Contacts of the helix formed by residues 110 - 122 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C THR* 1.3 70.0 - - + +
111C LEU* 1.3 66.0 + - - +
113C PHE* 2.8 15.3 + - - +
114C GLU* 2.9 15.7 + - - +
170C PHE 3.8 0.7 - - - -
171C HIS* 3.7 15.7 - - - -
217C VAL 2.8 14.6 + - - -
218C GLN* 3.6 34.9 + - - +
220C HIS* 3.5 26.0 - - + +
1004C BME 2.0 44.0 - - + -
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLN* 4.2 0.7 - - - +
72C PRO 3.7 2.9 - - - +
73C GLY* 3.8 0.2 - - - -
74C GLY* 3.4 44.4 - - - +
75C SER* 4.8 0.9 - - - -
76C VAL* 3.5 43.5 - - + +
78C LEU* 3.5 30.4 - - + +
83C TYR* 3.8 22.4 - - + -
109C THR 2.9 1.0 + - - -
110C CYS* 1.3 78.9 - - - +
112C GLY* 1.3 57.4 + - - +
114C GLU* 3.2 15.0 + - - +
115C GLU* 2.8 27.5 + - - +
1004C BME 3.1 5.3 - - - -
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Residues in contact with GLY 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PHE* 3.4 29.7 - - - -
83C TYR* 3.4 12.3 + - - -
108C GLY* 3.6 7.0 - - - -
109C THR 2.9 8.2 + - - -
111C LEU* 1.3 80.5 - - - +
113C PHE* 1.3 59.4 + - - +
115C GLU* 3.3 5.5 + - - +
116C LEU* 3.0 26.9 + - - +
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Residues in contact with PHE 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C GLY* 3.6 10.9 - - - +
110C CYS* 2.8 10.7 + - - +
112C GLY* 1.3 75.5 - - - +
114C GLU* 1.3 68.8 + - + +
116C LEU* 3.1 11.8 + - - +
117C SER* 3.1 19.4 + - - -
126C LEU* 5.7 0.2 - - + -
175C LEU* 4.1 20.4 - - + -
204C ILE* 3.6 39.0 - - + -
205C SER 4.5 3.1 - - - -
207C MET* 3.7 35.1 - - + +
216C GLY* 3.5 26.9 - - - -
217C VAL 3.3 23.8 - - - +
218C GLN* 3.3 28.3 - - - -
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Residues in contact with GLU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 3.4 25.4 - - + +
110C CYS* 2.9 17.1 + - - +
111C LEU* 3.4 16.1 - - - +
113C PHE* 1.3 77.6 - - + +
115C GLU* 1.3 64.0 + - - +
117C SER* 2.5 25.7 + - - -
118C LEU* 3.2 5.9 + - - +
126C LEU* 3.5 29.9 - - + +
171C HIS* 4.1 6.6 - - - +
173C TRP* 3.5 22.9 + - - +
218C GLN* 3.2 31.7 + - - +
1004C BME 4.6 2.2 - - - -
1005C BME 5.2 0.2 - - - +
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Residues in contact with GLU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PHE* 4.5 3.8 - - + -
78C LEU* 3.2 39.8 - - + +
83C TYR* 4.4 5.4 - - + -
84C ALA* 3.6 23.9 - - - +
87C ALA* 3.7 21.7 - - + +
88C LYS* 4.9 0.2 - - - +
111C LEU 2.8 13.6 + - - +
112C GLY* 3.5 13.0 - - - +
114C GLU* 1.3 75.7 - - - +
116C LEU* 1.3 58.0 + - - +
118C LEU* 3.2 10.3 + - - +
119C LEU* 2.8 63.6 + - + +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PHE* 4.1 23.3 - - + -
91C TYR* 4.6 5.6 - - + -
106C VAL* 4.3 5.8 - - + -
107C TRP 4.9 0.4 - - - -
108C GLY* 4.1 9.4 - - - +
112C GLY 3.0 19.1 + - - +
113C PHE* 3.1 8.0 + - - +
115C GLU* 1.3 75.1 - - - +
117C SER* 1.3 65.7 + - - +
119C LEU* 4.2 11.4 - - + -
120C ILE* 3.0 31.4 + - + +
190C PHE* 4.4 13.9 - - + -
207C MET* 4.7 3.4 - - + -
214C VAL* 3.7 29.6 - - + -
215C TYR 3.3 30.5 - - - +
216C GLY* 4.3 5.6 - - - +
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Residues in contact with SER 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PHE* 3.1 12.7 + - - -
114C GLU* 2.5 25.4 + - - -
116C LEU* 1.3 74.8 - - - +
118C LEU* 1.3 52.9 + - - +
121C SER* 2.7 39.9 + - - -
123C GLU 4.5 2.5 + - - -
125C LEU* 5.6 3.8 + - - -
126C LEU* 4.1 16.5 - - - +
175C LEU* 4.1 27.4 - - - -
186C LEU* 3.8 14.0 - - - +
207C MET* 4.8 5.1 - - - +
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C LEU* 3.2 31.4 - - + +
79C ARG* 4.1 24.2 - - - +
114C GLU 3.2 7.2 + - - +
115C GLU* 3.2 18.9 + - - +
117C SER* 1.3 80.2 + - - +
119C LEU* 1.3 59.4 + - + +
122C GLY* 2.7 37.9 + - - +
123C GLU* 3.4 33.0 - - - +
124C CYS* 4.2 2.5 - - - -
1005C BME 3.5 28.5 - - - -
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PHE* 4.3 2.5 - - + -
79C ARG* 5.9 1.3 - - - +
87C ALA 4.3 6.1 - - - +
88C LYS* 3.7 38.6 - - + -
91C TYR* 3.6 46.6 - - + -
115C GLU* 2.8 48.6 + - + +
116C LEU* 3.8 16.6 - - + +
118C LEU* 1.3 79.9 - - + +
120C ILE* 1.3 66.8 + - + +
122C GLY* 4.1 3.6 + - - -
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Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C TYR* 3.5 38.1 - - + +
116C LEU* 3.0 29.3 + - + +
119C LEU* 1.3 79.3 - - + +
121C SER* 1.3 61.9 + - - +
185C LYS* 3.5 42.1 + - + +
186C LEU* 3.7 15.3 - - + -
189C PHE* 3.8 26.7 - - + -
190C PHE* 3.6 26.0 - - + -
214C VAL* 4.8 0.2 - - + -
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Residues in contact with SER 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C SER 2.7 21.9 + - - -
120C ILE* 1.3 78.0 - - - +
122C GLY* 1.3 60.2 + - - +
123C GLU* 3.0 35.2 + - - +
125C LEU* 3.9 8.0 - - - +
183C ASN* 3.5 33.7 + - - -
185C LYS* 4.0 17.9 + - - +
186C LEU* 3.8 10.1 - - - -
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Residues in contact with GLY 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 2.7 29.9 + - - +
119C LEU 4.6 2.9 - - - -
120C ILE 3.5 1.8 - - - -
121C SER* 1.3 74.3 - - - +
123C GLU* 1.3 63.4 + - - +
185C LYS* 5.8 1.6 - - - -
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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