Contacts of the helix formed by residues 110 - 126 (chain T) 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 SER 110 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109T LEU* 1.4 79.5 - - - +
111T LYS* 1.4 60.6 + - - +
113T GLY* 3.5 9.2 + - - -
114T GLU* 3.9 16.9 + - - +
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Residues in contact with LYS 111 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63T LYS* 6.3 2.5 - - - -
67T ALA* 4.0 28.2 - - + +
109T LEU 5.3 2.9 - - - +
110T SER* 1.4 75.8 - - - +
112T CYS* 1.4 62.5 + - - +
114T GLU* 3.4 18.0 + - - +
115T GLU* 3.4 35.7 + - + +
118T ARG* 4.4 6.0 + - - +
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Residues in contact with CYS 112 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64T MET* 3.8 9.7 - - + +
67T ALA* 3.8 10.5 - - - -
68T ALA* 3.3 46.4 - - - -
109T LEU* 3.8 20.4 - - - +
110T SER 3.3 0.6 - - - -
111T LYS* 1.4 77.5 - - - +
113T GLY* 1.4 57.0 + - - +
115T GLU* 3.1 25.4 + - - +
116T LEU* 3.3 15.9 + - - +
154T TRP* 3.8 23.3 - - + +
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Residues in contact with GLY 113 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109T LEU 3.7 4.5 + - - -
110T SER 3.5 7.7 + - - -
111T LYS 3.4 1.0 - - - -
112T CYS* 1.4 75.1 - - - +
114T GLU* 1.4 61.3 + - - +
116T LEU* 3.4 22.8 - - - +
117T GLY 4.2 1.2 + - - -
154T TRP* 6.2 0.4 - - - -
158T ARG* 3.9 30.3 + - - +
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Residues in contact with GLU 114 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110T SER* 3.9 16.1 + - - +
111T LYS* 3.4 14.2 + - - +
112T CYS 3.3 0.6 - - - -
113T GLY* 1.4 73.8 - - - +
115T GLU* 1.4 63.6 + - - +
116T LEU 3.2 0.4 - - - -
117T GLY* 3.1 13.3 + - - -
118T ARG* 3.6 33.7 + - - +
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Residues in contact with GLU 115 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60T ALA* 5.6 0.2 - - - +
63T LYS* 3.9 28.6 - - - +
64T MET* 3.5 34.7 - - + +
67T ALA* 3.9 13.4 - - - +
111T LYS* 3.4 33.4 + - + +
112T CYS* 3.1 19.8 + - - +
114T GLU* 1.4 73.1 - - - +
116T LEU* 1.4 56.9 + - - +
118T ARG* 3.2 36.9 + - - +
119T LEU* 2.9 26.3 + - - +
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Residues in contact with LEU 116 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64T MET* 3.8 17.5 - - + -
112T CYS 3.3 8.9 + - - +
113T GLY* 3.4 16.2 - - - +
114T GLU 3.2 0.2 - - - -
115T GLU* 1.4 73.7 - - - +
117T GLY* 1.4 63.2 + - - +
119T LEU* 3.2 12.6 + - + +
120T LYS* 3.1 21.8 + - - +
151T GLY* 3.7 35.9 - - - +
154T TRP* 4.4 13.0 - - + -
158T ARG* 3.3 43.5 - - - +
167T TYR* 4.6 15.7 + - + +
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Residues in contact with GLY 117 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113T GLY 4.2 1.6 + - - -
114T GLU 3.1 9.7 + - - -
116T LEU* 1.4 80.2 - - - +
118T ARG* 1.3 60.9 + - - +
120T LYS* 3.2 23.7 + - - +
121T LEU* 3.6 12.4 - - - +
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Residues in contact with ARG 118 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63T LYS* 5.9 2.6 - - - +
111T LYS* 4.4 6.5 + - - +
114T GLU* 3.6 47.7 + - - +
115T GLU* 3.4 31.4 + - - +
117T GLY* 1.3 76.2 - - - +
119T LEU* 1.4 59.9 + - - +
121T LEU* 3.3 33.2 - - + +
122T VAL* 3.7 8.7 - - - +
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Residues in contact with LEU 119 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60T ALA* 4.2 22.7 - - + -
61T SER* 4.7 11.7 - - - +
64T MET* 4.0 20.6 - - + -
115T GLU 2.9 12.7 + - - +
116T LEU* 3.2 20.4 + - + +
118T ARG* 1.4 71.7 - - - +
120T LYS* 1.3 65.6 + - - +
122T VAL* 3.3 28.4 + - + +
123T LEU* 3.6 4.9 + - - +
147T ILE* 3.8 33.5 - - + +
150T ILE* 3.8 26.2 - - + -
151T GLY* 4.7 2.5 - - - +
167T TYR* 5.7 2.9 - - - +
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Residues in contact with LYS 120 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N LEU* 6.4 0.4 - - - -
14N GLU* 5.7 1.8 - - - +
16N GLU* 3.4 34.9 + - - +
19N LEU* 3.6 33.9 - - - +
116T LEU 3.1 11.8 + - - +
117T GLY* 3.2 15.9 - - - +
119T LEU* 1.3 78.6 - - - +
121T LEU* 1.4 67.8 + - + +
123T LEU* 3.1 28.9 + - + +
124T LEU* 3.4 14.6 + - + +
147T ILE* 6.0 0.2 - - - -
166T ARG* 5.1 22.9 - - - +
167T TYR* 5.8 3.6 - - - +
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Residues in contact with LEU 121 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N GLU* 5.4 7.4 - - - +
18N GLN* 5.4 4.7 - - - +
117T GLY 3.6 10.3 - - - +
118T ARG* 3.3 25.8 - - + +
120T LYS* 1.4 82.6 - - + +
122T VAL* 1.3 57.4 + - + +
124T LEU* 3.1 45.6 - - + +
125T GLU* 3.7 3.8 + - - +
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Residues in contact with VAL 122 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59T ALA* 6.1 5.8 - - + -
60T ALA* 5.8 4.9 - - + -
118T ARG 3.7 11.9 - - - +
119T LEU* 3.3 23.8 - - + +
120T LYS 3.3 0.2 - - - -
121T LEU* 1.3 74.8 - - + +
123T LEU* 1.4 63.0 + - - +
125T GLU* 3.3 21.5 + - + +
126T LEU* 3.7 13.3 + - + +
147T ILE* 4.8 13.9 - - + -
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Residues in contact with LEU 123 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N PHE* 5.3 0.9 - - - -
119T LEU 3.6 4.3 + - - +
120T LYS* 3.1 19.7 + - + +
122T VAL* 1.4 75.3 - - - +
124T LEU* 1.4 65.2 + - + +
126T LEU* 3.0 35.7 + - + +
129T LEU* 3.9 42.4 - - + +
144T ALA* 4.7 20.9 - - + +
147T ILE* 4.7 29.5 - - + +
148T LEU* 4.1 15.9 - - + -
166T ARG* 6.3 0.7 - - - +
167T TYR* 6.5 0.7 - - + -
170T GLN* 4.7 3.8 - - - +
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Residues in contact with LEU 124 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N GLU* 4.6 6.3 - - - +
18N GLN* 3.8 28.0 - - + +
19N LEU* 4.3 25.6 - - + -
22N PHE* 3.4 37.5 - - + -
120T LYS* 3.6 21.5 - - + +
121T LEU* 3.1 36.8 - - + +
123T LEU* 1.4 79.9 - - + +
125T GLU* 1.4 61.8 + - - +
126T LEU 3.3 7.3 - - - +
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Residues in contact with GLU 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121T LEU 3.7 3.2 + - - +
122T VAL* 3.3 14.8 + - + +
124T LEU* 1.4 76.0 - - - +
126T LEU* 1.4 76.0 + - - +
127T ASN* 3.5 18.7 + - - +
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Residues in contact with LEU 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N PHE* 3.9 9.2 - - - -
122T VAL* 3.8 16.8 - - + +
123T LEU* 3.0 28.6 + - + +
124T LEU 3.3 8.1 - - - +
125T GLU* 1.4 91.3 - - - +
127T ASN* 1.4 61.8 + - - +
128T PHE* 3.5 19.0 + - + +
129T LEU* 4.6 5.6 + - - +
140T GLN 5.9 0.9 - - - +
143T LEU* 3.9 34.1 - - + -
144T ALA* 5.1 7.9 - - + -
147T ILE* 3.9 25.1 - - + -
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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