Contacts of the helix formed by residues 81 - 89 (chain B) in PDB entry 1LDJ
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 PHE 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709A LEU* 3.5 44.6 - - + -
712A GLN* 5.4 0.9 - - - -
713A ALA* 6.5 0.9 - - + -
759A LYS* 4.9 7.4 - - - -
67B GLU* 5.0 4.3 - - - +
69B THR* 2.6 32.4 + - - +
71B ALA* 3.7 8.7 - - + +
79B PHE 3.5 0.2 + - - -
80B HIS* 1.3 77.3 - - - +
82B HIS* 1.3 69.3 + + + +
84B ILE* 2.9 22.9 + - - +
85B SER* 2.9 30.7 + - - -
103B PHE* 3.3 37.0 - + - -
106B TYR* 3.8 20.9 - + - -
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Residues in contact with HIS 82 (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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759A LYS* 4.1 21.5 + - - -
53B CYS* 4.2 2.2 - - - -
55B GLU* 5.9 0.2 - - - +
56B CYS* 3.5 2.4 - - - -
64B THR* 3.1 27.5 + - - -
67B GLU* 3.4 22.2 + - - +
68B CYS* 3.3 18.5 - - - -
80B HIS* 4.8 1.1 - - + -
81B PHE* 1.3 82.3 - + + +
83B CYS* 1.3 55.2 + - - +
84B ILE 2.6 17.3 + - - -
85B SER* 4.2 8.1 - - - -
86B ARG* 2.9 49.7 + - + +
203B ZN 2.0 40.1 - - - -
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Residues in contact with CYS 83 (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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42B CYS* 4.1 3.6 - - - -
44B ILE* 3.3 29.4 - - - +
45B CYS* 2.8 22.4 - - - -
53B CYS* 3.5 17.7 - - - -
79B PHE* 4.4 2.7 - - + -
80B HIS* 3.3 13.4 + - + +
81B PHE 3.3 1.8 + - - -
82B HIS* 1.3 77.4 - - - +
84B ILE* 1.3 58.5 + - - +
86B ARG* 3.5 10.8 + - - +
87B TRP* 3.4 17.6 + - - +
201B ZN 2.2 37.5 - - - -
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Residues in contact with ILE 84 (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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44B ILE* 5.3 0.2 - - + -
71B ALA* 5.1 0.4 - - + -
79B PHE* 3.5 29.6 - - + -
80B HIS 3.7 4.0 + - - +
81B PHE 2.9 9.6 + - - +
82B HIS 2.6 5.7 + - - -
83B CYS* 1.3 80.9 - - - +
85B SER* 1.3 61.9 + - - +
86B ARG 2.7 5.9 + - - -
87B TRP* 3.1 13.0 + - + +
88B LEU* 2.8 42.2 + - + +
95B PRO* 3.9 32.3 - - + -
101B TRP* 3.0 42.4 - - + +
103B PHE* 3.8 9.9 - - + -
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Residues in contact with SER 85 (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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759A LYS* 5.2 5.4 + - - -
761A TYR* 3.6 19.3 + - - -
81B PHE* 2.9 45.7 + - - -
82B HIS* 4.0 13.0 - - - -
84B ILE* 1.3 78.7 - - - +
86B ARG* 1.2 66.4 + - - +
88B LEU* 3.4 14.4 + - - +
89B LYS* 3.2 22.0 + - - +
103B PHE* 4.7 0.7 - - - -
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Residues in contact with ARG 86 (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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759A LYS* 6.3 6.3 - - - +
761A TYR* 4.8 8.7 - - + +
44B ILE 5.8 0.2 + - - -
45B CYS* 5.3 1.4 - - - +
53B CYS 3.8 10.5 + - - -
54B ILE* 5.7 0.4 - - - +
55B GLU* 3.8 32.2 + - - +
82B HIS* 2.9 29.4 + - + +
83B CYS* 3.5 36.6 + - - +
84B ILE 2.7 0.4 - - - -
85B SER* 1.2 90.3 - - - +
87B TRP* 1.0 70.0 + - - +
88B LEU 3.4 0.2 + - - -
89B LYS* 4.0 16.5 + - + +
90B THR* 3.5 12.3 - - - +
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Residues in contact with TRP 87 (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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44B ILE* 3.4 28.7 - - + +
83B CYS 3.4 14.1 + - - +
84B ILE* 3.1 17.1 + - + +
86B ARG* 1.0 90.8 - - - +
88B LEU* 1.3 59.0 + - + +
90B THR* 2.8 23.6 + - + +
91B ARG* 2.9 71.8 + - + +
93B VAL* 2.8 40.6 - - + -
95B PRO* 3.1 46.8 - - + +
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Residues in contact with LEU 88 (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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84B ILE* 2.8 35.6 + - + +
85B SER* 3.4 8.8 + - - +
87B TRP* 1.3 80.0 - - + +
89B LYS* 1.3 55.0 + - + +
90B THR 2.7 24.8 + - - +
91B ARG 3.0 19.5 - - - +
92B GLN* 3.9 18.9 + - + +
101B TRP* 3.6 44.0 - - + -
103B PHE* 3.9 15.0 - - + -
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Residues in contact with LYS 89 (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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759A LYS 4.3 2.6 + - - -
760A GLU 4.0 13.9 + - - -
761A TYR* 3.8 52.6 - - + +
775A LEU 5.8 0.2 + - - -
776A ALA* 4.6 18.9 + - - +
85B SER 3.2 16.6 - - - +
86B ARG* 4.1 17.5 - - + +
87B TRP 3.3 0.2 - - - -
88B LEU* 1.3 76.0 - - - +
90B THR* 1.3 59.9 + - + +
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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