Contacts of the helix formed by residues 110 - 122 (chain B) in PDB entry 1L9X
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 CYS 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLY* 4.1 0.2 - - - -
109B THR* 1.3 69.2 - - + +
111B LEU* 1.3 66.3 + - - +
113B PHE* 2.8 14.8 + - - +
114B GLU* 2.9 16.6 + - - +
170B PHE 3.8 0.7 - - - -
171B HIS* 3.8 11.4 - - - -
217B VAL 2.7 15.2 + - - -
218B GLN* 3.6 35.7 + - - +
220B HIS* 3.5 27.4 - - + +
1002B BME 2.0 46.4 - - - -
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Residues in contact with LEU 111 (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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17B GLN* 4.0 2.9 - - - +
72B PRO 3.6 4.3 - - - +
74B GLY* 3.5 43.7 - - - +
75B SER* 4.8 1.1 - - - -
76B VAL* 3.4 47.1 - - + +
78B LEU* 3.9 23.7 - - + +
83B TYR* 3.7 19.3 - - + +
109B THR 2.8 1.2 + - - -
110B CYS* 1.3 79.8 - - - +
112B GLY* 1.3 57.9 + - - +
114B GLU* 3.2 16.7 + - - +
115B GLU* 2.9 26.5 + - - +
1002B BME 3.1 4.7 - - - -
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.4 30.1 - - - -
83B TYR* 3.5 12.3 + - - -
108B GLY* 3.6 7.4 - - - -
109B THR 2.9 8.4 + - - -
111B LEU* 1.3 81.1 - - - +
113B PHE* 1.3 60.6 + - - +
115B GLU* 3.3 4.5 + - - +
116B LEU* 3.1 26.9 + - - +
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Residues in contact with PHE 113 (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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108B GLY 3.6 9.8 - - - +
110B CYS* 2.8 10.4 + - - +
112B GLY* 1.3 74.7 - - - +
114B GLU* 1.3 69.6 + - + +
116B LEU* 3.1 19.5 + - - +
117B SER* 3.1 12.4 + - - -
126B LEU* 5.7 0.4 - - + -
175B LEU* 4.1 20.9 - - + -
204B ILE* 3.6 39.0 - - + -
205B SER 4.5 2.9 - - - -
207B MET* 3.6 36.7 - - + +
216B GLY* 3.5 26.5 - - - -
217B VAL 3.4 23.1 - - - +
218B GLN* 3.3 27.6 - - - -
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 3.6 12.5 - - + +
110B CYS* 2.9 16.5 + - - +
111B LEU* 3.5 22.6 - - - +
113B PHE* 1.3 81.6 - - + +
115B GLU* 1.3 60.4 + - - +
117B SER* 3.2 9.7 + - - -
118B LEU* 3.2 20.3 + - - +
126B LEU* 3.4 36.2 - - + +
171B HIS* 4.1 6.1 - - - +
173B TRP* 3.5 21.6 + - - +
218B GLN* 3.2 31.9 + - - +
1002B BME 4.5 2.0 - - - -
1003B BME 4.6 2.8 - - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 4.2 6.1 - - + -
78B LEU* 3.4 30.7 - - + +
83B TYR* 4.4 5.2 - - + -
84B ALA* 3.6 28.7 - - - +
87B ALA* 3.6 20.9 - - + +
88B LYS* 4.7 0.7 - - - +
111B LEU 2.9 13.6 + - - +
112B GLY* 3.5 12.1 - - - +
113B PHE 3.2 0.2 - - - -
114B GLU* 1.3 75.5 - - - +
116B LEU* 1.3 58.4 + - - +
118B LEU* 3.2 10.7 + - - +
119B LEU* 2.8 66.9 + - + +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 4.1 23.6 - - + -
91B TYR* 4.8 4.3 - - + -
106B VAL* 4.2 6.3 - - + -
107B TRP 5.0 0.2 - - - -
108B GLY* 4.2 5.8 - - - +
112B GLY 3.1 18.2 + - - +
113B PHE* 3.1 9.5 + - - +
115B GLU* 1.3 75.2 - - - +
117B SER* 1.3 65.4 + - - +
119B LEU* 4.2 10.3 - - + -
120B ILE* 2.9 31.9 + - + +
190B PHE* 4.2 15.9 - - + -
207B MET* 4.6 3.6 - - + -
214B VAL* 3.7 26.9 - - + -
215B TYR 3.2 34.1 - - - +
216B GLY* 4.1 8.1 - - - -
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 3.1 11.8 + - - -
114B GLU* 3.2 13.2 + - - -
116B LEU* 1.3 74.6 - - - +
118B LEU* 1.3 54.7 + - - +
121B SER* 2.7 41.2 + - - -
123B GLU 4.6 1.7 + - - -
125B LEU* 4.9 4.9 + - - +
126B LEU* 4.4 11.2 - - - +
175B LEU* 3.7 35.9 - - - +
186B LEU* 3.9 16.7 - - - +
207B MET* 4.7 5.1 - - - +
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Residues in contact with LEU 118 (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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78B LEU* 3.8 27.1 - - + +
79B ARG* 5.0 3.6 - - + +
84B ALA* 5.5 0.4 - - + -
88B LYS* 6.4 3.4 - - - +
114B GLU 3.2 9.6 + - - +
115B GLU* 3.5 21.8 - - - +
116B LEU 3.1 0.4 - - - -
117B SER* 1.3 77.9 - - - +
119B LEU* 1.3 61.5 + - + +
122B GLY* 2.7 39.2 + - - +
123B GLU* 3.4 32.1 + - - +
124B CYS* 4.2 2.2 - - - -
1003B BME 3.5 28.5 - - - -
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 4.1 11.9 - - + -
87B ALA 4.3 1.8 - - - +
88B LYS* 3.7 39.7 - - + -
91B TYR* 3.6 44.8 - - + -
115B GLU* 2.8 54.7 + - + +
116B LEU* 3.2 11.6 + - + +
118B LEU* 1.3 77.6 - - + +
120B ILE* 1.3 68.7 + - + +
122B GLY* 4.2 3.3 + - - -
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Residues in contact with ILE 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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91B TYR* 3.4 39.5 - - + +
116B LEU* 2.9 27.1 + - + +
119B LEU* 1.3 82.5 - - + +
121B SER* 1.3 62.3 + - - +
185B LYS* 3.5 43.2 + - + +
186B LEU* 3.6 17.5 - - + -
189B PHE* 3.6 23.8 - - + -
190B PHE* 3.4 28.5 - - + -
214B VAL* 4.9 0.2 - - + -
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER 2.7 22.3 + - - -
120B ILE* 1.3 78.2 - - - +
122B GLY* 1.3 62.3 + - - +
123B GLU* 3.0 30.7 + - - +
125B LEU* 3.8 7.9 - - - +
183B ASN* 3.6 28.4 + - - -
185B LYS* 3.8 25.3 + - - +
186B LEU* 3.8 10.1 - - - -
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 2.7 28.7 + - - +
119B LEU 4.2 3.3 + - - -
120B ILE 3.5 1.4 - - - -
121B SER* 1.3 74.2 - - - +
123B GLU* 1.3 63.2 + - - +
185B LYS* 5.9 1.1 - - - -
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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
------------------------------------------------------------
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