Contacts of the helix formed by residues 93 - 103 (chain B) in PDB entry 4LL4
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 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.8 3.7 - - - +
77B PHE* 5.4 0.2 - - - -
89B PHE* 4.2 4.4 - - + -
91B GLY 3.0 12.8 + - - +
92B ALA* 1.3 73.1 - - - +
94B LYS* 1.3 66.1 + - - +
95B GLU* 3.0 21.7 - - - +
96B LYS* 3.1 32.2 + - + +
97B LEU* 3.0 18.5 + - - +
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Residues in contact with LYS 94 (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 MET* 5.2 4.7 - - - -
38B ILE* 3.6 14.9 - - + +
41B PHE* 3.4 59.9 - - + -
45B LEU* 4.7 3.9 - - + +
92B ALA 3.8 1.0 + - - +
93B ASN* 1.3 69.8 + - - +
95B GLU* 1.4 85.5 + - - +
97B LEU* 2.7 29.3 + - - +
98B GLU* 2.9 18.6 + - - +
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Residues in contact with GLU 95 (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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93B ASN* 3.0 15.5 + - - +
94B LYS* 1.4 107.3 + - - +
96B LYS* 1.3 57.8 + - - +
98B GLU* 3.4 6.3 + - - +
99B ALA* 2.7 39.1 + - - +
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.4 43.1 - - + +
90B SER 5.5 0.2 + - - -
93B ASN* 3.1 31.3 + - + +
95B GLU* 1.3 79.9 - - - +
97B LEU* 1.3 52.1 + - - +
99B ALA* 4.1 7.4 - - + -
100B THR* 2.6 55.6 + - - +
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Residues in contact with LEU 97 (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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24B VAL* 4.0 7.6 - - + -
38B ILE* 4.7 9.9 - - + -
41B PHE* 5.3 0.7 - - + -
42B PHE* 4.0 18.4 - - + +
45B LEU* 3.7 23.6 - - + -
77B PHE* 3.9 41.3 - - + -
79B PHE* 3.8 22.9 - - + -
89B PHE* 3.6 12.8 - - + -
93B ASN 3.0 11.3 + - - +
94B LYS* 2.7 18.2 + - - +
96B LYS* 1.3 70.2 - - - +
98B GLU* 1.3 57.7 + - - +
100B THR* 3.2 1.4 + - - -
101B ILE* 2.8 38.8 + - + +
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Residues in contact with GLU 98 (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 LEU* 3.9 29.4 - - + +
48B LYS* 4.5 9.4 - - - +
49B TYR* 2.7 27.6 + - + +
94B LYS 2.9 12.6 + - - +
95B GLU* 4.0 7.7 - - - +
97B LEU* 1.3 68.7 - - - +
99B ALA* 1.3 69.3 + - - +
101B ILE* 2.7 17.3 + - - -
102B ASN* 2.8 31.7 + - - +
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Residues in contact with ALA 99 (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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95B GLU 2.7 24.8 + - - +
96B LYS* 3.6 9.4 - - + +
98B GLU* 1.3 73.6 - - - +
100B THR* 1.3 57.1 + - - +
102B ASN* 3.7 7.9 + - - +
103B GLU* 2.8 34.3 + - - +
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Residues in contact with THR 100 (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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79B PHE* 3.8 29.4 - - + -
87B GLY* 5.3 3.1 - - - -
88B GLU 5.4 2.0 - - - +
89B PHE* 4.0 8.3 - - + -
96B LYS* 2.6 50.9 + - - +
97B LEU 3.9 2.9 - - - -
99B ALA* 1.3 73.2 - - - +
101B ILE* 1.3 63.9 + - - +
103B GLU* 3.3 13.7 + - - +
104B LEU* 3.0 37.8 + - + +
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Residues in contact with ILE 101 (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 LEU* 4.3 7.1 - - + +
24B VAL* 4.8 5.8 - - + -
45B LEU* 4.2 21.8 - - + -
49B TYR* 4.2 30.3 - - + -
52B VAL* 4.9 7.0 - - + -
54B PHE* 4.1 28.9 - - + -
79B PHE* 3.6 24.2 - - + -
97B LEU* 2.8 26.6 + - + +
98B GLU* 2.7 10.1 + - - +
100B THR* 1.3 73.6 - - - +
102B ASN* 1.3 74.7 + - - +
104B LEU* 3.0 3.1 + - - +
105B VAL* 2.9 29.3 + - + +
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Residues in contact with ASN 102 (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 TYR* 3.0 31.0 + - - -
98B GLU* 2.8 41.4 + - - +
99B ALA* 3.8 5.6 - - - +
101B ILE* 1.3 78.2 - - - +
103B GLU* 1.3 53.9 + - + +
104B LEU 2.3 17.0 + - - -
105B VAL* 2.9 21.5 + - - +
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Residues in contact with GLU 103 (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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99B ALA 2.8 23.7 + - - +
100B THR* 3.3 15.1 + - - +
102B ASN* 1.3 69.4 - - - +
104B LEU* 1.3 70.0 + - - +
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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