Contacts of the helix formed by residues 102 - 112 (chain Z) in PDB entry 5LN3
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 HIS 102 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60Z VAL* 3.5 37.5 - - + +
61Z GLU* 5.6 1.1 - - - -
63Z LEU* 4.2 7.6 - - + -
64Z GLY* 3.4 32.0 + - - -
99Z LEU* 3.1 15.0 + - + +
101Z PRO* 1.4 77.9 - - + +
103Z TYR* 1.4 62.8 + - - +
104Z GLY 3.2 1.1 - - - -
105Z LYS* 2.9 48.9 + - + +
106Z LEU* 3.1 38.5 + - + +
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Residues in contact with TYR 103 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Z LEU 3.9 1.6 + - - -
100Z ARG* 3.1 39.9 + - - +
101Z PRO 3.1 0.6 - - - -
102Z HIS* 1.4 77.4 - - - +
104Z GLY* 1.4 61.6 + - - +
106Z LEU* 3.5 10.7 + - + +
107Z LYS* 3.2 36.1 + - + +
126Z ILE* 4.1 31.8 - - + +
129Z LEU* 4.1 26.5 - - + -
130Z ALA* 5.0 7.2 - - - +
133Z MET* 4.4 23.8 - - + -
142Z TYR* 4.3 11.4 + - - -
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Residues in contact with GLY 104 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Z PRO 3.8 6.8 + - - -
102Z HIS 3.2 1.2 + - - -
103Z TYR* 1.4 80.1 - - - +
105Z LYS* 1.4 58.2 + - - +
107Z LYS* 3.6 17.6 + - - +
108Z GLU* 3.4 21.1 + - - +
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Residues in contact with LYS 105 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64Z GLY* 4.9 11.5 + - - -
66Z LYS* 5.8 3.2 - - - +
101Z PRO 4.7 1.6 + - - +
102Z HIS* 2.9 40.5 + - + +
104Z GLY* 1.4 72.9 - - - +
106Z LEU* 1.4 63.9 + - - +
108Z GLU* 3.6 28.2 + - - +
109Z ILE* 3.3 38.6 + - + +
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Residues in contact with LEU 106 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Z LEU* 3.7 17.9 - - + +
64Z GLY* 4.8 2.0 - - - +
71Z TYR* 4.1 13.0 - - - +
102Z HIS* 3.1 42.1 + - + +
103Z TYR* 3.6 12.1 - - + +
105Z LYS* 1.4 77.4 - - - +
107Z LYS* 1.4 59.9 + - - +
108Z GLU 3.4 0.3 + - - -
109Z ILE* 3.5 10.0 + - + +
110Z TYR* 3.1 21.9 + - - +
122Z ALA* 6.0 1.6 - - + +
125Z ILE* 3.8 24.7 - - + -
126Z ILE* 4.5 14.7 - - + +
129Z LEU* 3.3 34.1 - - + -
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Residues in contact with LYS 107 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Z TYR* 3.2 29.7 + - + +
104Z GLY* 3.8 14.8 + - - +
105Z LYS 3.4 0.2 - - - -
106Z LEU* 1.4 75.5 - - - +
108Z GLU* 1.4 68.5 - - - +
110Z TYR* 3.2 18.4 + - + +
111Z GLU* 3.3 21.0 + - + +
126Z ILE* 4.8 5.8 - - + +
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Residues in contact with GLU 108 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Z GLY 3.4 10.0 + - - +
105Z LYS* 3.6 35.1 - - - +
106Z LEU 3.3 0.4 - - - -
107Z LYS* 1.4 84.2 - - - +
109Z ILE* 1.3 71.9 + - + +
110Z TYR 3.5 0.5 + - - -
111Z GLU* 3.5 12.6 - - - +
112Z ASN* 3.3 35.5 + - - +
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Residues in contact with ILE 109 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Z GLY* 4.1 17.0 - - - +
65Z GLU 5.3 0.4 - - - +
66Z LYS* 3.8 37.7 - - + +
71Z TYR* 6.1 0.9 - - + +
105Z LYS* 3.3 25.4 - - - +
106Z LEU* 3.7 10.5 - - + +
107Z LYS 3.4 0.2 - - - -
108Z GLU* 1.3 88.2 - - + +
110Z TYR* 1.4 61.1 + - - +
112Z ASN* 3.3 19.5 + - + +
115Z PRO* 3.3 35.6 - - + +
118Z ASN* 3.8 16.2 - - - +
122Z ALA* 5.5 4.5 - - + -
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Residues in contact with TYR 110 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Z LEU 3.1 14.6 + - - +
107Z LYS* 3.2 13.0 + - + +
109Z ILE* 1.4 77.0 - - - +
111Z GLU* 1.4 59.3 + - - +
112Z ASN 3.6 5.5 + - - +
115Z PRO* 5.2 3.0 - - - +
119Z LYS* 3.7 32.3 - - + +
122Z ALA* 4.0 17.5 - - + -
123Z ALA* 3.8 19.8 - - + +
126Z ILE* 3.9 20.2 - - + -
142Z TYR* 4.3 22.2 - + - -
145Z VAL* 3.7 25.6 + - - +
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Residues in contact with GLU 111 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Z LYS* 3.3 15.3 + - + +
108Z GLU* 3.5 15.9 - - - +
110Z TYR* 1.4 73.2 - - - +
112Z ASN* 1.3 77.9 - - - +
113Z MET 3.9 0.3 + - - -
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Residues in contact with ASN 112 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Z LYS* 6.1 0.4 - - - +
108Z GLU* 3.3 26.9 + - - +
109Z ILE* 3.3 21.3 + - + +
110Z TYR 3.7 5.0 - - - +
111Z GLU* 1.3 96.0 - - - +
113Z MET* 1.3 61.2 + - - +
114Z ALA* 3.1 20.3 + - + +
115Z PRO* 3.6 14.7 - - + +
119Z LYS* 6.0 1.9 - - - +
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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