Contacts of the helix formed by residues 80 - 90 (chain D) in PDB entry 1LNU
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 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D TYR* 3.4 17.2 + - - -
64D VAL* 3.4 13.1 - - - +
75D ALA* 3.7 7.2 - - - -
77D THR 2.5 21.5 + - - -
78D GLU 2.8 0.6 + - - -
79D LEU* 1.3 73.1 - - - +
81D ARG* 1.3 64.0 + - - -
82D PRO 3.2 2.7 - - - -
83D ASP* 2.8 19.6 + - - +
84D ALA 3.0 9.9 + - - -
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Residues in contact with ARG 81 (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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75D ALA* 3.4 21.6 - - + +
78D GLU* 3.0 49.5 + - - +
80D GLY* 1.3 73.1 - - - +
82D PRO* 1.3 74.1 - - + +
84D ALA* 4.4 2.5 - - - -
85D GLU* 3.1 35.4 + - + +
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Residues in contact with PRO 82 (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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77C ARG* 3.6 17.3 - - + +
12D VAL* 3.3 26.0 - - + +
14D GLY* 6.2 0.2 - - - -
78D GLU 3.7 7.4 - - - +
79D LEU* 4.0 6.1 - - - -
80D GLY 3.3 4.3 - - - -
81D ARG* 1.3 97.8 - - + +
83D ASP* 1.3 65.3 - - - +
85D GLU* 3.8 2.9 - - + +
86D TYR* 3.2 20.8 + - - +
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Residues in contact with ASP 83 (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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77C ARG* 2.4 47.6 + - - -
11D ALA* 3.9 10.9 - - - +
12D VAL* 3.2 9.7 - - - +
63D TYR* 3.0 27.5 + - - -
64D VAL* 4.0 3.8 - - + -
80D GLY 2.8 10.6 + - - +
82D PRO* 1.3 68.5 - - - +
84D ALA* 1.3 64.4 + - - +
87D TRP* 3.0 61.9 + - + -
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Residues in contact with ALA 84 (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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64D VAL* 4.5 4.6 - - + +
73D HIS* 4.0 22.8 - - + +
74D ARG* 4.2 1.6 - - - -
75D ALA* 3.7 31.4 - - + +
80D GLY 3.0 10.9 + - - +
81D ARG* 3.9 6.3 - - - +
83D ASP* 1.3 76.2 - - - +
85D GLU* 1.3 63.1 + - + +
87D TRP* 4.5 0.2 - - - -
88D ASN* 2.9 35.7 + - - +
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Residues in contact with GLU 85 (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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81D ARG* 3.1 26.8 + - + +
82D PRO* 3.8 2.9 - - + +
84D ALA* 1.3 77.8 - - + +
86D TYR* 1.3 66.9 + - - +
88D ASN* 3.1 12.6 + - - +
89D SER* 3.0 23.7 + - - -
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Residues in contact with TYR 86 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D LYS 5.3 1.3 - - - -
12D VAL* 3.1 36.1 - - + -
82D PRO 3.2 7.2 + - - +
83D ASP 4.2 1.1 - - - +
85D GLU* 1.3 78.7 - - - +
87D TRP* 1.3 73.0 + + + +
89D SER* 2.5 33.0 + - - -
90D GLN* 3.3 27.8 + - + +
93D ILE* 3.8 19.7 - - + -
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Residues in contact with TRP 87 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C ASN* 4.2 3.6 - - - -
9D ASN* 3.1 40.9 - - + +
10D LYS 2.5 35.9 + - - +
11D ALA* 4.0 2.5 - - - -
12D VAL 5.0 0.6 - - - +
56D TYR* 3.7 34.3 - + - -
63D TYR* 4.4 2.2 - - - -
64D VAL* 3.5 28.3 - - + -
73D HIS* 3.6 23.7 - + + +
83D ASP* 3.0 45.9 + - + +
86D TYR* 1.3 84.9 - + + +
88D ASN* 1.3 58.5 + - - +
89D SER 3.2 0.6 + - - -
90D GLN 3.9 1.3 - - - +
93D ILE* 3.5 31.7 - - + +
94D LEU* 3.1 30.0 + - - +
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Residues in contact with ASN 88 (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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72D GLU* 3.0 22.2 + - - +
73D HIS* 2.7 40.2 + - - +
84D ALA* 2.9 23.6 + - - +
85D GLU* 3.1 15.3 + - - +
87D TRP* 1.3 77.6 - - - +
89D SER* 1.3 58.8 + - - +
94D LEU* 2.8 41.0 - - - +
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Residues in contact with SER 89 (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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85D GLU 3.0 9.4 + - - -
86D TYR* 2.5 33.0 + - - -
88D ASN* 1.3 79.9 - - - +
90D GLN* 1.3 64.7 + - - +
91D PRO* 3.3 14.0 - - - +
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Residues in contact with GLN 90 (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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86D TYR* 3.3 34.9 + - + +
87D TRP 4.0 0.6 + - - -
88D ASN 3.7 0.2 - - - -
89D SER* 1.3 83.3 + - - +
91D PRO* 1.3 68.7 - - - +
92D GLU* 3.3 24.6 - - - +
93D ILE* 2.7 45.6 + - + +
94D LEU* 2.8 16.5 + - - +
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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