Contacts of the helix formed by residues 86 - 95 (chain A) in PDB entry 1LH9
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A LEU* 1.3 86.1 - - - +
87A SER* 1.3 57.8 + - - +
89A LEU* 3.6 14.8 - - - +
90A SER* 3.2 18.4 + - - -
100A PHE* 4.0 2.8 - - - -
102A LEU* 5.1 2.5 - - - -
150A ALA* 3.3 28.7 - - - +
153A PHE* 3.8 18.2 - - - -
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLU* 2.7 30.0 + - - -
85A LEU 3.1 3.6 + - - -
86A GLY* 1.3 71.1 - - - +
88A ARG* 1.3 74.3 + - - +
89A LEU 3.1 0.9 - - - -
90A SER* 2.5 25.9 + - - -
91A LYS* 3.4 6.4 + - - +
150A ALA* 3.5 4.8 + - - -
151A GLU* 2.8 30.1 - - - -
154A ASN* 3.3 6.3 + - - -
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A THR* 3.3 18.6 + - - +
82A ILE* 3.3 15.2 - - - +
84A GLU* 2.5 62.5 + - - +
85A LEU* 2.3 51.0 - - + +
87A SER* 1.3 82.9 + - - +
89A LEU* 1.3 63.9 + - - +
91A LYS* 3.8 11.3 + - - +
92A GLU* 3.9 6.8 + - - +
288A GLY* 5.9 2.6 + - - -
290A ILE* 5.9 0.2 - - - -
291A LEU* 3.4 16.1 - - + +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.4 13.5 - - + -
67A TYR* 6.3 1.8 - - + -
85A LEU* 3.6 19.0 - - + +
86A GLY* 3.6 14.8 - - - +
87A SER 3.1 0.2 - - - -
88A ARG* 1.3 76.8 - - - +
90A SER* 1.3 67.9 + - - +
92A GLU* 3.1 14.7 + - - +
93A MET* 3.1 30.5 + - + +
100A PHE* 4.8 6.5 - - + -
102A LEU* 3.7 30.1 - - + -
153A PHE* 6.1 0.9 - - + -
291A LEU* 3.8 23.8 - - + -
294A ILE* 4.4 21.1 - - + -
295A ILE* 4.2 9.9 - - + -
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLY 3.2 6.6 + - - -
87A SER* 2.5 25.6 + - - -
89A LEU* 1.3 78.4 - - - +
91A LYS* 1.3 54.9 + - - +
93A MET* 3.1 1.2 + - - +
94A SER* 2.5 47.4 + - - -
100A PHE* 3.6 32.9 - - - -
150A ALA* 4.1 7.9 - - - +
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A SER 3.4 5.3 + - - +
88A ARG* 4.0 10.3 - - - +
89A LEU 3.2 0.8 + - - -
90A SER* 1.3 83.8 + - - +
92A GLU* 1.3 68.2 + - + +
94A SER* 3.6 15.0 - - - -
95A LYS* 3.0 36.2 + - - +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ARG 4.0 3.4 - - - +
89A LEU 3.1 7.4 + - - +
91A LYS* 1.3 81.5 - - + +
93A MET* 1.3 64.7 + - - +
94A SER 3.2 0.7 + - - -
95A LYS* 3.2 41.3 + - - +
96A LEU* 4.1 5.6 + - - +
291A LEU* 3.6 25.6 - - + -
292A GLN* 3.7 24.1 + - - +
295A ILE* 4.2 27.7 - - + +
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Residues in contact with MET 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL* 3.5 44.4 - - + -
65A LEU* 4.5 14.6 - - + -
89A LEU* 3.1 32.9 + - + +
90A SER* 3.8 6.3 - - - +
92A GLU* 1.3 77.1 - - - +
94A SER* 1.3 61.4 + - - +
95A LYS 3.2 0.2 - - - -
96A LEU* 3.0 24.8 + - + +
97A THR* 2.8 30.9 + - - +
100A PHE* 4.6 15.9 - - + -
294A ILE* 5.3 1.3 - - - -
295A ILE* 4.6 18.8 - - + -
298A TYR* 4.1 18.4 - - + -
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER* 2.5 35.2 + - - -
91A LYS* 3.6 10.6 - - - -
92A GLU 3.1 0.4 - - - -
93A MET* 1.3 69.1 - - - +
95A LYS* 1.3 55.3 + - - +
96A LEU 2.8 15.6 + - - -
97A THR 3.0 23.2 + - - +
100A PHE* 5.8 2.6 - - - +
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Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS* 3.0 44.5 + - - +
92A GLU* 3.2 30.1 + - - +
94A SER* 1.3 76.3 - - - +
96A LEU* 1.3 71.4 + - + +
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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