Contacts of the helix formed by residues 115 - 127 (chain B) in PDB entry 3LX9
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 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B GLU* 2.7 32.6 + - - +
114B PRO* 1.3 87.9 - - + +
116B GLY* 1.3 63.0 + - - +
118B ARG* 5.8 0.2 - - - +
119B GLN* 3.4 52.7 + - + +
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLU* 4.1 3.4 + - - +
108B ALA* 4.5 7.9 - - - -
113B PHE* 3.0 19.7 + - - +
114B PRO 3.3 1.6 + - - -
115B HIS* 1.3 84.3 - - - +
117B ILE* 1.3 67.7 + - - -
118B ARG 3.4 2.2 - - - -
119B GLN* 3.7 0.3 + - - +
120B LEU* 3.4 17.7 + - - +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ILE* 4.0 18.4 - - + -
95B TRP* 4.1 13.0 - - + -
108B ALA* 3.8 19.9 - - + +
113B PHE* 4.0 27.4 - - + -
116B GLY* 1.3 71.1 - - - -
118B ARG* 1.3 56.1 + - - +
120B LEU* 3.2 5.2 + - + +
121B ALA* 2.7 32.4 + - + +
131B LEU* 3.8 20.9 - - + -
133B ILE* 4.1 8.5 - - + -
162B TRP* 3.7 48.3 - - + -
164B VAL* 4.6 1.8 - - + -
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B HIS 5.8 0.2 - - - +
116B GLY 3.4 1.0 - - - -
117B ILE* 1.3 77.0 - - - +
119B GLN* 1.3 60.2 + - + +
121B ALA* 3.2 3.1 + - - +
122B ASN* 2.8 49.3 + - - +
161B ASP* 3.1 34.1 + - - +
162B TRP* 3.8 45.5 - - + +
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Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B HIS* 3.4 55.9 + - + +
116B GLY 3.7 2.3 + - - +
117B ILE 3.3 0.4 - - - -
118B ARG* 1.3 78.9 - - + +
120B LEU* 1.3 60.5 + - - +
122B ASN* 3.8 11.5 - - - +
123B TYR* 3.0 28.9 + - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLU* 4.1 13.7 - - + +
69B PHE* 4.1 18.6 - - + -
70B MET* 3.8 31.0 - - + +
91B ILE* 3.8 28.5 - - + -
113B PHE* 3.9 23.6 - - + -
116B GLY 3.4 12.1 + - - +
117B ILE* 3.2 11.8 + - + +
119B GLN* 1.3 77.1 - - - +
121B ALA* 1.3 58.7 + - - +
123B TYR* 3.3 6.0 + - + +
124B VAL* 2.9 41.9 + - + +
131B LEU* 4.5 11.7 - - + -
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ILE* 2.7 21.2 + - + +
118B ARG 3.4 5.2 - - - +
120B LEU* 1.3 73.8 - - - +
122B ASN* 1.3 56.2 + - - +
124B VAL* 3.3 3.4 + - - +
125B HIS* 2.8 48.4 + - + -
131B LEU* 3.6 22.4 - - + +
162B TRP 3.4 20.9 - - - +
163B GLY 4.3 4.3 - - - +
164B VAL 5.0 0.2 - - - +
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Residues in contact with ASN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 2.8 43.4 + - - +
119B GLN* 3.8 10.3 - - - +
121B ALA* 1.3 74.6 - - - +
123B TYR* 1.3 57.8 + - - +
125B HIS* 3.8 13.1 + - - +
126B SER* 2.9 30.2 + - - -
162B TRP 4.8 2.3 - - - +
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Residues in contact with TYR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B MET* 3.8 59.9 - - + -
73B ALA* 4.5 6.5 - - + -
74B GLU* 2.7 32.0 + - - +
119B GLN 3.0 19.0 + - - +
120B LEU* 3.5 7.2 - - - +
122B ASN* 1.3 75.0 - - - +
124B VAL* 1.3 66.4 + - + +
126B SER* 2.5 27.3 + - - -
127B LYS* 3.4 36.5 + - - +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA* 4.4 6.3 - - + -
89B LEU* 3.8 27.6 - - + -
120B LEU* 2.9 29.8 + - + +
121B ALA* 3.6 7.0 - - - +
123B TYR* 1.3 76.8 - - + +
125B HIS* 1.3 62.0 + - + +
127B LYS* 3.1 15.6 + - - +
129B LEU* 3.2 41.3 + - + +
130B LYS 3.7 26.0 - - - +
131B LEU* 3.9 16.6 - - + +
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Residues in contact with HIS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ALA* 2.8 31.5 + - + +
122B ASN* 3.8 13.2 + - - +
124B VAL* 1.3 73.0 - - + +
126B SER* 1.3 57.4 + - - +
128B GLY* 3.0 19.1 + - - -
129B LEU 3.5 17.2 - - - +
130B LYS* 4.4 2.7 - - + -
131B LEU* 4.4 3.8 + - - +
163B GLY* 3.1 27.1 + - - -
165B ASP* 2.7 30.5 + - - -
196B ARG* 3.7 12.8 + - - -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ASN 2.9 15.4 + - - -
123B TYR* 2.5 27.5 + - - -
125B HIS* 1.3 76.4 - - - +
127B LYS* 1.3 67.4 + - - +
128B GLY 3.3 1.5 + - - -
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA* 4.4 15.7 - - + +
74B GLU* 4.0 16.4 - - - +
77B VAL* 3.5 36.8 - - + +
82B LYS* 3.7 10.9 - - - +
123B TYR* 3.4 53.9 + - - +
124B VAL 3.1 8.2 + - - +
125B HIS 3.1 1.0 - - - -
126B SER* 1.3 82.2 - - - +
128B GLY* 1.3 59.3 + - - +
129B LEU* 3.6 8.6 + - + -
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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