Contacts of the helix formed by residues 49 - 58 (chain B) in PDB entry 4L9T
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 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B LEU* 1.3 75.7 - - - +
50B GLN* 1.3 65.5 + - - +
51B ASN* 3.3 18.2 + - - +
52B ASP* 2.9 23.9 + - - +
53B ILE* 3.1 24.3 + - - +
88B ARG* 3.7 38.4 - - + +
89B LYS 3.6 19.3 - - - +
90B ASN* 3.9 0.4 - - - +
91B ILE* 3.6 5.4 - - - -
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Residues in contact with GLN 50 (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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49B THR* 1.3 75.4 - - - +
51B ASN* 1.3 64.2 + - - +
53B ILE* 3.2 5.4 + - - +
54B ALA* 2.8 29.8 + - + +
61B GLY* 3.4 13.0 - - - +
64B VAL* 3.6 18.4 - - + -
65B SER* 2.8 35.6 + - - +
68B LEU* 3.7 18.0 - - + +
79B ARG* 4.2 10.5 - - - +
89B LYS 4.4 2.4 + - - -
91B ILE* 3.5 12.4 - - + +
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Residues in contact with ASN 51 (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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49B THR* 3.2 10.3 + - - +
50B GLN* 1.3 84.0 - - - +
52B ASP* 1.3 63.4 + - - +
54B ALA* 3.7 7.6 - - - +
55B LYS* 3.1 23.9 + - - +
61B GLY* 6.2 0.2 - - - -
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Residues in contact with ASP 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 4.0 17.1 + - - +
47B GLY 4.1 4.0 - - - +
48B LEU* 3.5 18.4 - - + +
49B THR* 2.9 36.5 + - - +
51B ASN* 1.3 76.0 - - - +
53B ILE* 1.3 65.3 + - - +
55B LYS* 3.4 6.7 + - - +
56B ALA* 3.1 22.7 + - - +
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Residues in contact with ILE 53 (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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36B THR* 4.1 15.9 - - + -
39B TYR* 3.5 33.4 - - + -
40B LEU* 3.6 27.6 - - + -
48B LEU* 4.7 3.1 - - + -
49B THR 3.2 14.4 - - - +
50B GLN* 3.4 6.5 - - - +
52B ASP* 1.3 76.3 - - - +
54B ALA* 1.3 63.5 + - - +
56B ALA* 3.0 3.9 + - - +
57B LEU* 2.9 42.2 + - + +
64B VAL* 3.7 20.4 - - + -
68B LEU* 4.8 3.8 - - + -
91B ILE* 4.0 15.7 - - + -
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Residues in contact with ALA 54 (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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50B GLN 2.8 20.8 + - - +
51B ASN* 3.7 10.1 - - - +
52B ASP 3.3 0.2 - - - -
53B ILE* 1.3 73.1 - - - +
55B LYS* 1.3 58.0 + - - +
57B LEU* 3.5 0.4 + - - -
58B GLN* 3.0 8.3 + - - -
59B ARG 3.0 41.3 + - - +
61B GLY* 4.6 10.8 - - - +
64B VAL* 3.6 22.6 - - + +
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Residues in contact with LYS 55 (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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51B ASN 3.1 16.7 + - - +
52B ASP* 3.8 5.2 - - - +
54B ALA* 1.3 76.0 - - - +
56B ALA* 1.3 63.5 + - - +
58B GLN* 2.8 31.3 + - - +
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Residues in contact with ALA 56 (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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35B HIS* 4.2 12.7 + - - +
39B TYR* 3.5 44.9 - - + +
52B ASP 3.1 11.1 + - - +
53B ILE 3.0 8.8 + - - +
55B LYS* 1.3 78.7 - - - +
57B LEU* 1.3 61.7 + - + +
58B GLN* 3.2 3.4 + - - +
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Residues in contact with LEU 57 (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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32B GLU* 4.3 19.4 - - + +
35B HIS* 3.4 45.1 - - + +
36B THR* 3.1 33.9 - - - +
39B TYR* 5.3 2.5 - - + -
53B ILE* 2.9 34.7 + - + +
54B ALA* 4.3 0.7 - - - +
56B ALA* 1.3 79.2 - - + +
58B GLN* 1.3 70.2 + - - +
59B ARG* 3.6 21.5 - - + +
64B VAL* 4.6 11.4 - - + -
67B LEU* 4.7 4.7 - - + -
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Residues in contact with GLN 58 (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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54B ALA 3.0 5.6 + - - -
55B LYS* 2.8 30.9 + - - +
56B ALA 3.2 4.1 - - - +
57B LEU* 1.3 81.9 - - - +
59B ARG* 1.3 62.7 + - - +
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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