Contacts of the helix formed by residues 116 - 128 (chain P) 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 THR 116 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80P TRP* 6.1 0.2 - - + -
115P ILE* 1.4 80.6 - - + +
117P ASP* 1.4 73.5 + - - +
118P LEU 3.1 4.4 + - - -
119P PRO* 3.4 19.1 - - - +
120P ILE* 4.3 7.8 + - - +
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Residues in contact with ASP 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75P TYR* 5.2 2.1 + - - -
80P TRP* 3.1 46.1 + - + +
112P VAL* 3.4 26.5 - - + +
114P GLU* 3.4 28.8 - - - +
115P ILE* 3.2 13.3 - - - +
116P THR* 1.4 86.5 - - - +
118P LEU* 1.4 57.4 + - - +
119P PRO 3.7 0.2 - - - -
120P ILE* 3.0 29.9 - - + +
121P LYS 3.2 6.2 + - - -
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Residues in contact with LEU 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112P VAL 4.7 0.2 - - - -
113P GLU* 4.0 7.6 - - + -
114P GLU* 3.1 31.8 + - - +
115P ILE 3.5 13.2 - - - +
116P THR 3.1 2.2 + - - -
117P ASP* 1.4 76.3 - - - +
119P PRO* 1.4 69.6 - - + +
121P LYS* 3.3 49.2 + - - +
122P LEU* 3.6 6.6 + - - +
152P ILE* 3.9 24.3 - - + +
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Residues in contact with PRO 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P ILE 4.4 1.6 - - - +
116P THR* 3.4 18.8 - - - +
118P LEU* 1.4 95.0 - - + +
120P ILE* 1.4 62.0 + - + +
122P LEU* 3.3 18.0 - - + +
123P ARG* 3.3 32.9 + - - +
152P ILE* 6.4 0.7 - - + -
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Residues in contact with ILE 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P TRP* 3.6 37.9 - - + +
81P ASP* 5.2 0.9 - - - +
84P ASN* 3.6 14.7 - - - +
112P VAL* 5.1 3.6 - - + -
116P THR 4.3 4.3 - - - +
117P ASP* 3.0 35.7 - - + +
119P PRO* 1.4 72.9 - - + +
121P LYS* 1.4 64.6 + - - +
122P LEU 3.2 0.7 - - - -
123P ARG* 3.2 39.6 + - - +
124P LEU 3.5 4.3 + - - -
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Residues in contact with LYS 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P CYS* 4.0 22.4 + - + +
112P VAL* 3.6 29.4 - - + -
113P GLU* 3.4 28.9 + - - +
117P ASP 3.2 8.4 + - - +
118P LEU* 3.3 35.2 - - + +
119P PRO 3.3 0.2 - - - -
120P ILE* 1.4 74.5 - - - +
122P LEU* 1.4 63.9 + - - +
124P LEU* 3.0 20.8 + - + +
125P ILE* 3.1 40.6 + - + +
148P THR* 4.0 11.5 - - - +
152P ILE* 3.9 18.6 - - - +
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Residues in contact with LEU 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P LEU 3.6 4.7 + - - +
119P PRO* 3.3 20.4 + - + +
120P ILE 3.2 0.4 - - - -
121P LYS* 1.4 75.1 - - - +
123P ARG* 1.3 71.5 + - - +
125P ILE* 3.5 14.1 - - + +
126P ASP* 3.1 42.8 + - - +
149P LEU* 5.0 5.8 - - + -
152P ILE* 4.2 29.8 - - + -
153P LYS* 4.5 28.7 - - + +
156P ASN* 4.8 6.1 - - - +
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Residues in contact with ARG 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P ASN* 4.6 9.9 - - - +
119P PRO* 3.3 38.2 + - - +
120P ILE* 3.2 30.4 + - - +
121P LYS 3.2 0.4 - - - -
122P LEU* 1.3 90.9 - - - +
124P LEU* 1.4 55.9 + - - +
126P ASP* 3.5 4.6 + - - +
127P THR* 2.8 33.9 + - - +
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Residues in contact with LEU 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P ASN* 3.6 52.9 + - - +
87P ILE* 4.2 23.1 - - + -
88P MET* 5.1 3.6 - - + +
108P CYS* 6.3 3.4 - - + -
109P CYS* 4.8 8.5 - - - -
112P VAL* 6.0 7.9 - - + -
120P ILE 3.5 2.3 + - - +
121P LYS* 3.0 15.1 + - + +
123P ARG* 1.4 61.7 - - - +
125P ILE* 1.3 72.3 + - + +
127P THR* 3.2 16.8 + - - -
128P LEU* 3.2 37.5 + - + +
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Residues in contact with ILE 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P CYS* 4.1 27.1 - - + -
121P LYS* 3.4 41.5 - - + +
122P LEU* 3.5 19.3 - - + +
124P LEU* 1.3 82.2 - - + +
126P ASP* 1.4 55.3 + - - +
128P LEU* 2.9 31.4 - - + +
131P VAL* 3.3 22.1 - - + +
145P LEU* 5.2 5.4 - - + +
148P THR* 5.7 2.2 - - + -
149P LEU* 3.9 40.4 - - + +
152P ILE* 5.2 2.2 - - + -
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Residues in contact with ASP 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P LEU* 3.1 35.8 + - - +
123P ARG* 3.7 5.2 - - - +
125P ILE* 1.4 70.8 - - - +
127P THR* 1.3 65.6 + - - +
128P LEU 3.5 6.1 + - - +
129P ARG* 4.7 4.3 - - - +
131P VAL* 5.4 0.2 - - - -
132P THR* 4.6 14.1 + - - +
149P LEU* 4.0 17.9 - - - +
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Residues in contact with THR 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P ASN* 5.1 4.1 + - - -
88P MET* 3.6 37.9 - - + -
123P ARG* 2.8 24.0 + - - +
124P LEU* 3.2 11.5 + - - -
126P ASP* 1.3 76.7 - - - +
128P LEU* 1.4 60.2 + - - +
129P ARG* 3.7 6.8 + - - +
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Residues in contact with LEU 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87P ILE* 5.2 5.8 - - + -
88P MET* 6.4 1.8 - - - -
91P SER* 4.7 16.8 - - - +
105P VAL* 4.9 25.8 - - + -
109P CYS* 5.0 4.5 - - - -
124P LEU* 3.2 35.1 + - + +
125P ILE* 2.9 34.5 - - + +
126P ASP 3.5 4.9 - - - +
127P THR* 1.4 77.8 - - - +
129P ARG* 1.3 60.6 + - - +
130P MET* 4.3 12.8 - - + +
131P VAL* 3.8 25.2 - - + +
132P THR* 4.4 1.0 + - - -
145P LEU* 6.0 4.5 - - + -
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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