Contacts of the helix formed by residues 83 - 94 (chain A) in PDB entry 1L4E
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 ILE 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 3.9 15.9 - - + -
82A LYS* 1.3 74.1 - - + +
84A VAL* 1.3 94.8 + - + +
85A THR 3.0 2.5 - - - -
86A ALA* 3.0 21.3 + - + +
87A ILE* 3.0 37.5 + - + +
118A ASP 6.0 1.8 - - - +
119A ALA* 6.4 2.2 - - + -
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Residues in contact with VAL 84 (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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80A SER* 4.5 3.1 - - - -
81A PRO* 3.4 37.5 - - + +
82A LYS 3.1 0.8 - - - -
83A ILE* 1.3 88.1 - - + +
85A THR* 1.3 56.7 + - - +
87A ILE* 4.3 8.3 - - + -
88A GLN* 2.9 33.8 + - + +
177A MET* 3.8 23.3 - - + -
990A RBZ 3.8 30.5 - - + -
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Residues in contact with THR 85 (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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67A CYS* 4.6 1.8 - - + -
68A ALA 4.0 6.1 - - - +
69A ASP* 2.7 30.6 + - - +
82A LYS 3.3 6.2 + - - -
83A ILE 3.0 0.8 + - - -
84A VAL* 1.3 77.4 - - - +
86A ALA* 1.3 57.6 + - - +
89A ALA* 2.9 29.6 + - - +
117A ILE* 3.9 24.7 - - + -
175A LEU* 3.8 31.2 - - + +
176A GLY* 4.1 1.1 - - - -
177A MET* 3.2 27.3 + - - +
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Residues in contact with ALA 86 (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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69A ASP* 5.7 0.2 - - - +
83A ILE* 3.0 13.2 + - + +
85A THR* 1.3 76.9 - - - +
87A ILE* 1.3 67.0 + - + +
89A ALA* 3.4 1.0 + - - -
90A ALA* 3.1 20.8 + - - +
117A ILE* 4.0 10.5 - - + -
119A ALA* 3.9 28.0 - - + -
122A ILE* 3.5 22.4 - - + +
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Residues in contact with ILE 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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83A ILE* 3.0 45.3 + - + +
84A VAL* 3.9 8.1 - - + +
86A ALA* 1.3 77.3 - - + +
88A GLN* 1.3 59.3 + - + +
90A ALA* 3.2 9.3 + - + +
91A ASN* 2.9 40.8 + - - +
94A ARG* 5.9 1.1 - - - +
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Residues in contact with GLN 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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84A VAL* 2.9 26.6 + - + +
87A ILE* 1.3 74.5 - - + +
89A ALA* 1.3 67.0 + - - +
91A ASN* 3.0 35.4 + - - +
92A MET* 2.9 26.2 + - - +
97A THR* 3.7 20.3 - - - +
98A GLY 5.5 0.2 - - - +
175A LEU* 3.5 21.5 - - + -
317A GLU* 3.3 25.3 + - - -
990A RBZ 3.6 30.1 - - + +
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Residues in contact with ALA 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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67A CYS* 4.3 7.0 - - - -
85A THR 2.9 19.4 + - - +
86A ALA 3.6 5.8 - - - +
87A ILE 3.2 0.2 - - - -
88A GLN* 1.3 76.2 - - - +
90A ALA* 1.3 63.4 + - - +
92A MET* 3.1 21.7 + - - +
93A THR* 3.6 9.7 + - - +
112A VAL* 4.1 7.9 - - + +
117A ILE* 3.8 14.4 - - + -
122A ILE* 3.7 16.8 - - + -
125A VAL* 4.2 5.6 - - + +
175A LEU* 3.5 12.5 - - + +
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Residues in contact with ALA 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 ALA 3.1 13.5 + - - +
87A ILE* 3.3 11.7 - - - +
89A ALA* 1.3 73.2 - - - +
91A ASN* 1.3 64.8 + - - +
93A THR* 2.7 28.2 + - - -
94A ARG* 3.5 28.8 + - - +
122A ILE* 4.1 22.1 - - + +
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Residues in contact with ASN 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 ILE* 2.9 28.8 + - - +
88A GLN* 3.0 31.0 + - - +
90A ALA* 1.3 76.0 - - - +
92A MET* 1.3 62.6 + - - +
94A ARG* 2.9 40.3 + - - +
95A GLY 3.2 9.9 + - - -
96A THR* 3.5 25.2 + - - +
97A THR* 3.6 6.7 - - + -
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Residues in contact with MET 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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65A VAL* 4.2 18.4 - - + -
88A GLN* 2.9 16.5 + - - +
89A ALA* 3.2 16.8 - - - +
90A ALA 3.1 0.4 - - - -
91A ASN* 1.3 77.5 - - - +
93A THR* 1.3 60.2 + - - +
94A ARG 3.4 0.3 + - - -
95A GLY* 3.5 1.7 + - - -
97A THR* 3.3 24.9 - - + +
99A VAL* 3.5 15.5 - - + -
100A CYS* 3.3 25.1 - - - -
110A VAL* 4.8 3.0 - - - +
112A VAL* 3.3 29.2 - - + +
175A LEU* 3.9 19.7 - - + -
317A GLU* 3.6 41.1 - - + +
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Residues in contact with THR 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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89A ALA 3.8 3.8 - - - +
90A ALA* 2.7 23.0 + - - +
92A MET* 1.3 77.7 - - - +
94A ARG* 1.3 66.7 + - - +
95A GLY 3.7 0.2 + - - -
112A VAL* 4.7 7.4 - - + -
122A ILE* 5.7 0.2 - - - +
123A PRO 4.2 8.7 + - - +
124A GLY* 4.1 19.3 - - - +
125A VAL* 3.8 29.2 - - + -
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Residues in contact with ARG 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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87A ILE* 4.8 2.0 + - - +
90A ALA* 3.9 31.7 + - - +
91A ASN* 2.9 32.5 + - - +
93A THR* 1.3 85.9 + - - +
95A GLY* 1.3 61.0 + - - +
96A THR* 3.5 18.1 + - + +
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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