Contacts of the helix formed by residues 93 - 105 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D ILE* 3.3 6.9 - - - +
89D PHE* 4.4 5.3 - - + -
90D SER 5.5 0.7 - - - +
91D GLY* 2.8 14.4 + - - +
92D ALA* 1.3 73.8 - - - +
94D LYS* 1.3 63.8 + - - +
95D GLU* 3.3 13.7 + - - +
96D LYS* 3.0 37.1 + - + +
97D LEU* 2.9 20.3 + - - +
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Residues in contact with LYS 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D MET* 5.2 8.3 - - - -
38D ILE* 3.7 10.1 - - + +
41D PHE* 3.4 58.1 - - + -
45D LEU* 5.0 2.3 - - + +
92D ALA 4.1 0.8 + - - +
93D ASN* 1.3 71.0 + - - +
95D GLU* 1.3 82.7 + - - +
97D LEU* 3.1 13.4 - - - +
98D GLU* 2.8 30.6 + - - +
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Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ASN* 3.2 10.7 - - - +
94D LYS* 1.3 106.1 + - - +
96D LYS* 1.3 65.3 + - - +
98D GLU* 3.1 6.6 + - - +
99D ALA* 3.0 23.8 + - - +
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Residues in contact with LYS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D PHE* 3.9 43.0 - - + +
90D SER 5.5 1.1 + - - +
93D ASN* 3.0 33.8 + - + +
95D GLU* 1.3 76.1 - - - +
97D LEU* 1.3 53.6 + - - +
99D ALA* 3.4 7.2 + - + +
100D THR* 2.9 42.3 + - - +
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 4.6 0.7 - - + -
38D ILE* 4.3 24.0 - - + -
41D PHE* 5.2 0.9 - - + -
42D PHE* 4.1 25.6 - - + +
45D LEU* 3.4 27.1 - - + -
77D PHE* 4.0 28.9 - - + -
79D PHE* 4.6 8.3 - - + -
89D PHE* 3.7 14.2 - - + -
93D ASN 2.9 12.2 + - - +
94D LYS* 3.1 11.7 - - - +
96D LYS* 1.3 73.2 - - - +
98D GLU* 1.3 64.1 + - - +
100D THR* 3.5 3.1 + - - -
101D ILE* 3.1 40.2 + - + +
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Residues in contact with GLU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 4.1 21.4 - - + +
48D LYS* 3.9 10.6 - - - +
49D TYR* 2.4 38.7 + - + +
94D LYS 2.8 17.7 + - - +
95D GLU* 3.1 5.1 + - - +
97D LEU* 1.3 74.0 - - - +
99D ALA* 1.3 62.7 + - - +
101D ILE* 3.1 6.9 + - - +
102D ASN* 3.0 34.7 + - - +
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Residues in contact with ALA 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D GLU 3.0 11.3 + - - +
96D LYS* 3.6 11.4 - - + +
98D GLU* 1.3 75.3 - - - +
100D THR* 1.3 68.6 + - - +
101D ILE 3.0 0.3 + - - -
102D ASN* 3.2 6.9 + - - +
103D GLU* 2.8 29.6 + - + +
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Residues in contact with THR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PHE* 3.6 31.5 - - + -
87D GLY* 5.1 2.0 - - - -
88D GLU 5.4 1.3 - - - +
89D PHE* 3.7 16.3 - - + -
96D LYS* 2.9 27.3 + - - +
97D LEU 4.0 0.9 - - - -
99D ALA* 1.3 72.3 - - - +
101D ILE* 1.4 63.8 + - - +
103D GLU* 3.6 16.1 + - - +
104D LEU* 2.9 51.8 + - + +
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Residues in contact with ILE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.0 5.8 - - + +
24D VAL* 4.6 6.5 - - + -
45D LEU* 4.2 22.9 - - + -
49D TYR* 4.2 30.3 - - + -
52D VAL* 4.4 8.1 - - + -
54D PHE* 4.0 29.4 - - + -
79D PHE* 4.1 20.2 - - + -
97D LEU* 3.1 26.9 + - + +
98D GLU* 3.4 8.5 - - - +
99D ALA 3.0 1.2 + - - -
100D THR* 1.4 75.2 - - - +
102D ASN* 1.3 56.0 + - - +
104D LEU 3.0 3.1 + - - -
105D VAL* 2.8 42.6 + - + +
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Residues in contact with ASN 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D TYR* 3.2 39.9 + - - -
98D GLU* 3.0 30.5 + - - +
99D ALA* 3.8 6.0 - - - +
101D ILE* 1.3 73.6 - - - +
103D GLU* 1.3 59.6 + - - +
105D VAL* 3.8 19.1 - - - +
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Residues in contact with GLU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ALA* 2.8 19.7 + - + +
100D THR* 3.7 21.3 + - - +
101D ILE 3.0 0.2 - - - -
102D ASN* 1.3 79.7 - - + +
104D LEU* 1.3 71.3 + - + +
105D VAL 3.9 1.7 - - - +
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 3.7 18.7 - - + +
79D PHE* 4.4 7.0 - - + -
81D LYS* 3.2 19.2 - - - -
86D VAL* 3.7 37.9 - - + +
87D GLY* 4.0 10.5 - - - -
100D THR* 2.9 38.4 + - + +
103D GLU* 1.3 96.1 - - + +
105D VAL* 1.3 70.0 - - - +
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 3.9 12.7 + - + +
49D TYR* 5.3 4.7 - - + -
51D ASN* 5.1 5.8 - - - +
52D VAL* 3.7 30.3 - - + -
81D LYS* 3.2 22.6 + - - -
101D ILE* 2.8 27.3 + - + +
102D ASN* 3.8 22.7 - - - +
103D GLU 5.0 1.4 - - - +
104D LEU* 1.3 84.3 + - - +
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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