101F SCN 5.0 0.7 - - - -
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Residues in contact with ALA 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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82A GLY* 5.2 1.7 - - - -
11F LEU* 3.8 7.7 - - + +
12F ALA 3.1 27.8 - - - +
13F LYS 4.2 0.2 - - - -
14F ASN* 3.9 11.5 - - + +
17F SER 3.7 15.0 + - - +
18F LEU* 3.4 16.2 + - - +
19F GLY* 4.2 2.0 - - - -
44F GLY* 1.3 72.4 - - - +
46F ALA* 1.3 64.7 + - - +
48F SER* 3.3 1.9 + - - -
49F ASP* 3.1 23.2 + - - +
101F SCN 4.4 11.4 - - - +
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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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11F LEU* 4.1 16.3 - - + +
18F LEU 3.0 12.9 + - - +
19F GLY 3.7 3.8 + - - +
20F ILE* 3.2 35.9 - - + -
40F VAL* 4.1 9.6 - - + -
44F GLY 3.4 0.2 - - - -
45F ALA* 1.3 74.2 - - - +
47F GLU* 1.3 63.5 + - - +
49F ASP* 3.4 3.5 + - - +
50F GLY* 3.0 20.3 + - - -
51F ARG 4.4 2.1 + - - -
52F ILE* 4.6 16.6 + - + +
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Residues in contact with GLU 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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19F GLY 4.8 0.4 + - - -
40F VAL* 4.4 24.2 - - + +
41F ILE 3.6 15.7 + - - +
42F PRO* 3.4 17.0 - - - +
43F GLN* 2.8 28.5 + - - +
44F GLY 3.4 5.2 + - - +
45F ALA 3.2 0.8 - - - -
46F ALA* 1.3 79.3 - - - +
48F SER* 1.3 64.6 + - - +
50F GLY* 3.3 14.3 + - - -
52F ILE 5.7 0.7 - - - -
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Residues in contact with SER 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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80A ASN* 4.3 9.0 - - - +
81A THR* 3.6 18.4 + - - +
82A GLY* 4.0 5.2 - - - -
43F GLN* 4.3 8.8 + - - -
44F GLY 3.1 17.3 + - - -
45F ALA 3.3 3.3 + - - -
47F GLU* 1.3 78.3 + - - +
49F ASP* 1.3 62.9 + - - +
50F GLY* 4.4 0.7 - - - -
101F SCN 3.8 31.4 - - - -
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Residues in contact with ASP 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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62A ASN* 3.7 18.5 + - - +
80A ASN 4.8 6.1 - - - +
82A GLY* 3.8 14.9 + - - +
84A VAL 4.3 7.8 - - - +
9F VAL* 4.2 5.2 - - - +
10F GLU 5.0 0.7 - - - +
11F LEU* 3.9 18.8 - - + +
45F ALA 3.1 16.9 + - - +
46F ALA* 3.7 4.2 - - - +
48F SER* 1.3 78.7 - - - +
50F GLY* 1.3 58.3 + - - +
51F ARG* 2.8 59.6 + - - +
52F ILE* 4.7 2.8 + - - +
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Residues in contact with GLY 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 3.0 10.6 + - - -
47F GLU 3.3 12.7 + - - -
48F SER 4.4 0.7 - - - -
49F ASP* 1.3 76.6 - - - +
51F ARG* 1.3 60.8 + - - +
52F ILE 3.6 2.7 - - - -
53F HIS* 3.1 24.8 + - - -
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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